ДНК-нанотехнологии 1 введение и основные методы / sun2014
.pdfDNA Nanotechnology and Its Applications in Biomedical Research |
Sun et al. |
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Figure 10. Schematic showing of the 4 × 4-tile-formed DNA 2D barcode array and its detection mechanism. (a) shows the tile design, different-colored array formation, and color changes after binding with target molecules; (b) the mechanism of the interaction between the probe and target molecules. Reprinted with permission from [170], C. Lin, et al., Self-assembled combinatorial encoding nanoarrays for multiplexed biosensing. Nano Lett. 7, 507 (2007). © 2007, American Chemical Society.
technique, makes DNA nanostructures ideal for label-free |
with electrochemical techniques, they were able to detect a |
nucleic acids detections, which can avoid the tedious pro- |
variety of interested targeted molecules.177–180 Research on |
cess of the multi-coded fluorescence DNA array system. |
patterning DNA nanostructures on gold surfaces with the |
An origami chip for label-free RNA detection173 was |
help of lithography also made great progress.181–184 The |
first reported by Yan’ group; a rectangular DNA origami |
combination of top-down and bottom-up technology will |
Delivered by Publishing Technology to: Rice University |
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tile was used as the chip, multiple single-stranded DNA |
greatly help DNA nanostructures’ application in biosens- |
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probes targeting specific RNA sequences were precisely |
ing field. |
Copyright: American Scientific Publishers patterned on the origami scaffold; upon binding of the tar-
geted RNA molecules on DNA probes, a designed double helical DNA-RNA-V-Shaped junctions formed, created designed features visualized by AFM. Index spots were created on each origami tile so that the detection tiles could be differentiated, allowing for simultaneously, multi-target detection. Later, an asymmetric map-like DNA origami tile was used to replace the rectangular tile, which eliminated the symmetry feature, avoids the use of index spots.174
A different approach was used to detect single nucleotide polymorphisms on DNA origami.175 Four visible letters features corresponding to A, T, G, C were created first on the origami, with each letter contains distinct sequences; when target DNA strand with the right nucleotide variation was added onto the surface of the origami, the letter strand was replaced and the corresponding letter pattern disappeared. Most recently, DNA origami single-molecule-beacons were prepared also for label-free detection. By adding different control features, the devices were able to detect a range of targets, including miRNA and proteins,176 by AFM imaging. A DNA tetrahedral structure was used by Fan’s group to improve the conventional DNA-on-gold surface microarray detection. By attaching the DNA probes on the vertex of the DNA tetrahedron, which deposited onto the gold surface through thio groups modified on three of its vertexes, the accessibility of the probes vastly improved. Combining
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DNA Nanotechnology and Its Applications in Biomedical Research |
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tissues, of improving cell-uptake of small drugs, of real- |
cytotoxicity test showed no significant cell death was |
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time monitoring the delivery process, among others. Some |
observed, which proved DNA nanotubes are biocompati- |
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drug delivery nanosystems, including liposome and poly- |
ble as expected. But the relative large size of the DNA |
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mer nanoparticles, have already had some success and |
nanotubes they used, 10–40 m, might make the nano- |
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been approved for clinical use, but still haven’t had signif- |
tubes difficult to maintain their designed structure during |
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icant impact yet.185 Developing biocompatible, multifunc- |
the cell uptaking process. |
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tional drug delivery nanosystems remains the key for the |
Sleiman’s group later reported their DNA nanotubes |
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application of nanotechnology on drug delivery. It is desir- |
with controlled length, assembled with rolling-circle- |
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able to develop multifunctional drug nanocarriers, which |
amplification (RCA), had good cell-uptaking efficacy, and |
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have cage-like structures that can encapsulate one or multi- |
they also demonstrate the integrity of their DNA nano- |
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ple drugs inside the cage, so the drugs will only be released |
tubes inside the human cervical cancer (HeLa) cells.104 |
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when the nanocarriers get to the targeted sites and receive |
The more compact DNA tetrahedron nanostructure devel- |
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specific signals; the drug nanocarriers also should have |
oped by Turberfield’s group50 51 was later explored as |
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modification sites for targeting ligands to deliver drugs to |
another potential drug delivery carrier. The DNA tetra- |
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interested cell or tissues; the drug nanocarriers also should |
hedron structure was first tested for its resistance against |
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contain imaging reagents (or they are luminescent them- |
enzymatic digestions,187 and the results showed that the |
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selves) allowing real-time monitoring the drug delivery |
DNA tetrahedron structure has superior stability over DNA |
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processes and their efficacy. |
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single strands against enzymatic digestions. In 10% fetal |
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DNA 3D nanostructures have all the features to be |
bovine serum (consisting complex mixture of nucleases |
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promising candidates for multifunction drug delivery: |
and other proteins), the DNA tetrahedron structure can |
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they are biocompatible; can be easily modified at multi- |
be stable for 42 hours, comparing to only 0.8 hours for |
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ple addressable positions; some well-developed cage-like |
DNA single strands. This indicates that the DNA tetra- |
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DNA 3D structures have the |
cavities to accommo- |
hedron structure can exist inside cells with integrity for |
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date drug cargos; and 3D DNA nanostructures can be |
a certain period of time, and could be used as drug |
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reconfigurable with special designs and control methods. |
delivery carrier. Later, the transfection efficacy of this |
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In recent years, some excellent researches have already |
DNA tetrahedron nanostructure into plated human embry- |
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been done to explore the application of DNA nano- |
onic kidney cells was tested. Fluorescence dyes, Cy5 |
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structures as multifunctional drug delivery nanosystems. |
and Cy3 were attached to the DNA tetrahedron at spe- |
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A dual-functionalized DNA nanotube structure was first |
cific positions, fluorescence study results clearly showed |
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Copyright: American Scientific Publishers |
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used to deliver covalently linked fluorescence dye Cy3 |
the DNA tetrahedron can easily transfect into the cells, |
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into the nasopharyngeal epidermal carcinoma KB cells by |
and the DNA tetrahedron structure remain intact in cells |
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Mao’s group;186 folate molecules were conjugated onto |
even 48 hours after transfection.188 Then, Fan’s group |
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the DNA nanotube as targeting ligands for targeting folate |
attached unmethylated cytosine-phosphate-guanine (CpG) |
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receptors (FRs) over-expressed on the surface of the KB |
motifs to the DNA tetrahedron structure for immunostim- |
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cells (see Fig. 12). Comparing to single-stranded DNAs, |
ulatory study (see Fig. 13),189 once getting into the cells, |
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fluorescence images clearly showed that some of the |
the therapeutic CpG oligodeoxynucleotides will bind and |
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DNA nanotubes transfect into the targeted cells, and the |
allosterically activates Toll-like receptor 9 (TLR9), which |
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then activates downstream pathways to induce immunos- |
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timulatory effects, producing high-level secretion of vari- |
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ous pro-inflammatory cytokines including tumor necrosis |
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factor (TNF)-R, interleukin (IL)-6, and IL-12. They found |
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that the DNA tetrahedron structures could noninvasively |
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and efficiently enter macrophage-like RAW264.7 cells |
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without the aid of transfection agents. And their ELISA |
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assays results showed that functional CpG-DNA tetrahe- |
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dron nanostructures dramatically induced the production of |
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various proinflammatory cytokines including tumor necro- |
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sis factor (TNF)-R, interleukin (IL)-6, and IL-12. The level |
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of immunostimulatory effects of CpG attached on DNA |
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tetrahedron nanostructures increased by 9 to 18 times com- |
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Figure 12. Schematic showing of |
the construction of the |
paring to free CpG oligodeoxynucleotides. |
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dual-functionalized DNA nanotube and its delivery process. |
Langer and Anderson’s group later tested the therapeu- |
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(a) The design of the DNA nanotube; (b) cell targeting and |
tic potential of DNA tetrahedron nanostructures as siRNA |
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delivery mechanism. Reprinted with permission from [186], |
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nanocarrier in vivo.190 They used DNA tetrahedron nano- |
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S. H. Ko, et al., DNA nanotubes as combinatorial vehicles for |
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structures as nanocarriers, attached anti-luciferase siRNA |
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cellular delivery. Biomacromolecules 9, 3039 (2008). © 2008, |
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American Chemical Society. |
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onto specific sites of the DNA tetrahedral, also with |
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DNA Nanotechnology and Its Applications in Biomedical Research
Figure 13. Schematic showing of the assembly of CpG bearing DNA tetrahedron and its immunostimulatory effect. Reprinted with permission from [189], J. Li, et al., Selfassembled multivalent DNA nanostructures for noninvasive intracellular delivery of immunostimulatory CpG oligonucleotides. ACS Nano 5, 8783 (2011). © 2011, American Chemical Society.
conjugated folate (FA) targeting folate receptor overex- |
Figure 14. |
Schematic showing of DNA tetrahedral nano- |
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structures as scaffold for the assembly of adjuvant-antigen |
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pressing KB cells. Either by tail-vein injection or intratu- |
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vaccine complex. The CpG adjuvant molecules shown in pur- |
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mor injection, folate (FA)-conjugated DNA tetrahedra with |
ple hangers at the outside of the tetrahedral; the streptavidin |
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anti-luciferase siRNA were delivered into mice. By silenc- |
antigen shown in red. The vaccine complexes were injected |
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ing gene of firefly luciferase expressing KB xenografts, |
into mice, and bound specifically to B cells and nonspecifi- |
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cally to dendritic cells and macrophages. The complexes are |
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one should expect a decrease of bioluminescent intensity |
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internalized by the three types of antigen-presenting cells, |
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in the tumor, their results clearly showed that a decrease |
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disassembled, and the individual peptide antigens are subse- |
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of 60% in bioluminescent intensity for both tail-vein and |
quently presented to T cells to activate B cell response and |
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intratumor injections, which means that DNA tetrahedron |
antibody production. Reprinted with permission from [191], |
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nanostructures have a promising future as nanocarriers for |
X. Liu, et |
al., A DNA nanostructure platform for directed |
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assembly of synthetic vaccines. Nano Lett. 12, 4254 (2012). |
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siRNA and possible other drugs molecules. |
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© 2012, American Chemical Society. |
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Yan’s group later used DNA tetrahedral nanostructures |
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as platform for the assembly of synthetic |
vaccine, and |
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191 |
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tested the immune |
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response in vivo. |
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They utilized |
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the addressability of the DNA tetrahedral nanostructures, |
epithelial cancer cells. |
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Copyright: American Scientific Publishers |
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attached a model antigen, streptavidin (STV), and a rep- |
Krishnan’s group used their DNA icosahedral nano- |
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resentative adjuvant, CpG oligodeoxynucleotides onto the |
structures made from DNA five-way junction motif as |
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designed sites, and assembled a synthetic vaccine complex |
nanocarrier cages, encapsulated Fluorescein isothiocyanate |
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(see Fig. 14), once the vaccine complex were injected into |
(FITC)-Dextran (FD) as cargos inside the cages.194 Their |
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mice, they bound specifically to B cells and nonspecif- |
results showed that the host–cargo complex was uptaken |
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ically to dendritic cells and macrophages, and activated |
only by specific cells (coelomocytes) in Caenorhabditis |
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T cells and triggered antibody production. This synthetic |
elegans that expressed the anionic ligand-binding receptor |
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vaccine complex has similar size and shape as a natural |
(ALBR). Later, by redesigning their icosahedral structures, |
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viral particle. Their results showed that, comparing to free |
they divided their icosahedra into two half parts, which |
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CpG plus free STV, fully-assembled tetrahedral-STV-CpG |
added a cyclic-di-GMP (cdGMP) binding aptamer struc- |
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synthetic vaccine complex generated a much higher level |
ture into the middle connection part which associating the |
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of anti-STV IgG antibodies in vivo. And no antibody was |
two half parts together. Then their DNA icosahedral struc- |
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detected against the DNA tetrahedral structures alone. This |
tures become drug delivery nanosystems capable releas- |
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experiment shows that DNA tetrahedral structures not only |
ing drug cargos in a controlled manner, in response to an |
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can serve as a nanocarrier system for drug, but also can |
external trigger, namely cyclic-di-GMP (cdGMP).195 |
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be used to assemble vaccine like structures for biomedical |
All the polyhedral DNA nanostructures mentioned |
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purpose. |
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above showed great promise as efficient drug delivery |
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Polypod-like DNA structures were also developed for |
nanocarriers, even in a controlled-release function. But |
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efficient delivery of immunostimulatory CpG to immune |
one of the concerns regarding the polyhedral DNA nano- |
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cells.192 Their results showed that increasing pod num- |
