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Publications


Schmidt TL, Beliveau BJ, Uca YO, Theilmann M, Da Cruz F, Wu CT, Shih WM. Scalable amplification of strand subsets from chip-synthesized oligonucleotide libraries. Nat Comm Accepted.


Tellechea A, Silva EA, Min J, Leal EC, Auster ME, Pradhan-Nabzdyk L, Shih W, Mooney DJ, Veves A. Alginate and DNA Gels Are Suitable Delivery Systems for Diabetic Wound Healing. Int J Low Extrem Wounds 14, 146–153, 2015. [journal link]


Tian Y, Wang T, Liu W, Xin HL, Li H, Ke Y, Shih WM, Gang O. Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames. Nat Nanotechnol 10, 637–644, 2015. [journal link] [zip]


Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu CT. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. Nat Comm 6, 7147, 2015. [journal link] [zip]


Shih WM. Materials Science. Exploiting weak interactions in DNA self-assembly. Science 347, 1417–1418, 2015. [journal link] [zip