structures is that they all have porous surfaces, which |
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ber is directly linked with efficient cellular uptake, and |
could limit their application as totally-closed cage-like |
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large amount of cytokine production from TLR9-positive |
drug delivery nanosystems. DNA origami 3D nano- |
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cells. A distinct five-point-star motif and aptamer- |
structures have their structural advantages as topological- |
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conjugated six-point-star motif were developed to inter- |
closed drug delivery nanocarriers. Some wonderful works |
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molecularly construct DNA icosahedra as a nanocarrier |
have already done to explore DNA origami structures as |
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for doxorubicin.193 |
Aptamer-conjugated doxorubicin- |
potential drug delivery nanocarriers. First, Yan’s group |
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intercalated DNA icosahedra (Doxo@Apt-DNA-icosa) |
tested the |
stabilities of different shaped DNA origami |
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Sun et al. |
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DNA Nanotechnology and Its Applications in Biomedical Research |
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nanostructures in lysates from various normal and can- |
visualization of the intracellular location and stability of |
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cerous cell lines. After incubating DNA origami nano- |
DNA origami;203 this technique will bring more alterna- |
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structures with cell lysates for up to 12 hours, they |
tives to monitor the drug delivery process of DNA nano- |
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found the DNA origami structures were still intact.196 And |
structures, especially in some environment, where small |
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the functional DNA origami structures could be sepa- |
organic dye molecules might be difficult to stay intact. |
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rated from the cell lysates and maintaining their structural |
Because their biocompatibility, and promising features |
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integrity and functionality.197 |
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as multifunctional drug nanocarriers, DNA nanostructures |
Liedl’s group then used a DNA |
origami |
nanotubu- |
could become import nanosystems for smart, controlled |
lar structure as delivery nanocarrier |
for the |
therapeu- |
drug delivery applications. The stability concern about the |
tic CpG oligodeoxynucleotides.198 Their results showed |
DNA nanostructures might be solved by using stable DNA |
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that the DNA origami nanotube also can enter the cell |
analog-DNA heterostructures,204 or by chemical modifica- |
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effectively and activate Toll-like receptor 9 (TLR9) and |
tion DNA nanostructures at designed positions. |
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then the downstream pathway. A twisted DNA origami |
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nanostructure was also used for optimal delivery of the |
Biomimetic Assemblies |
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anthracycline doxorubicin (Dox) to human breast cancer |
One best way to understand the function of the living cells |
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cells.199 Another triangular DNA origami structure also |
and cell networks, is to assemble synthetic cells or cell net- |
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was used for the delivery of doxorubicin anticancer drug |
works, which can mimic all the functions of the living cells |
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to human breast cancer cell.200 In both cases, doxorubicin |
and cell networks. Because of its excellent self-assembly |
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was attached to the DNA origami structure by intercalating |
properties, DNA is a promising material for synthetic biol- |
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between the DNA bases. |
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ogy applications. Some works have already proven that |
But the DNA origami nanotube198 used for the delivery |
DNA nanostructures can be used for biomimetic appli- |
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of CpG oligodeoxynucleotides, and the two DNA origami |
cations. Luo’ group created a cell-free protein-producing |
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structures199 200 used for doxorubicin drug delivery men- |
DNA hydrogel system.205 By joining genomic DNA frag- |
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tioned above, all don’t have the controlled-drug-release |
ments together with a DNA four-way-junction motif |
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function. Recently, A DNA origami nanorobot,201 with a |
(called X-DNA) using ligase, they assembled a gene- |
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hexagonal barrel shaped cage-like structure was developed |
containing DNA hydrogel system inside polydimethyl- |
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for controlled delivery of cargos. Two domains of the |
siloxane (PDMS) moulds, thus prepared DNA hydrogel |
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DNA origami barrel structure are covalently attached in |
pads with well-defined dimensions with controlled poros- |
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the rear by single-stranded scaffold hinges; two specific |
ity. When immersed in cell extracts containing compo- |
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Copyright: American Scientific Publishers |
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DNA aptamer–based locks are created to close the barrel |
nents, such as RNA polymerase and ribosome, the DNA |
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in the front. Once a correct combination of two protein |
hydrogel pads can serve as gene template for in vitro cell |
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antigen are met, the aptamers will undergo target-induced |
free protein synthesis. They tested a total of 16 different |
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switching between an aptamer-complement duplex and |
protein-producing DNA hydrogels containing 16 different |
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an aptamer-target complex, in turn, open the barrel, and |
genes, and successfully produced all 16 proteins includ- |
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release the inside payloads. In their experiment, different |
ing membrane and toxic proteins. Their results proved |
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aptamer-based locks were used for testing the open and |
that their DNA hydrogel system can serve as a general |
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close function of their DNA origami nanorobot; and differ- |
protein production technology. Their work represented an |
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ent antibody payloads were added into the nanorobot cage |
important milestone for the use of DNA nanostructures |
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to investigate their nanorobot application on interfering |
on engineering higher functional complexity in synthetic |
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with cell signaling pathways. Their results clearly showed |
biological systems.206 |
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their DNA origami nanorobot can release drug payloads in |
Also it is important for biomedical research to gain clear |
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a controlled manner, and can carry multiple drug payloads |
information about individual cells, and cell-cell interac- |
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at the same time. This is big step towards developing a |
tions. Krishnan’s group developed a DNA nanomachine |
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multifunctional controlled drug delivery nanosystem. |
system based on I-motif DNA. This DNA nanomachine, |
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One concern about DNA origami structure as drug |
called the I-switch, consists of two DNA duplexes con- |
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delivery nanocarrier is that it requires too many short |
nected to each other by a flexible hinge and bearing cyto- |
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DNA staple strands to build; some of the staple strands |
sine rich single-stranded overhangs at the duplex termini. |
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might possess biological effects to the cell by themselves. |
At acidic and neutral pH conditions, the I-switch DNA |
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A Rolling-Circle-Amplification (RCA)-based approach to |
nanomachine will adapt “closed” and “open” conforma- |
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fold well-defined DNA origami nanostructures with only |
tions respectively. By attaching a pair of fluorescent dyes |
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several staple strands was developed recently, and was |
at designed positions of this I-switch DNA nanomachine, |
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used as efficient delivery carriers for CpG immunos- |
it forms the molecular basis of a fluorescence resonance |
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timulatory drugs;202 this approach might pave the way |
energy transfer (FRET)-based pH sensor. They used this |
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to simplify the structure design of other DNA origami |
DNA nanomachine successfully mapped spatiotemporal |
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nanocarriers to eliminate possible interfering DNA strands. |
pH changes associated with endosome maturation inside |
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Also a label-free fluorescent probe |
was developed for |
living cells in culture;207 and later in multicellular living |
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organisms, Caenorhabditis elegans;208 and most recently, |
the DNA origami structures at the gate of glass nanocap- |
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they used two distinct DNA nanomachines within the |
illaries. By tuning the pore size they were able to control |
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same living cell to simultaneously map pH gradients along |
the folding of dsDNA passing through the nanopore; and |
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two different but intersecting cellular entry pathways,209 |
by specific introduction of binding sites (a short ssDNA |
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the furin retrograde endocytic pathway and the transfer- |
with designed sequence) in the DNA origami nanopore, |
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rin endocytic/recycling pathway. This approach represents |
they were able to selectively detect ssDNA molecules.217 |
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a first successful application of DNA nanotechnology on |
And recently, a breakthrough was made by Dietz and |
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cell analysis. Liu’s group used Y-DNA motif and linkers to |
Simmel’s group. Inspired by the structure of the bac- |
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form DNA hydrogel, served as a cover to a polydimethyl- |
terial protein pore a-hemolysin, they constructed a syn- |
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siloxane (PDMS) chip with circular microwells at different |
thetic lipid membrane channel218 made entirely from DNA |
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diameters are designed and prepared by soft lithography, |
origami nanostructure, with cholesterol modification at |
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cells are trapped inside those microwells separately, one |
designed positions. The barrel-like structure contains a |
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cell in one well.210 Since the DNA hydrogel is permeable, |
stem that penetrated and spanned a lipid membrane, and |
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nutrients for the cell can pass through the hydrogel cover. |
a cap adhered to the membrane via 26 cholesterol moi- |
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Also the DNA hydrogel can be specifically digested by |
ety. The stem protrudes centrally from the barrel and |
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restriction enzymes, which open the hydrogel cover for a |
consists of six double-helical DNA domains that form a |
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specific cell and release it. This design allows successful |
hollow tube which acts as a transmembrane channel, with |
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single cell level analysis, and can avoid the misinterpreta- |
a diameter of 2 nm and a length of 42 nm. Single- |
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tion for specific cell properties by bulk cell analysis. |
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channel electrophysiological experiments showed that the |
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Meanwhile, understanding the cell–cell interactions is |
channel conducted an electrical current proportional to |
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essential to understand the function of multicellular organ- |
the potential that is placed across the membrane, and |
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isms. Yan’s group utilized DNA 4 × 4 tiles as scaffold, |
demonstrated stochastic gating-fluctuations between open |
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attached cell-targeting aptamers as directing reagents, suc- |
and closed conformations resemble those seen in natural |
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cessfully aligned two types of cell into close vicinity, and |
biological transmembrane protein channels. The synthetic |
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analyzed cell–cell interactions.211 This might be a first step |
origami channel could also be used for molecular detec- |
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towards building multicellular organism; also might has |
tion applications, as their results showed that their channel |
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significance in disease treatment, for example, it might fos- |
was able to monitor the zipping-unzipping of DNA hair- |
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ter the T–B cell interactions required to generate an effec- |
pin structures and folding-unfolding of DNA G-quadruplex |
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tive immune response. The development of methods for |
structures. This synthetic DNA origami lipid membrane |
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Copyright: American Scientific Publishers |
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the modification of cell surfaces with single-stranded DNA |
channel has the potential to make great impact on biomed- |
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oligomers212 provided the means to use different designs |
ical research, such as manipulation of the cells and drug |
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DNA nanoscaffold for the alignment of various interested |
delivery.219 220 |
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cells. |
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Later, |
Howorka’s |
group used |
chemical modification |
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In nature, a lot of protein and peptide channels inserted |
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methods |
to |
prepare |
DNA |
origami |
nanopores |
which |
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into the |
lipid bilayer membranes |
of living cells act as |
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have better interaction with lipid membranes. First, they |
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transporting pathway water, ions and others for the cells’ |
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used ethyl-modified |
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phosphorothioate |
groups to |
form a |
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normal |
growth. Many |
synthetic |
nanopores mimic |
the |
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hydrophobic belt around the DNA origami nanopores to |
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protein |
channel were |
created for |
the biodetecting |
and |
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minimize the negative charges and mimic natural pro- |
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biosensing purpose. DNA nanostructures have also been |
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tein pores.221 |
And |
then |
they |
used only |
two porphyrin- |
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explored for the application as nanopore materials, |
but |
based hydrophobic |
tags |
attached |
on |
the |
DNA |
origami |
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mostly as gating purpose. First, Liu’s group G-quadruplex |
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nanopore |
to |
successfully anchor |
the |
highly negatively |
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DNA was immobilized onto a |
synthetic nanopore,213 |
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charged DNA nanostructure into the hydrophobic core of |
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which undergoes a potassium-responsive conformational |
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lipid bilayers.222 Their works greatly improved the stabil- |
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change at a certain potassium concentration range, as a |
ity of the synthetic DNA origami lipid membrane channel, |
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result, changed the pore size of their synthetic nanopore. |
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enhanced the possibility of its application in biomedical |
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Then Dietz’s group utilized the |
permeability of DNA |
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research.
origami,214 applied a DNA origami nanoplate as gatekeepers for solid-state nanopores, and successfully gained control over both the geometrical and chemical specifications of solid-state nanopores.215 Keyser’s group explored different approaches. In one experiment, they inserted a DNA origami nanopore-like structure inside a solid-state nanopore,216 and employed their hybrid nanopore system for the successful detection of -DNA molecules. In another experiment, they used a DNA origami nanoplate structure with a pore opening in the middle, and attached
2364
DNA Nanotechnology and Its Applications in Biomedical Research
and solving biomedical problems, especially in disease |
20. |
D. Han, S. Pal, Y. Yang, S. Jiang, J. Nangeave, Y. Liu, and H. Yan, |
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early diagnosis and targeted treatment. And we can foresee |
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DNA gridiron nanostructures based on four-arm junctions. Science |
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that DNA nanotechnology will make even greater impacts |
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339, 1412 (2013). |
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21. |
D. Liu, M. Wang, Z. Deng, R. Walulu, and C. Mao, Tensegrity: |
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on biomedical research in the near future. |
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Construction of rigid DNA triangles with flexible four-arm DNA |
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Acknowledgments: We are grateful to Dr. Nadrian |
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junctions. J. Am. Chem. Soc. 126, 2324 (2004). |
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22. |
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and T. H. LaBean, |
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H. Yan, S. H. Park, G. Ginkelstein, J. H. Reif, |
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C. Seeman for the courtesy images used in Figures 1 and 2. |
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DNA templated self-assembly of protein arrays and highly conduc- |
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We also thank the financial supports from National Sci- |
23. |
tive nanowires. Science 301, 1882 (2003) |
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E. Ribbe, and C. Mao, |
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ence Foundation China (21373151) and Tianjin Medical |
Y. He, Y. Tian, Y. Chen, Z. Deng, A. |
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University (TMU start-up fund). |
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Sequence symmetry as a tool for designing DNA nanostructures. |
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Angew. Chem., Int. Ed. 44, 6694 (2005) |
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24. |
K. Lund, Y. Liu, S. Lindsay, and |
H. Yan, |
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Self-assembling a molec- |
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REFERENCES |
|
|
|
|
|
|
|
|
|
ular pegboard. J. Am. Chem. Soc. 127, 17606 (2005). |
||||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
25. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||
|
|
|
|
|
|
|
|
S. H. Park, C. Pistol, S. J. Ahn, J. H. Reif, A. R. Lebeck, C. Dwyer, |
||||||||||||||||||||||||||||||||||||||||||||
1. |
G. M. Whitesides, Nanoscience, nanotechnology, and |
chemistry. |
||||||||||||||||||||||||||||||||||||||||||||||||||
|
and T. H. LaBean, Finite-size, fully addressable DNA tile lattices |
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
Small 1, 172 (2005). |
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
formed by hierarchical assembly procedures. Angew. Chem., Int. |
||||||||||||||||||||||||||||||||||||||||||
2. |
H. S. Nalwa (ed.), Encyclopedia of Nanoscience |
and Nano- |
|
|||||||||||||||||||||||||||||||||||||||||||||||||
|
Ed. 45, 735 (2006). |
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
technology, American Scientific Publishers, Los Angeles, CA |
|
||||||||||||||||||||||||||||||||||||||||||||||||||
|
26. |
Y. Liu, Y. Ke, and H. Yan, Self-assembly of symmetric finite-size |
||||||||||||||||||||||||||||||||||||||||||||||||||
|
(2004/2011), Vols. 1–25. |
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
DNA nanoarrays. J. Am. Chem. Soc. 127, 17140 (2005). |
||||||||||||||||||||||||||||||||||||||||||
3. |
H. S. Nalwa (ed.), Handbook of Nanostructured Materials and Nan- |
|
||||||||||||||||||||||||||||||||||||||||||||||||||
27. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||
Y. He, Y. Chen, H. Liu, A. E. Ribbe, and C. Mao, Self assembly of |
||||||||||||||||||||||||||||||||||||||||||||||||||||
|
otechnology, Academic Press, San Diego, CA (2000), Vols. 1–5. |
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
hexagonal DNA two-dimensional (2D) arrays. J. Am. Chem. Soc. |
||||||||||||||||||||||||||||||||||||||||||||||||||
4. |
N. C. Seeman, DNA in a material world. Nature 421, 427 (2003). |
|
||||||||||||||||||||||||||||||||||||||||||||||||||
|
127, 12202 (2005). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||||
5. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||
N. C. Seeman, Nucleic acid junctions and lattices. J. Theor. Biol. |
28. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||||
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|
|
|
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|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||
Y. He, Y. Tian, A. E. Ribbe, and C. Mao, Highly connected two- |
||||||||||||||||||||||||||||||||||||||||||||||||||||
|
99, 237 (1982). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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||||||||||||||||||||||||||||
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
dimensional crystals of DNA six-point-stars. J. Am. Chem. Soc. |
|||||||||||||||||||||||||||
6. |
|
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|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||
N. R. Kallenbach, R. I. Ma, and N. C. Seeman, An immobile |
|
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
128, 15978 (2006). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||||
|
nucleic acid junction constructed from oligonucleotides. Nature |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||||||
|
29. |
B. Wei, M. Dai and P. Yin, Complex shapes self-assembled from |
||||||||||||||||||||||||||||||||||||||||||||||||||
|
305, 829 (1983). |
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
single-stranded DNA tiles. Nature 485, 623 (2012). |
||||||||||||||||||||||||||||
7. |
|
|
|
|
|
|
|
|
|
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|
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|
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|
||||||||||||||||||||||
T. J. Fu and N. C. Seeman, DNA double crossover molecules. |
30. |
|||||||||||||||||||||||||||||||||||||||||||||||||||
B. Wei, M. Dai, C. Myhrvold, Y. Ke, R. Jungmann, and P. Yin, |
||||||||||||||||||||||||||||||||||||||||||||||||||||
|
Biochemistry 32, 3211 (1993). |
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
Design space for complex DNA structures. J. Am. Chem. Soc. |
||||||||||||||||||||||||||||||||||||||||||
8. |
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|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||
X. Li, X. Yang, J. Qi, and N. C. Seeman, Antiparallel DNA double |
|
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
135, 18080 (2013). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||||
|
crossover molecules as components for nanoconstruction. J. Am. |
|
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|
|
|
|
|
|
|
|
|
|
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|||||||||||||||||||||||||||||||||||
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31. |
F. Zhang, Y. Liu, and H. Yan, Complex Archimedean tiling self- |
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|
|
|
|
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|
|
|
|
|
|
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|
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|||||||||||||||||||||||
|
Chem. Soc. 118, 6131 (1996). Delivered by Publishing Technology to: Rice University |
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
assembled from DNA nanostructures. J. Am. Chem. Soc. 135, 7458 |
|||||||||||||||||||||
9. |
|
|
|
|
|
|
|
|
|
|
|
|
IP: 206.214.8.80 On: Fri, 15 Jan 2016 06:47:27 |
|||||||||||||||||||||||||||||||||||||||
T. LaBean, H. Yan, J. Kopatsch, F. Liu, E. Winfree, J. H. Reif, |
|
(2013). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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||||||||||||||||||||||||||||||
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|
|
Copyright: American Scientific Publishers |
|||||||||||||||||||||||||||||||||||||||
|
and N. C. Seeman, The construction, analysis, ligation and self- |
32. |
P. W. K. Rothemund, Folding DNA to create nanoscale shapes and |
|||||||||||||||||||||||||||||||||||||||||||||||||
|
assembly of DNA triple crossover complexes. J. Am. Chem. Soc. |
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
patterns. Nature 440, 297 (2006). |
||||||||||||||||||||||||||||||||||||||||||||||||||
|
122, 1848 (2000). |
|
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|
|
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33. |
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10. |
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M. Endo, T. Sugita, Y. Katsuda, K. Hidaka, and H. Sugiyama, |
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|
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||||||||||||||||||||||||
Z. Shen, H. Yan, T. Wang, and N. C. Seeman, Paranemic crossover |
||||||||||||||||||||||||||||||||||||||||||||||||||||
|
Programmed-assembly system using DNA Jigsaw pieces. Chem. |
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
DNA: A generalized holliday structure with applications in nan- |
|
||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
Eur. J. 16, 5362 (2010). |
||||||||||||||||||||||||||||||||||||||||||||||||||
|
otechnology. J. Am. Chem. Soc. 126, 1666 (2004). |
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||||||||||
|
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34. |
A. Rajendran, M. Endo, Y. Katsuda, K. Hidaka, and H. Sugiyama, |
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11. |
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N. C. Seeman, De Novo design of sequences for nucleic acid struc- |
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|
Programmed two-dimensional self-assembly of multiple DNA |
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
ture engineering. J. Biomol. Str. Dyns. 8, 573 (1990). |
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
origami jigsaw pieces. ACS Nano 5, 665 (2011). |
||||||||||||||||||||||||||||||||||||||||||
12. |
J. J. Birac, W. B. Sherman, J. Kopatsh, P. E. Constantinou, and |
|
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35. |
Z. Zhao, H. Yan, and Y. Liu, A route to scale up DNA origami |
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
N. C. Seeman, GIDEON, A program for design in structural DNA |
|||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
using DNA tiles as folding staples. Angew. Chem., Int. Ed. 49, 1414 |
||||||||||||||||||||||||||||||||||||||||||||||||||
|
nanotechnology. J. Mol. Graphics Modell. 25, 470 (2006) |
|
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13. |
|
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|
|
H. Yan, |
|
(2010). |
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S. Williams, K. Lund, C. Lin, P. Wonka, S. Lindsay, and |
36. |
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Tiamat: A three-dimensional editing tool for complex DNA struc- |
Z. Zhao, Y. Liu, and H. Yan, Organizing DNA origami tiles |
||||||||||||||||||||||||||||||||||||||||||||||||||
|
tures, The 14th International Meeting on DNA Computing, Prague, |
|
into larger structures using preformed scaffold frames. Nano Lett. |
|||||||||||||||||||||||||||||||||||||||||||||||||
|
Czech Republic (2008). |
|
|
|
|
|
|
|
|
37. |
11, 2997 (2011). |
|
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|
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|||||||||||||||||||||||||
14. |
S. M. Douglas, A. H. Marblestone, S. Teerapittayanon, A. Vazquez, |
Z. Li, M. Liu, L. Wang, J. Nangreave, H. Yan, and Y. Liu, Molecu- |
||||||||||||||||||||||||||||||||||||||||||||||||||
|
G. M. Church, and W. M. Shih, Rapid prototyping of 3D DNA- |
|
lar behavior of DNA origami in higher-order self-assembly. J. Am. |
|||||||||||||||||||||||||||||||||||||||||||||||||
|
origami shapes with caDNAno. Nucleic Acids Res. 37, 5001 (2009) |
38. |
Chem. Soc. 132, 13545 (2010). |
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15. |
C. E. Castro, F. Kilchherr, D. E. Kim, E. L. Shiao, T. Wauer, |
M. Endo, T. Sugita, A. Rajendran, Y. Katsuda, T. Emura, |
||||||||||||||||||||||||||||||||||||||||||||||||||
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P. Wortmann, M. Bathe, and H. Dietz, A primer to scaffolded DNA |
|
K. Hidaka, and H. Sugiyama, Two-dimensional DNA origami |
|||||||||||||||||||||||||||||||||||||||||||||||||
|
origami. Nat. Methods 8, 221 (2011) |
|
|
|
|
|
|
|
|
|
assemblies using a four-way connector. Chem. Commun. 47, 3213 |
|||||||||||||||||||||||||||||||||||||||||
16. |
E. Winfree, F. Liu, L. A. Wenzler, and N. C. Seeman, Design and |
39. |
(2011). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||
|
self-assembly of two-dimensional DNA crystals. Nature 394, 539 |
W. Liu, H. Zhong, R. Wang, and N. C. Seeman, Crystalline two- |
||||||||||||||||||||||||||||||||||||||||||||||||||
|
(1998). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
dimensional DNA-origami arrays. Angew. Chem. Int. Ed. 50, 264 |
||||||||||||||||||||||
17. |
F. Liu, |
R. Sha, and N. C. Seeman, Modifying the surface features of |
|
(2011). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||
|
two-dimensional DNA crystals. J. Am. Chem. Soc. 121, 917 (1999). |
40. |
Y. Ma, H. Zheng, C. Wang, Q. Yan, J. Chao, C. Fan, and S.-J. |
|||||||||||||||||||||||||||||||||||||||||||||||||
18. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Xiao, RCA strands as scaffold to create nanoscale shapes by a few |
|||||||||||||||||||||||||
P. W. K. Rothemund, N. Papadakis, and E. Winfree, Algorithmic |
|
|
|
|||||||||||||||||||||||||||||||||||||||||||||||||
|
self-assembly of DNA Sierpinski triangles. PLoS Biol. 2, 2041 |
|
staple strands. J. Am. Chem. Soc. 135, 2959 (2013). |
|||||||||||||||||||||||||||||||||||||||||||||||||
|
(2004). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
41. |
E. Pound, J. R. Ashton, H. C. A. Becerril, and A. T. Woolley, Poly- |
||||||||||||||||||||||
19. |
C. Mao, W. Sun, and N. C. Seeman, Designed two dimen- |
|
merase Chain reaction based scaffold preparation for the production |
|||||||||||||||||||||||||||||||||||||||||||||||||
|
sional DNA Holliday junction arrays visualized by atomic force |
|
of thin, branched DNA origami nanostructures of arbitrary sizes. |
|||||||||||||||||||||||||||||||||||||||||||||||||
|
microscopy. J. Am. Chem. Soc. 121, 5437 (1999). |
|
|
|
|
|
|
|
|
|
Nano Lett. 9, 4302 (2009). |
|||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
J. Biomed. Nanotechnol. 10, 2350–2370, 2014
DNA Nanotechnology and Its Applications in Biomedical Research |
|
|
|
|
|
|
|
|
|
Sun et al. |
||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||
42. |
H. Zhang, J. Chao, D. Pan, H. Liu, Q. Huang, and C. Fan, Folding |
63. |
C. Zhang, S. H. Ko, M. Su, Y. Leng, A. E. Ribbe, W. Jiang, and |
|||||||||||||||||||||||||||||||||||||||
|
super-sized DNA origami with scaffold strands from long-range |
|
Mao, Symmetry controls the face geometry of DNA polyhedra. |
|||||||||||||||||||||||||||||||||||||||
|
PCR. Chem. Commun. 48, 6405 (2012). |
|
|
|
|
|
|
|
64. |
J. Am. Chem. Soc. 131, 1413 (2009). |
|
|
|
|
||||||||||||||||||||||||||||
43. |
B. R. Högberg, T. Liedl, and W. M. Shih, Folding DNA origami |
S. Hamada and S. Murata, Substrate-assisted assembly of intercon- |
||||||||||||||||||||||||||||||||||||||||
|
from a double-stranded source of scaffold. J. Am. Chem. Soc. |
|
nected single-duplex DNA nanostructures. Angew. Chem., Int. Ed. |
|||||||||||||||||||||||||||||||||||||||
|
131, 9154 (2009). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
65. |
48, 6820 (2009). |
|
|
|
|
|
|
|
|
||||||||||
44. |
Y. Yang, D. Han, J. Nangreave, Y. Liu, and H. Yan, DNA origami |
X. Li, C. Zhang, C. Hao, C. Tian, G. Wang, and C. Mao, DNA |
||||||||||||||||||||||||||||||||||||||||
|
with double-stranded DNA as a unified scaffold. ACS Nano 6, 8209 |
|
polyhedral with T-linkage. ACS Nano 6, 8209 (2012). |
|
|
|||||||||||||||||||||||||||||||||||||
|
(2012). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
66. Z. Liu, Y. Li, C. Tian, and C. Mao, A smart DNA tetrahedron that |
||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
isothermally assembles or dissociates in response to the solution |
||||||||||||||
45. |
P. Wang, S. H. Ko, C. Tian, C. Hao, and C. Mao, RNA-DNA |
|
||||||||||||||||||||||||||||||||||||||||
|
pH value changes. Biomacromolecules 14, 1711 (2013). |
|
|
|||||||||||||||||||||||||||||||||||||||
|
hybrid origami: Folding of a long RNA single strand into complex |
|
|
|
||||||||||||||||||||||||||||||||||||||
|
67. C. Zhang, C. Tian, X. Li, H. Qian, C. Hao, W. Jiang, and C. Mao, |
|||||||||||||||||||||||||||||||||||||||||
|
nanostructures using short DNA helper strands. Chem. Commun. |
|||||||||||||||||||||||||||||||||||||||||
|
|
Reversibly switching the surface porosity of a DNA tetrahedron. |
||||||||||||||||||||||||||||||||||||||||
|
49, 5462 (2013). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
J. Am. Chem. Soc. 134, 11998 (2012). |
|
|
|
|
|||||||||||||||
46. |
M. Endo, S. Yamamoto, K. Tatsumi, T. Emura, K. Hidaka, and |
|
|
|
|
|
||||||||||||||||||||||||||||||||||||
68. C. Zhang, M. Su, Y. He, Y. Leng, A. E. Ribbe, G. Wang, W. Jiang, |
||||||||||||||||||||||||||||||||||||||||||
|
H. Sugiyama, |
RNA-templated |
|
DNA |
origami |
structures. Chem. |
||||||||||||||||||||||||||||||||||||
|
|
|
and C. Mao, Exterior modification of a DNA tetrahedron. Chem. |
|||||||||||||||||||||||||||||||||||||||
|
Commun. 49, 2879 (2013). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Commun. 46, 6792 (2010). |
|
|
|
|
|
|
||||||||||||||||||||
47. |
J. Chen and N. C. Seeman, The synthesis from DNA of a molecule |
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||
69. |
J. Zheng, J. |
J. Birktoft, Y. Chen, |
T. |
Wang, R. Sha, |
P. E. |
|||||||||||||||||||||||||||||||||||||
|
with the connectivity of a cube. Nature 350, 631 (1991). |
|||||||||||||||||||||||||||||||||||||||||
|
|
Constantinou, |
S. L. Ginell, |
C. Mao, |
and |
N. C. Seeman, |
From |
|||||||||||||||||||||||||||||||||||
48. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||
Y. Zhang and N. C. Seeman, The construction of a DNA truncated |
|
|||||||||||||||||||||||||||||||||||||||||
|
molecular to |
macroscopic |
via the |
rational design of a |
self- |
|||||||||||||||||||||||||||||||||||||
|
Octahedron. J. Am. Chem. Soc. 116, 1661 (1994). |
|
|
|
|
|
|
|||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
assembled 3D DNA crystal. Nature 461, 74 (2009). |
|
|
|||||||||||||||||||||||||||||||||
49. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||
W. M. Shih, J. D. Quispe, and G. F. Joyce, A 1.7-kilobase single- |
|
|
|
|||||||||||||||||||||||||||||||||||||||
70. R. Sha, J. J. Birktoft, N. Nguyen, A. R. Chandrasekaran, J. Zheng, |
||||||||||||||||||||||||||||||||||||||||||
|
stranded DNA |
that |
folds into |
|
a nanoscale octahedron. Nature |
|||||||||||||||||||||||||||||||||||||
|
|
|
X. Zhao, C. Mao, and N. C. Seeman, Self-assembled DNA crystals: |
|||||||||||||||||||||||||||||||||||||||
|
427, 618 |
(2004). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
The impact on resolution of 5 -phosphates and the DNA source. |
|||||||||||||||||||
50. |
|
|
|
|
|
|
|
R. M. Berry, and A. J. Turberfield, The single-step |
|
|||||||||||||||||||||||||||||||||
R. P. Goodman, |
|
Nano Lett. 13, 793 (2013). |
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||
|
synthesis of a DNA tetrahedron. Chem. Commun. 40, 1372 (2004). |
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||
|
71. T. Wang, R. Sha, J. J. Birktoft, J. Zheng, C. Mao, and N. C. |
|||||||||||||||||||||||||||||||||||||||||
51. |
R. P. Goodman, I. A. T. Schaap, C. F. Tardin, C. M. Erben, R. M. |
|||||||||||||||||||||||||||||||||||||||||
|
Seeman, A DNA crystal designed to contain two molecules per |
|||||||||||||||||||||||||||||||||||||||||
|
Berry, C. F. Schmidt, and A. J. Turberfield, Rapid chiral assem- |
|
asymmetric unit. J. Am. Chem. Soc. 132, 15471 (2010). |
|
|
|||||||||||||||||||||||||||||||||||||
|
bly of rigid DNA building blocks for molecular nanofabrication. |
72. |
D. Bhatia, S. Mehtab, R. Krishnan, S. S. Indi, A. Basu, and |
|||||||||||||||||||||||||||||||||||||||
52. |
Science 310, 1661 (2005). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y. Krishnan, Icosahedral DNA nanocapsules by modular assembly. |
|||||||||||||||||||||||||
Z. Li, B. Wei, J. |
Nangreave, C. Lin, Y. Liu, Y. Mi, and H. Yao, |
|
Angew. Chem., Int. Ed. 48, 4134 (2009). |
|
|
|
||||||||||||||||||||||||||||||||||||
|
A replicable tetrahedral nanostructure self-assembled from a single |
73. |
Y. Li, Y. D. Tseng, S. Y. Kwon, L. D’Espaux, J. S. Bunch, P. L. |
|||||||||||||||||||||||||||||||||||||||
|
DNA strand. J. Am. Chem. Soc. 131, 13093 (2009). |
|
|
|
|
|
|
Mceuen, and D. Luo, Controlled assembly of dendrimer-like DNA. |
||||||||||||||||||||||||||||||||||
53. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Delivered by Publishing Technology to: Rice University |
|
|
|
|
|
|
||||||||||||||||||||
T. Kato, R. P. Goodman, C. M. Erben, A. J. Turberfield, and |
|
Nat. Mater. 3, 38 (2004). |
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
IP: 206.214.8.80 On: Fri, 15 Jan 2016 06:47:27 |
|
|
|
|
|
|
|||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Copyright: American Scientific Publishers |
|
|
|
|
|
|
||||||||||||||||
|
K. Namba, High-resolution structural analysis of a DNA nano- |
74. |
Y. Ke, L. L. Ong, W. M. Shih, and P. Yin, Three-dimensional struc- |
|||||||||||||||||||||||||||||||||||||||
|
structure by cryoEM. Nano Lett. 9, 2747 (2009). |
|
|
|
|
|
|
tures self-assembled from DNA bricks. Science 338, 1177 (2012). |
||||||||||||||||||||||||||||||||||
54. |
R. P. Goodman, M. Heilemann, S. Doose, C. M. Erben, A. N. |
75. |
F. A. Aldaye and H. F. Sleiman, Modular access tostructurally |
|||||||||||||||||||||||||||||||||||||||
|
Kapanidis, and A. J. Turberfield, Reconfigurable, braced, three- |
|
switchable 3D discrete DNA assemblies. J. Am. Chem. Soc. |
|||||||||||||||||||||||||||||||||||||||
|
dimensional DNA nanostructures. Nat. Nanotechnol. 3, 93 (2008). |
76. |
129, 13376 (2007). |
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||
55. |
H. Pei, L. Liang, G. Yao, J. Li, Q. Huang, and C. Fan, Recon- |
S. M. Douglas, H. Dietz, T. Liedl, B. Hogberg, F. Graf, and W. M. |
||||||||||||||||||||||||||||||||||||||||
|
figurable three-dimensional DNA nanostructures for the construc- |
|
Shih, Self-assembly of DNA into nanoscale three-dimensional |
|||||||||||||||||||||||||||||||||||||||
|
tion of intracellular logic sensors. Angew. Chem., Int. Ed. 51, 9020 |
|
shapes. Nature 459, 414 (2009). |
|
|
|
|
|||||||||||||||||||||||||||||||||||
|
77. H. Dietz, S. M. Douglas, and W. M. Shih, Folding DNA into |
|||||||||||||||||||||||||||||||||||||||||
|
(2012). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
twisted and curved nanoscale shapes. Science 325, 725 (2009). |
||||||||||||||
56. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||
D. Han, J. Huang, Z. Zhu, Q. Yuan, M. You, Y. Chen, and W. Tan, |
|
|||||||||||||||||||||||||||||||||||||||||
78. Y. Ke, N. V. Voigt, K. V. Gothelf, and W. M. Shih, Multilayer DNA |
||||||||||||||||||||||||||||||||||||||||||
|
Molecular engineering of photoresponsive three-dimensional DNA |
|||||||||||||||||||||||||||||||||||||||||
|
|
origami packed on hexagonal and hybrid lattices. J. Am. Chem. |
||||||||||||||||||||||||||||||||||||||||
|
nanostructures. Chem. Commun. 47, 4670 (2011). |
|
|
|
|
|
|
|||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
Soc. 134, 1770 (2011). |
|
|
|
|
|
|
|||||||||||||||||||||||||||||
57. |
N. |
Mitchell, |
R. |
Schlapak, |
|
|
M. |
Kastner, |
|
D. |
|
Armitage, |
|
|
|
|
|
|
|
|||||||||||||||||||||||
|
|
|
|
79. Y. Ke, S. M. Douglas, M. Liu, J. Sharma, A. Cheng, A. Leung, |
||||||||||||||||||||||||||||||||||||||
|
W. |
Chrzanowski, J. |
Riener, |
P. Hinterdorfer, |
|
A. |
Ebner, and |
|||||||||||||||||||||||||||||||||||
|
|
|
Y. Liu, W. M. Shih, and H. Yan, Multilayer DNA origami packed |
|||||||||||||||||||||||||||||||||||||||
|
S. Howorka, A DNA nanostructure for the functional assembly of |
|
||||||||||||||||||||||||||||||||||||||||
|
|
on a square lattice. J. Am. Chem. Soc. 131, 15903 (2009). |
|
|
||||||||||||||||||||||||||||||||||||||
|
chemical groups with tunable stoichiometry and defined nanoscale |
|
|
|
||||||||||||||||||||||||||||||||||||||
|
80. T. Liedl, B. Hogberg, J. Tytell, D. E. Ingber, and W. M. Shih, |
|||||||||||||||||||||||||||||||||||||||||
|
geometry. Angew. Chem. Int. Ed. 48, 525 (2009). |
|
|
|
|
|
||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
Self-assembly of three-dimensional prestressed tensegrity structures |
|||||||||||||||||||||||||||||||||||
58. |
C. M. Erben, |
R. P. Goodman, and |
A. J. Turberfield, A self- |
|
||||||||||||||||||||||||||||||||||||||
|
from DNA. Nat. Nanotechnol 5, 520 (2010). |
|
|
|||||||||||||||||||||||||||||||||||||||
|
assembled DNA bipyramid. J. Am. Chem. Soc. 129, 6992 (2007). |
|
|
|
||||||||||||||||||||||||||||||||||||||
|
81. E. S. Andersen, M. Dong, M. M. Nielsen, K. Jahn, R. Subramani, |
|||||||||||||||||||||||||||||||||||||||||
59. |
Y. He, T. Ye, M. Su, C. Zhang, A. E. Ribbe, W. Jiang, and C. Mao, |
|||||||||||||||||||||||||||||||||||||||||
|
W. Mamdouh, M. M. Golas, B. Sander, H. Stark, C. L. P. Oliveira, |
|||||||||||||||||||||||||||||||||||||||||
|
Hierarchical self-assembly of DNA into symmetric supramolecular |
|
||||||||||||||||||||||||||||||||||||||||
|
|
J. S. Pedersen, V. Birkedal, |
F. Besenbacher, K. V. Gothelf, and |
|||||||||||||||||||||||||||||||||||||||
|
polyhedra. Nature 452, 198 (2008). |
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
J. Kjems, Self-assembly of a nanoscale DNA box with a control- |
||||||||||||||||||||||||||||||
60. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||
C. Zhang, M. Su, Y. He, X. |
Zhao, |
P. Fang, A. E. Ribbe, W. Jiang, |
|
lable lid. Nature 459, 73 (2009). |
|
|
|
|
||||||||||||||||||||||||||||||||||
|
and C. Mao, Conformational flexibility facilitates self-assembly |
|
|
|
|
|
||||||||||||||||||||||||||||||||||||
|
82. |
|
|
|
|
|
||||||||||||||||||||||||||||||||||||
|
R. M. Zadegan, M. D. E. |
Jepsen, K. E. Thomsen, A. H. Okholm, |
||||||||||||||||||||||||||||||||||||||||
|
of complex DNA nanostructures. Proc. Natl. Acad. Sci. USA |
|
D. H. Schaffert, E. S. Andersen, V. Birkedal, and J. Kjems, Con- |
|||||||||||||||||||||||||||||||||||||||
61. |
105, 10665 (2008). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
struction of a 4 zeptoliters switchable 3D DNA box origami. ACS |
|||||||||||||||||||
Y. He, M. Su, P. Fang, C. Zhang, A. E. Ribbe, W. Jiang, and |
|
Nano 6, 10050 (2012). |
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||
|
C. Mao, On the chirality of self-assembled DNA octahedra. Angew. |
83. |
A. Kuzuya and M. Komiyama, Design and construction of box- |
|||||||||||||||||||||||||||||||||||||||
|
Chem., Int. Ed. 49, 748 (2010). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
shaped 3D-DNA origami. Chem. Commun. 45, 4182 (2009). |
|
|
|||||||||||||||||||||||
62. |
C. Zhang, W. Wu, X. Li, C. Tian, H. Qian, G. Wang, W. Jiang, |
84. |
M. Endo, K. Hidaka, and H. Sugiyama, Direct observation of an |
|||||||||||||||||||||||||||||||||||||||
|
and C. Mao, Controlling the chirality of DNA nanocages. Angew. |
|
opening event of a DNA cuboid constructed via a prism structure. |
|||||||||||||||||||||||||||||||||||||||
|
Chem., Int. Ed. 51, 7999 (2012). |
|
|
|
|
|
|
|
|
|
|
|
Org. Biomol. Chem. 9, 2075 (2011). |
|
|
|
|
|||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
2366 |
J. Biomed. Nanotechnol. 10, 2350–2370, 2014 |
Sun et al. |
|
|
|
|
|
|
|
|
|
|
DNA Nanotechnology and Its Applications in Biomedical Research |
||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||
85. |
Y. Ke, J. Sharma, M. Liu, K. Jahn, Y. Liu, and H. Yan, Scaffolded |
106. |
O. I. Wilner, A. Henning, B. Shlyahovsky, and I. Willner, Cova- |
||||||||||||||||||||||||||||||||||||||||||||||
|
DNA origami of a DNA tetrahedron molecular container. Nano |
|
lently linked DNA nanotubes. Nano Lett. 10, 1458 (2010). |
||||||||||||||||||||||||||||||||||||||||||||||
|
Lett. 9, 2445 (2009). |
|
|
|
|
|
|
|
|
|
|
107. |
J. Sharma, R. Chhabra, A. Cheng, J. Brownell, Y. Liu, and H. Yan, |
||||||||||||||||||||||||||||||||||||
86. |
D. Liu, S. H. |
Park, |
J. H. Reif, and T. H. LaBean, DNA nanotubes |
|
Control of self-assembly of DNA tubules through integration of |
||||||||||||||||||||||||||||||||||||||||||||
|
self-assembled from triple-crossover tiles as templates for conduc- |
|
gold nanoparticles. Science 323, 112 (2009). |
||||||||||||||||||||||||||||||||||||||||||||||
87. |
tive nanowires. Proc. Nat. Acad. Sci. USA 101, 717 (2004). |
108. |
C. Mao, W. Sun, Z. Shen, and N. C. Seeman, A DNA nanomechan- |
||||||||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||||||||||||
J. C. Mitchell, R. Harris, J. Maio, J. Bath, and A. |
J. Turberfield, |
|
ical device based on the B-Z transition. Nature 397, 144 (1999). |
||||||||||||||||||||||||||||||||||||||||||||||
|
Self-assembly of chiral DNA nanotubes. J. Am. Chem. Soc. |
109. |
|
|
and |
||||||||||||||||||||||||||||||||||||||||||||
|
B. Yurke, A. J. Turberfield, A. P. Mills Jr., F. C. Simmel, |
||||||||||||||||||||||||||||||||||||||||||||||||
88. |
126, 16342 (2004). |
|
|
|
|
|
|
|
|
|
|
|
|
J. L. Neumann, A DNA-fuelled molecular machine made of DNA. |
|||||||||||||||||||||||||||||||||||
P. W. K. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||
Rothemund, A. Ekani-Nkodo, N. Papadakis, A. Kumar, |
|
Nature 406, 605 (2000). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||
|
D. K. Fygenson, and E. Winfree, Design and characterization of |
110. |
W. U. Dittmer and F. C. Simmel, Transcriptional control of DNA- |
||||||||||||||||||||||||||||||||||||||||||||||
|
programmable DNA nanotubes. |
J. Am. Chem. Soc. 126, 16344 |
|
|
based nanomachines. Nano Lett. 4, 689 (2004). |
||||||||||||||||||||||||||||||||||||||||||||
89. |
(2004). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
111. |
S. Beyer, W. U. Dittmer, and F. C. Simmel, Design variations for |
|||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||||||
P. O’Neill, P. W. K. Rothemund, A. Kumar, and D. K. Fygenson, |
|
an aptamer-based DNA nanodevice. J. Biomed. Nanotechnol. 1, 96 |
|||||||||||||||||||||||||||||||||||||||||||||||
90. |
Sturdier DNA nanotubes via ligation. Nano Lett. 6, 1379 (2006). |
|
(2005). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||
A. M. Mohammed and R. Schulman, Directing self-assembly of |
112. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||
H. Yan, H.; X. Zhang, Z. Shen, and N. C. Seeman, A robust DNA |
|||||||||||||||||||||||||||||||||||||||||||||||||
|
DNA nanotubes using programmable seeds. Nano Lett. 13, 4006 |
||||||||||||||||||||||||||||||||||||||||||||||||
|
|
mechanical device controlled by hybridization topology. Nature |
|||||||||||||||||||||||||||||||||||||||||||||||
|
(2013). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||
91. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
415, 62 (2002). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||
M. Endo, N. C. Seeman, and T. Majima, DNA tube structures con- |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||
113. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||
B. Ding and N. C. Seeman, Operation of a DNA robot arm inserted |
|||||||||||||||||||||||||||||||||||||||||||||||||
|
trolled by a four-way-branched DNA connector. Angew. Chem., Int. |
||||||||||||||||||||||||||||||||||||||||||||||||
|
|
into a 2D DNA crystalline substrate. Science 31, 1583 (2006). |
|||||||||||||||||||||||||||||||||||||||||||||||
|
Ed. 44, 6074 (2005). |
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
114. |
S. Liao and N. C. Seeman, Translation of DNA signals into polymer |
|||||||||||||||||||||||||||||||||||||
92. |
H. Liu, Y. Chen, Y. He, A. E. Ribbe, and C. Mao, Approaching |
||||||||||||||||||||||||||||||||||||||||||||||||
|
assembly instructions. Science 306, 2072 (2004). |
||||||||||||||||||||||||||||||||||||||||||||||||
|
the limit: Can one DNA oligonucleotide assemble into large nano- |
|
|||||||||||||||||||||||||||||||||||||||||||||||
|
115. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||
|
H. Gu, J. Chao, S. J. Xiao, and N. C. Seeman, Dynamic patterning |
||||||||||||||||||||||||||||||||||||||||||||||||
|
structures? Angew. Chem. Int. Ed. 45, 1942 (2006). |
||||||||||||||||||||||||||||||||||||||||||||||||
|
|
programmed by DNA tiles captured on a DNA origami substrate. |
|||||||||||||||||||||||||||||||||||||||||||||||
93. |
F. Mathieu, S. Liao, J. Kopatsch, T. Wang, C. Mao, and N. C. |
|
|||||||||||||||||||||||||||||||||||||||||||||||
|
Nat. Nanotechnol. 4, 245 (2009). |
||||||||||||||||||||||||||||||||||||||||||||||||
|
Seeman, Six-helix bundles designed from DNA. Nano Lett. 5, 661 |
|
|||||||||||||||||||||||||||||||||||||||||||||||
|
116. |
W. Shen, M. F. Bruist, |
S. D. Goodman, and N. C. Seeman, |
||||||||||||||||||||||||||||||||||||||||||||||
|
(2005). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
A protein-driven DNA |
device that measures the excess bind- |
|||||||||||||||||||||||||||
94. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||
T. Wang, D. Schifells, S. M. Cuesta, D. K. Fygenson, and N. C. |
|
||||||||||||||||||||||||||||||||||||||||||||||||
|
ing energy of proteins that distort DNA. Angew. Chem., Int. Ed. |
||||||||||||||||||||||||||||||||||||||||||||||||
|
Seeman, Design and characterization of 1D nanotubes and 2D peri- |
|
|||||||||||||||||||||||||||||||||||||||||||||||
|
|
43, 4906 (2004). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||
|
odic arrays self-assembled from DNA multi-helix bundles. J. Am. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||
|
117. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||
|
X. Han, Z. Zhou, F. Yang, and Z. Deng, Catch and release: DNA |
||||||||||||||||||||||||||||||||||||||||||||||||
|
Chem. Soc. 134, 1606 (2012). |
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
tweezers that can catch, hold, and release an object under control. |
|||||||||||||||||||||||||||||||||||||
95. |
R. Wang, W. Liu, and N. C. Seeman, Prototyping nanorod con- |
|
|||||||||||||||||||||||||||||||||||||||||||||||
|
J. Am. Chem. Soc. 130, 14414 (2008). |
||||||||||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
Delivered by Publishing Technology to: Rice University |
||||||||||||||||||||||||||||||||||||||
|
trol: A DNA double helix sheathed within a DNA six-helix bundle. |
118. W. B. Sherman and N. C. Seeman, A precisely controlled DNA |
|||||||||||||||||||||||||||||||||||||||||||||||
|
Chem. Biol. 16, 862 (2009). |
|
IP: 206.214.8.80 On: Fri, 15 Jan 2016 06:47:27 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
biped walking device. Nano Lett. 4, 1203 (2004). |
|||||||||||||||||||||||||||||||||||||
96. |
|
|
|
|
|
|
|
|
|
|
|
Copyright: American Scientific Publishers |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||
A. Kuzuya, R. Wang, R. Sha, and N. C. Seeman, Six-helix and |
119. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||
P. Yin, H. Yan, X. G. Daniell, A. J. Turberfield, and J. H. Reif, |
|||||||||||||||||||||||||||||||||||||||||||||||||
|
eight-helix DNA nanotubes assembled from half-tubes. Nano Lett. |
||||||||||||||||||||||||||||||||||||||||||||||||
|
|
A unidirectional DNA walker that moves autonomously along a |
|||||||||||||||||||||||||||||||||||||||||||||||
|
7, 1757 (2007). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
track. Angew. Chem., Int. Ed. 43, 4906 (2004). |
||||||||||||||||||||||||||||||||||
97. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||
Y. Ke, Y. Liu, J. Zhang, and H. Yan, A study of DNA tube forma- |
120. |
||||||||||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||
Y. Tian, Y. He, Y. Chen, P. Yin, and C. Mao, A DNAzyme |
|||||||||||||||||||||||||||||||||||||||||||||||||
|
tion mechanisms using 4-, 8-, and 12-helix DNA nanostructures. |
||||||||||||||||||||||||||||||||||||||||||||||||
|
|
that walks processively and autonomously along a one-dimensional |
|||||||||||||||||||||||||||||||||||||||||||||||
|
J. Am. Chem. Soc. 128, 4414 (2006). |
|
|||||||||||||||||||||||||||||||||||||||||||||||
|
|
track. Angew. Chem., Int. Ed. 44, 4355 (2005). |
|||||||||||||||||||||||||||||||||||||||||||||||
98. |
P. Yin, R. F. Hariadi, S. Sahu, H. M. T. Choi, S. H. Park, T. H. |
|
|||||||||||||||||||||||||||||||||||||||||||||||
121. |
Z. G. Wang, J. Elbaz, and I. Willner, DNA machines: Bipedal |
||||||||||||||||||||||||||||||||||||||||||||||||
|
LaBean, and J. H. Reif, Programming DNA tube circumferences. |
||||||||||||||||||||||||||||||||||||||||||||||||
|
|
walker and stepper. Nano Lett. 11, 304 (2011). |
|||||||||||||||||||||||||||||||||||||||||||||||
|
Science 321, 824 (2008). |
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
122. |
T. Omabegho, R. Sha, and N. C. Seeman, A bipedal DNA Brownian |
|||||||||||||||||||||||||||||||||||||
99. |
W. B. Sherman and N. C. Seeman, Design of minimally strained |
||||||||||||||||||||||||||||||||||||||||||||||||
|
motor with coordinated legs. Science 324, 67 (2009). |
||||||||||||||||||||||||||||||||||||||||||||||||
|
nucleic acid nanotubes. Biophys. J. 90, 4546 (2006). |
|
|||||||||||||||||||||||||||||||||||||||||||||||
|
123. |
Y. He and D. R. Liu, Autonomous multistep organic synthesis |
|||||||||||||||||||||||||||||||||||||||||||||||
100. |
H. Qian, C. Tian, J. Yu, F. Guo, M.-S. Zheng, W. Jiang, Q.-F. |
||||||||||||||||||||||||||||||||||||||||||||||||
|
in a single isothermal solution mediated by a DNA walker. Nat. |
||||||||||||||||||||||||||||||||||||||||||||||||
|
Dong, and C. Mao, Self-assembly of DNA nanotubes with defined |
|
|||||||||||||||||||||||||||||||||||||||||||||||
|
|
Nanotechnol. 5, 778 (2010). |
|||||||||||||||||||||||||||||||||||||||||||||||
|
diameters and lengths. Small 10, 855 (2014). |
|
|||||||||||||||||||||||||||||||||||||||||||||||
|
124. |
K. Lund, A. J. Manzo, N. Dabby, N. Michelotti, A. Johnson-Buck, |
|||||||||||||||||||||||||||||||||||||||||||||||
101. |
S. M. Douglas, J. J. Chou, and W. M. Shih, DNA-nanotube-induced |
||||||||||||||||||||||||||||||||||||||||||||||||
|
J. Nangreave, S. Taylor, R. J. Pei, M. N. Stojanovic, N. G. Walter, |
||||||||||||||||||||||||||||||||||||||||||||||||
|
alignment of membrane proteins for NMR structure determination. |
|
|||||||||||||||||||||||||||||||||||||||||||||||
|
|
E. Winfree, and H. Yan, Molecular robots guided by prescriptive |
|||||||||||||||||||||||||||||||||||||||||||||||
|
Proc. Natl. Acad. Sci. USA 104, 6644 (2007). |
|
|||||||||||||||||||||||||||||||||||||||||||||||
102. |
F. A. Aldaye, P. K. Lo, P. Karam, C. K. McLaughlin, G. Cosa, |
|
landscapes. |
Nature 465, 206 |
(2010). |
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
125. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||
|
and H. F. Sleiman, Modular construction of DNA nanotubes of |
S. F. Wickham, M. Endo, |
Y. |
Katsuda, K. Hidaka, J. Bath, |
|||||||||||||||||||||||||||||||||||||||||||||
|
tunable geometry and singleor double-stranded character. Nat. |
|
H. Sugiyama, and A. J. Turberfield, Direct observation of stepwise |
||||||||||||||||||||||||||||||||||||||||||||||
|
Nanotechnol. 4, 349 (2009). |
|
|
|
|
|
|
|
|
|
|
|
movement of a synthetic molecular transporter. Nat. Nanotechnol. |
||||||||||||||||||||||||||||||||||||
103. |
P. K. Lo, F. Altvater, and H. F. Sleiman, Templated synthesis of |
126. |
6, 166 (2011). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||
|
DNA nanotubes with controlled, predetermined lengths. J. Am. |
S. F. Wickham, J. Bath, Y. Katsuda, M. Endo, K. Hidaka, |
|||||||||||||||||||||||||||||||||||||||||||||||
|
Chem. Soc. 132, 10212 (2010). |
|
|
|
|
|
|
|
|
|
|
|
H. Sugiyama, and A. J. Turberfield, A DNA-based molecular motor |
||||||||||||||||||||||||||||||||||||
104. |
G. D. Hamblin, K. M. Carneiro, J. F. Fakhoury, K. E. Bujold, and |
|
that can navigate a network of tracks. Nat. Nanotechnol. 7, 169 |
||||||||||||||||||||||||||||||||||||||||||||||
|
H. F. Sleiman, Rolling circle amplification-templated DNA nano- |
127. |
(2012). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||
|
tubes show increased stability and cell penetration ability. J. Am. |
H. Gu, J. Chao, S. J. Xiao, and N. C. Seeman, A proximity-based |
|||||||||||||||||||||||||||||||||||||||||||||||
|
Chem. Soc. 134, 2888 (2012). |
|
|
|
|
|
|
|
|
|
|
|
programmable DNA nanoscale assembly line. Nature 465, 202 |
||||||||||||||||||||||||||||||||||||
105. |
G. D. Hamlin, A. A. Hariri, K. M. M. Carneiro, K. L. Lao, G. Cosa, |
|
(2010). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||
|
and H. F. Sleiman, Simple design for DNA nanotubes from a min- |
128. |
H. Li, S. H. Park, J. H. Reif, T. H. LaBean, and H. Yan, DNA- |
||||||||||||||||||||||||||||||||||||||||||||||
|
imal set of unmodified strands: Rapid, room-temperature assembly |
|
templated self-assembly of protein and nanoparticle linear arrays. |
||||||||||||||||||||||||||||||||||||||||||||||
|
and readily tunable structure. ACS Nano 7, 3022 (2013). |
|
J. Am. Chem. Soc. 126, 418 (2004). |
||||||||||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
J. Biomed. Nanotechnol. 10, 2350–2370, 2014 |
2367 |
DNA Nanotechnology and Its Applications in Biomedical Research |
|
|
|
|
|
|
|
|
|
|
|
|
Sun et al. |
||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||
129. |
S. H. Park, P. Yin, Y. Liu, J. H. Reif, T. H. LaBean, and H. Yan, |
|
factor encapsulation inside a DNA cage. Angew. Chem., Int. Ed. |
||||||||||||||||||||||||||||||||||||||
|
Programmable DNA self-assemblies for nanoscale organization of |
|
52, 2284 (2013). |
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||
|
ligands and proteins. Nano Lett. 5, 729 (2005). |
150. |
J. D. Flory, S. |
Shinde, S. Lin, Y. Liu, H. Yan, G. Ghirlanda, and |
|||||||||||||||||||||||||||||||||||||
130. |
|
|
Accommodation of a |
|
P. Fromme, PNA-peptide assembly in a 3D DNA nanocage at room |
||||||||||||||||||||||||||||||||||||
A. Kuzuya, K. Numajiri, and M. Komiyama, |
|
||||||||||||||||||||||||||||||||||||||||
|
single protein guest in nanometer-scale wells embedded in a DNA |
|
temperature. J. Am. Chem. Soc. 135, 6985 (2013). |
|
|
|
|||||||||||||||||||||||||||||||||||
131. |
nanotape. Angew. Chem., Int. Ed. 47, 3400 (2008). |
151. |
G. Bellot, M. A. McClintock, J. J. Chou, and W. M. Shih, DNA |
||||||||||||||||||||||||||||||||||||||
A. Kuzuya, |
M. Kimura, K. Numajiri, N. Hoshi, T. Ohnishi, |
|
nanotubes for NMR structure determination of membrane proteins. |
||||||||||||||||||||||||||||||||||||||
|
F. Okada, and M. Komiyama, Precisely programmed and robust 2D |
|
Nat. Protoc. 8, 755 (2013). |
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||
|
streptavidin nanoarrays by using periodical nanometer-scale wells |
152. N. D. Derr, B. S. Goodman, R. Jungmann, A. E. Leschziner, W. M. |
|||||||||||||||||||||||||||||||||||||||
|
embedded in |
DNA origami assembly. ChemBioChem 10, 1811 |
|
Shih, and S. L. Reck-Peterson, Tug-of-war in motor protein ensem- |
|||||||||||||||||||||||||||||||||||||
|
(2009). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
bles revealed with a programmable DNA origami scaffold. Science |
||||||||||||||||
132. |
K. Numajiri, M. Kimura, A. Kuzuya, and M. Komiyama, Stepwise |
|
|||||||||||||||||||||||||||||||||||||||
|
338, 662 (2012). |
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||
|
and reversible nanopatterning of proteins on a DNA origami scaf- |
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||
|
153. R. Subramani, S. Juul, A. Rotaru, F. F. Andersen, K. V. Gothelf, |
||||||||||||||||||||||||||||||||||||||||
|
fold. Chem. Commun. 46, 5127 (2010). |
||||||||||||||||||||||||||||||||||||||||
|
|
W. Mamdouh, F. Bensenbacher, M. Dong, and B. Knudsen, A novel |
|||||||||||||||||||||||||||||||||||||||
133. |
Y. He, Y. Tian, A. E. Ribbe, and C. Mao, Antibody nanoarrays with |
|
|||||||||||||||||||||||||||||||||||||||
|
secondary DNA binding site in human topoisomerase I unraveled |
||||||||||||||||||||||||||||||||||||||||
|
a pitch of 20 nanometers. J. Am. Chem. Soc. 128, 12664 (2006). |
|
|||||||||||||||||||||||||||||||||||||||
|
|
by using a 2D DNA origami platform. ACS Nano 10, 5969 (2010). |
|||||||||||||||||||||||||||||||||||||||
134. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||
Y. Liu, C. Lin, H. Li, and H. Yan, Aptamer-directed self-assembly |
154. |
||||||||||||||||||||||||||||||||||||||||
M. Endo, Y. Katsuda, K. Hidaka, and H. Sugiyama, Regulation |
|||||||||||||||||||||||||||||||||||||||||
|
of protein arrays on a DNA nanostructure. Angew. Chem., Int. Ed. |
||||||||||||||||||||||||||||||||||||||||
|
|
of |
DNA methylation using different |
tensions |
of |
double strands |
|||||||||||||||||||||||||||||||||||
|
44, 4333 (2005). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
constructed in a defined DNA nanostructure. J. Am. Chem. Soc. |
||||||||||||||||||||
135. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||
C. Lin, E. Katilius, Y. Liu, J. Zhang, and H. Yan, Self-assembled |
|
||||||||||||||||||||||||||||||||||||||||
|
132, 1592 (2010). |
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||
|
signaling aptamer DNA arrays for protein detection. Angew. Chem., |
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||
|
155. |
M. Endo, Y. Katsuda, K. Hidaka, and H. Sugiyama, A versatile |
|||||||||||||||||||||||||||||||||||||||
|
Int. Ed. 45, 5296 (2006). |
|
|
||||||||||||||||||||||||||||||||||||||
|
|
DNA nanochip for direct analysis of DNA base-excision repair. |
|||||||||||||||||||||||||||||||||||||||
136. |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||
R. Chhabra, |
J. Sharma, Y. Ke, Y. Liu, S. Rinker, S. Lindsay, |
|
|||||||||||||||||||||||||||||||||||||||
|
Angew. Chem., Int. Ed. 49, 9412 (2010). |
|
|
|
|
|
|||||||||||||||||||||||||||||||||||
|
and H. Yan, |
Spatially addressable multiprotein nanoarrays tem- |
|
|
|
|
|
|
|||||||||||||||||||||||||||||||||
|
156. A. Rajendran, M. Endo, K. Hidaka, P. L. T. Tran, J.-L. Mergny, |
||||||||||||||||||||||||||||||||||||||||
|
plated by aptamer-tagged DNA nanoarchitectures. J. Am. Chem. |
||||||||||||||||||||||||||||||||||||||||
|
|
R. J. Gorelick, and H. Sugiyama, HIV-1 nucleocapsid proteins as |
|||||||||||||||||||||||||||||||||||||||
|
Soc. 129, 10304 (2007). |
|
|||||||||||||||||||||||||||||||||||||||
137. |
S. Rinker, Y. Ke, Y. Liu, R. Chhabra, and H. Yan, Self-assembled |
|
molecular chaperones for tetramolecular antiparallel G-quadruplex |
||||||||||||||||||||||||||||||||||||||
|
DNA nanostructures for distance-dependent multivalent ligand- |
157. |
formation. J. Am. Chem. Soc. 135, 18575 (2013). |
|
|
|
|||||||||||||||||||||||||||||||||||
|
protein binding. Nat. Nanotechnol. 3, 418 (2008). |
Y. Suzuki, M. Endo, Y. Katsuda, K. Ou, |
K. |
Hidaka, |
and |
||||||||||||||||||||||||||||||||||||
138. |
J. Malo, J. C. Mitchell, C. Venien-Bryan, J. R. Harris, H. Wille, |
|
H. Sugiyama, DNA origami based visualization system for study- |
||||||||||||||||||||||||||||||||||||||
|
D. J. Sherratt, and A. J. Turberfield, Engineering a 2D protein-DNA |
|
ing site-specific recombination events, J. Am. Chem. Soc. 136, 211 |
||||||||||||||||||||||||||||||||||||||
|
crystal. Angew. Chem., Int. Ed. 44, 3057 (2005). |
|
(2014). |
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||
139. |
E. Nakata, F. F. Liew, C. Uwatoko, S. Kiyonaka, Y. Mori, |
158. M. Endo, K. Tatsumi, K. Terushima, Y. Katsuda, K. Hidaka, |
|||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
Delivered by Publishing Technology to: Rice University |
|
|
|
|
|
|
|
|
|||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
IP: 206.214.8.80 On: Fri, 15 Jan 2016 06:47:27 |
|
|
|
|
|
|
|
|
|||||||||||||||||||||
|
Y. Katsuda, M. Endo, H. Sugiyama, and T. Morii, Zinc-finger pro- |
|
Y. Harada, and H. Sugiyama, Direct visualization of the movement |
||||||||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Copyright: American Scienti ic Publishers |
|
|
|
|
|
|
|
|
|||||||||||||||||
|
teins for site-specific protein positioning on DNA origami struc- |
|
of a single T7 RNA polymerase and transcription on a DNA nano- |
||||||||||||||||||||||||||||||||||||||
140. |
tures. Angew. Chem., Int. Ed. 51, 2421 (2012). |
|
structure. Angew. Chem., Int. Ed. 51, 8778 (2012). |
|
|
|
|||||||||||||||||||||||||||||||||||
B. A. |
R. Williams, K. Lund, Y. Liu, H. |
|
|
|
|
|
|
|
|
|
|
|
159. |
|
|
|
|
|
|
|
|||||||||||||||||||||
Yan, and J. C. Chaput, Self- |
H. Gu, W. Yang, and N. C. Seeman, DNA scissors device used |
||||||||||||||||||||||||||||||||||||||||
|
assembled peptide nanoarrays: An approach to studying protein- |
|
to measure MutS binding to DNA mis-pairs. J. Am. Chem. Soc. |
||||||||||||||||||||||||||||||||||||||
141. |
protein interactions. Angew. Chem., Int. Ed. 46, 3051 (2007). |
|
132, 4352 (2010). |
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||
N. Stephanopoulos, M. Liu, G. J. Tong, Z. Li, Y. Liu, H. Yan, and |
160. |
C. Liu, E. Kim, B. Demple, and N. C. Seeman, A DNA-based |
|||||||||||||||||||||||||||||||||||||||
|
M. B. Francis, Immobilization and one-dimensional arrangement of |
|
nanomechanical device used to characterize the distortion of DNA |
||||||||||||||||||||||||||||||||||||||
|
virus capsids with nanoscale precision using DNA origami. Nano |
|
by apo-SoxR protein. Biochemistry 51, 937 (2012). |
|
|
|
|||||||||||||||||||||||||||||||||||
|
Lett. 10, 2714 (2010). |
161. O. I. Wilner, Y. Weizmann, R. Gill, O. Lioubashevski, R. Freeman, |
|||||||||||||||||||||||||||||||||||||||
142. |
W. Shen, H. Zhong, D. Neff, and M. L. Norton, NTA directed pro- |
||||||||||||||||||||||||||||||||||||||||
|
and I. Willner, Enzyme cascades activated on topologically pro- |
||||||||||||||||||||||||||||||||||||||||
|
tein nanopatterning on DNA origami nanoconstructs. J. Am. Chem. |
|
|||||||||||||||||||||||||||||||||||||||
|
|
grammed DNA scaffolds. Nat. Nanotechnol. 4, 249 (2009). |
|
|
|||||||||||||||||||||||||||||||||||||
|
Soc. 131, 6660 (2009). |
|
|
|
|||||||||||||||||||||||||||||||||||||
|
162. O. I. Wilner, S. Shimron, Y. Weizmann, Z. G. Wang, and I. Willner, |
||||||||||||||||||||||||||||||||||||||||
143. |
R. P. Goodman, C. M. Erben, J. Malo, W. M. Ho, M. L. McKee, |
||||||||||||||||||||||||||||||||||||||||
|
Self-assembly of enzymes on DNA scaffolds: En route to biocat- |
||||||||||||||||||||||||||||||||||||||||
|
A. N. Kapanidis, and A. J. Turberfield, A facile method for |
|
|||||||||||||||||||||||||||||||||||||||
|
|
alytic cascades and the synthesis of metallic nanowires. Nano Lett. |
|||||||||||||||||||||||||||||||||||||||
|
reversibly linking a recombinant protein to DNA. ChemBioChem |
|
|||||||||||||||||||||||||||||||||||||||
|
|
9, 2040 (2009). |
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||
|
10, 1551 (2009). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
163. J. Fu, M. Liu, Y. Liu, N. W. Woodbury, and H. Yan, Interenzyme |
|||||||||||||||||||||
144. |
W. Huang, J. Chao, Q. Yan, and S. J. Xiao, Binding His-tagged |
||||||||||||||||||||||||||||||||||||||||
|
substrate diffusion for an enzyme cascade organized on spatially |
||||||||||||||||||||||||||||||||||||||||
|
proteins to DNA stripes assembled in 2D DNA scaffold. Chin. J. |
|
|||||||||||||||||||||||||||||||||||||||
|
|
addressable DNA |
nanostructures. J. Am. Chem. Soc. 134, |
5516 |
|||||||||||||||||||||||||||||||||||||
|
Chem. 28, 1795 (2010). |
|
|||||||||||||||||||||||||||||||||||||||
|
|
(2012). |
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||
145. |
B. Sacca, R. Meyer, M. Erkelenz, K. Kiko, A. Arndt, H. Schroeder, |
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||
164. |
K. |
Numajiri, T. |
Yamazaki, M. |
Kimura, |
A. |
Kuzuya, |
and |
||||||||||||||||||||||||||||||||||
|
K. S. Rabe, and C. M. Niemeyer, Orthogonal protein decoration of |
||||||||||||||||||||||||||||||||||||||||
|
|
M. Komiyama, Discrete and active enzyme nanoarrays on DNA |
|||||||||||||||||||||||||||||||||||||||
|
DNA origami. Angew. Chem., Int. Ed. 49, 9378 (2010). |
|
|||||||||||||||||||||||||||||||||||||||
|
|
origami scaffolds purified by affinity tag separation. J. Am. Chem. |
|||||||||||||||||||||||||||||||||||||||
146. |
C. M. Erben, R. P. Goodman, and A. J. Turberfield, single-molecule |
|
|||||||||||||||||||||||||||||||||||||||
|
Soc. 132, 9937 (2010). |
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||||||||
|
protein encapsulation in a rigid DNA cage. Angew. Chem., Int. Ed. |
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||||
|
165. |
M. Erkelenz, C. H. Kuo, and C. M. Niemeyer, DNA-mediated |
|||||||||||||||||||||||||||||||||||||||
|
45, 7414 (2006). |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
assembly of cytochrome P450 BM3 subdomains. J. Am. Chem. Soc. |
||||||||||||||||||||
147. |
N. Y. Wong, C. Zhang, L. H. Tan, and Y. Lu, Site-specific attach- |
|
|||||||||||||||||||||||||||||||||||||||
|
ment of proteins onto a 3D DNA tetrahedron through backbone- |
166. |
133, 16111 (2011). |
|
|
|
|
|
|
|
|
|
|||||||||||||||||||||||||||||
|
modified phosphorothioate DNA. Small 7, 1427 (2011). |
C. Zhou, Z. Yang, and D. Liu, Reversible regulation of protein |
|||||||||||||||||||||||||||||||||||||||
148. |
C. Zhang, C. Tian, F. Guo, Z. Liu, W. Jiang, and C. Mao, DNA- |
|
binding affinity by a DNA machine. J. Am. Chem. Soc. 134, 1416 |
||||||||||||||||||||||||||||||||||||||
|
directed three-dimensional protein organization. Angew. Chem., Int. |
167. |
(2012). |
|
|
|
|
|
|
|
|
|
|
|
|
||||||||||||||||||||||||||
149. |
Ed. 51, 3382 (2012). |
|
|
|
|
|
|
M. Liu, J. Fu, C. Hejesen, Y. Yang, N. W. Woodury, K. Gothelf, |
|||||||||||||||||||||||||||||||||
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Y. Liu, and H. Yan, A DNA tweezer-actuated enzyme nanoreactor. |
||||||||||||||||||
R. Crawford, |
C. M. |
Erben, J. Periz, L. M. Hall, T. Brown, A. J. |
|
||||||||||||||||||||||||||||||||||||||
|
Turberfield, and A. N. Kapanidis, Non-covalent single transcription |
|
Nat. Commun. 4, 2127 (2013). |
|
|
|
|
|
|
|
|
2368 |
J. Biomed. Nanotechnol. 10, 2350–2370, 2014 |
Sun et al. |
|
|
DNA Nanotechnology and Its Applications in Biomedical Research |
||||||
|
|
|
|
||||||
168. |
Y. Li, Y. T. H. Cu, and D. Luo, Multiplexed detection of pathogen |
189. |
J. Li, H. Pei, B. Zhu, L. Liang, M. Wei, Y. He, N. Chen, D. Li, |
||||||
|
DNA with DNA-based fluorescence nanobarcodes, Nat. Biotechnol. |
|
Q. Huang, and C. Fan, Self-assembled multivalent DNA nano- |
||||||
|
23, 885 (2005). |
|
|
structures for noninvasive intracellular delivery of immunostimula- |
|||||
169. |
D. Han, J. Hong, H. C. Kim, J. H. Sung, and J. B. Lee, Multi- |
|
tory CpG oligonucleotides. ACS Nano 5, 8783 (2011). |
||||||
|
plexing enhancement for the detection of multiple pathogen DNA. |
190. H. Lee, A. K. R. Lytton-Jean, Y. Chen, K. T. Love, A. I. Park, E. D. |
|||||||
170. |
J. Nanosci. Nanotechnol. 13, 7295 (2013). |
|
Karagiannis, A. Sehgal, W. Querbes, C. S. Zurenko, M. Jayaraman, |
||||||
C. Lin, Y. Liu, and H. Yan, Self-assembled combinatorial encoding |
|
C. G. Peng, K. Charisse, A. Borodovsky, M. Manoharan, J. S. |
|||||||
171. |
nanoarrays for multiplexed biosensing, Nano Lett. 7, 507 (2007). |
|
Donahoe, |
J. Truelove, |
M. Nahrendorf, R. Langer, and D. G. |
||||
C. Lin, R. Jungmann, A. M. Leifer, C. Li, D. levner, G. M. Church, |
|
Anderson, |
Molecularly |
self-assembled nucleic acid nanoparticles |
|||||
|
and P. Yin, Submicrometre geometrically encoded fluorescent bar- |
|
|||||||
|
|
for targeted in vivo SiRNA delivery. Nat. Nanotechnol. 7, 389 |
|||||||
|
codes self-assembled from DNA. Nat. Chem. 4, 832 (2012). |
|
|||||||
|
|
(2012). |
|
|
|
||||
172. |
C. Steinhauer, |
R. Jungmann, |
T. L. Sobey, F. C. Simmel, and |
|
|
|
|
||
191. X. Liu, Y. Xu, T. Yu, C. Clifford, Y. Liu, H. Yan, and Y. Chang, |
|||||||||
|
P. Tinnefeld, |
DNA origami |
as a nanoscopic ruler for super- |
||||||
|
|
A DNA nanostructure platform for directed assembly of synthetic |
|||||||
|
resolution microscopy. Angew. Chem., Int. Ed. 48, 8870 (2009). |
|
|||||||
|
|
vaccines. Nano Lett. 12, 4254 (2012). |
|||||||
173. |
Y. Ke, S. Lindsay, Y. Chang, Y. Liu, and H. Yan, Self-assembled |
|
|||||||
192. K. Mohri, M. Nishikawa, N. Takahashi, T. Shiomi, N. Matsuoka, |
|||||||||
|
water-soluble nucleic acid probe tiles for label-free RNA hybridiza- |
||||||||
|
|
K. Ogawa, M. Endo, K. Hidaka, H. Sugiyama, Y. Takahashi, and |
|||||||
|
tion assays. Science 319, 180 (2008). |
|
|||||||
|
|
Y. Takakura, Design and development of nanosized DNA assem- |
|||||||
174. |
Z. Zhang, Y. Wang, C. Fan, C. Li, Y. Li, L. Qian, Y. Fu, |
|
|||||||
|
blies in polypod-like structures as efficient vehicles for immunos- |
||||||||
|
Y. Shi, J. Hu, and L. He, Asymmetric DNA origami for spatially |
|
|||||||
|
|
timulatory CpG motifs to immune cells. ACS Nano 6, 5931 (2012). |
|||||||
|
addressable and index-free solution-phase DNA chips. Adv. Mater. |
|
|||||||
|
193. |
M. Chang, C. S. Yang, and D.-M. Huang, Aptamer-conjugated |
|||||||
|
22, 2672 (2010). |
|
|||||||
|
|
|
DNA icosahedral nanoparticles as a carrier of doxorubicin for can- |
||||||
175. |
H. K. K. Subramanian, B. Chakraborty, R. Sha, and N. C. Seeman, |
|
|||||||
|
cer therapy. ACS Nano 5, 6156 (2011). |
||||||||
|
The label-free unambiguous detection and symbolic display of sin- |
|
|||||||
|
194. |
D. Bhatia, S. Surana, |
S. Chakraborty, S. P. Koushika, and |
||||||
|
gle nucleotide polymorphisms on DNA origami. Nano Lett. 11, 910 |
||||||||
|
|
Y. Krishnan, A synthetic icosahedral DNA-based host-cargo com- |
|||||||
|
(2011). |
|
|
|
|||||
|
|
|
|
plex for functional in vivo imaging. Nat. Commun. 2, 339 (2011). |
|||||
176. |
A. Kuzuya, Y. Sakai, T. Yamazaki, Y. Xu, and M. Kumiyama, |
|
|||||||
195. |
A. Banerjee, D. Bhatia, A. Saminathan, S. Chakraborty, S. Kar, |
||||||||
|
Nanomechanical DNA origami ‘single-molecule-beacons’ directly |
||||||||
|
imaged by atomic force microscopy. Nat. Commun. 2, 449 (2011). |
|
and Y. Krishnan, Controlled release of encapsulated cargo from a |
||||||
177. |
H. Pei, N. Lu, Y. Wen, S. Song, Y. Liu, H. Yan, and C. Fan, A DNA |
|
DNA icosahedron using a chemical rigger. Angew. Chem., Int. Ed. |
||||||
|
nanostructure-based biomolecular probe carrier platform for elec- |
196. |
52, 6854 (2013). |
|
|
||||
|
trochemical sensing. Adv. Mater. 22, 4754 (2010). |
Q. Mei, |
X. Wei, F. Su, Y. Liu, C. Youngbull, R. Johnson, |
||||||
178. |
Y. Wen, H. Pei, Y. Wan, Y. Su, Q. Huang, S. Song, and C. Fan, |
|
S. Lindsay, H. Yan, and D. Meldrum, Stability of DNA Origami |
||||||
|
DNA nanostructure-decorated surfaces for enhanced aptamer-target |
|
Nanoarrays in Cell Lysate. Nano Lett. 11, 1477 (2011). |
||||||
|
|
|
Delivered by Publishing Technology to: Rice University |
|
|||||
|
|
|
IP: 206.214.8.80 On: Fri, 15 Jan 2016 06:47:27 |
|
|
||||
|
binding and electrochemical cocaine sensors. Anal. Chem. 83, 7418 |
197. |
Q. Mei, R. H. Johnson, X. Wei, F. Su, Y. Liu, L. Kelbauskas, |
||||||
|
(2011). |
|
|
|
S. Lindsay, D. R. Meldrum, and H. Yan, On-chip isotachophoresis |
||||
179. |
|
|
Copyright: American Scientific Publishers |
|
|
||||
H. Pei, Y. Wan, J. Li, H. Hu, Y. Su, Q. Huang, and C. Fan, Regener- |
|
separation of functional DNA origami capture nanoarrays from cell |
|||||||
|
able electrochemical immunological sensing at DNA nanostructure- |
|
lysate. Nano Res. 6, 712 (2013). |
|
|||||
180. |
decorated gold surfaces. Chem. Commun. 47, 6254 (2011). |
198. |
V. J. Schuller, S. Heidegger, N. Sandholzer, P. C. Nickels, N. A. |
||||||
Y. Wen, H. Pei, Y. Shen, J. Xi, M. Lin, N. Lu, X. Shen, J. Li, and |
|
Suhartha, S. Endres, C. Bourquin, and T. Liedl, Cellular immunos- |
|||||||
|
C. Fan, DNA nanostructure-based interfacial engineering for PCR- |
|
timulation by CpG sequence-coated DNA origami structures. ACS |
||||||
|
free ultrasensitive electrochemical analysis of microRNA. Sci. Rep. |
|
Nano 5, 9696 (2011). |
|
|
||||
|
2, 867 (2012). |
|
|
199. Y. X. Zhao, A. Shaw, X. Zeng, E. Benson, A. M. Nystrom, and |
|||||
181. |
C. Lin, Y. Ke, Y. Liu, M. Mertig, J. Gu, and H. Yan, Functional |
||||||||
|
B. Hogberg, DNA origami delivery system for cancer therapy with |
||||||||
|
DNA nanotube arrays: Bottom-up meets top-down. Angew. Chem., |
|
|||||||
|
|
tunable release properties. ACS Nano 6, 8684 (2012). |
|||||||
|
Int. Ed. 46, 6089 (2007). |
|
|
||||||
|
|
200. |
Q. Jiang, C. Song, J. Nangreave, X. Liu, L. Lin, D. Qiu, Z. G. |
||||||
182. |
A. E. Gerdon, S. S. Oh, K. Hsieh, Y. Ke, H. Yan, and H. T. Soh, |
||||||||
|
Wang, G. Zou, X. Liang, H. Yan, and B. Ding, DNA origami as |
||||||||
|
Controlled delivery of DNA origami on patterned surfaces. Small |
|
|||||||
|
|
a carrier for circumvention of drug resistance. J. Am. Chem. Soc. |
|||||||
|
5, 1942 (2009). |
|
|
||||||
|
|
|
134, 13396 (2012). |
|
|
||||
183. |
R. J. Kershner, L. D. Buzano, C. M. Micheel, A. M. Hung, A. R. |
|
|
|
|||||
201. |
S. M. Douglas, I. Bachelet, and |
G. M. Church, A logic-gated |
|||||||
|
Fornof, J. N. Cha, C. T. Rettner, M. Bersani, J. Frommer, P. W. |
||||||||
|
|
nanorobot |
for targeted |
transport |
of molecular payloads. Science |
||||
|
K. Rothemund, and G. M. Wallraff, Placement and orientation of |
|
|||||||
|
|
335, 831 (2012). |
|
|
|||||
|
individual DNA shapes on lithographically patterned surfaces. Nat. |
|
|
|
|||||
|
202. X. Ouyang, J. Li, H. Liu, B. Zhao, J. Yan, Y. Ma, S. Xiao, S. Song, |
||||||||
|
Nanotechnol. 4, 557 (2009). |
|
|||||||
|
|
|
Q. Huang, J. Chao, and C. Fan, Rolling circle amplification-based |
||||||
184. |
A. M. Hung, C. M. Micheel, L. D. Buzano, L. W. Osterbur, G. M. |
|
|||||||
|
DNA origami nanostructures for intracellular delivery of immunos- |
||||||||
|
Wallraff, and J. N. Cha, Large-area spatially ordered arrays of gold |
|
|||||||
|
|
timulatory drugs. Small 9, 3082 (2013). |
|||||||
|
nanoparticles directed by lithographically confined DNA origami. |
|
|||||||
|
203. X. Shen, Q. Jiang, J. Wang, L. Dai, G. Zou, Z. G. Wang, W. Q. |
||||||||
|
Nat. Nanotechnol. 5, 121 (2010). |
||||||||
|
|
Chen, W. Jiang, and B. Ding, Visualization of the intracellular loca- |
|||||||
185. |
O. C. Farokhzad and R. Langer, Impact of nanotechnology on drug |
|
|||||||
|
tion and stability of DNA origami with a label-free fluorescent |
||||||||
|
delivery. ACS Nano 3, 16 (2009). |
|
|||||||
186. |
S. H. Ko, H. Liu, Y. Chen, and C. Mao, DNA nanotubes as combi- |
204. |
probe. Chem. Commun. 48, 11301 (2012). |
||||||
|
natorial vehicles for cellular delivery. Biomacromolecules 9, 3039 |
S. Rinker, Y. Liu, and H. Yan, Two-dimensional LNA/DNA arrays: |
|||||||
|
(2008). |
|
|
|
Estimating the helicity of LNA/DNA hybrid duplex. Chem. Com- |
||||
187. |
J. W. Keuma and H. Bermudez, Enhanced resistance of DNA nano- |
205. |
mun. 42, 2675 (2006). |
|
|
||||
|
structures to enzymatic digestion. Chem. Commun. 45, 7036 (2009). |
N. Park, S. H. Um, H. Funabashi, J. Xu, and D. Luo, A cell-free |
|||||||
188. |
A. S. Walsh, H. Yin, C. M. Erben, M. J. A. Wood, and A. J. |
|
protein-producing gel. Nat. Mater. 8, 432 (2009). |
||||||
|
Turberfield, DNA cage delivery to mammalian cells. ACS Nano |
206. |
K. S. Rabe and C. M. Niemeyer, Gene jelly. Nat. Mater. 8, 370 |
||||||
|
5, 5427 (2011). |
|
|
(2009). |
|
|
|
J. Biomed. Nanotechnol. 10, 2350–2370, 2014 |
2369 |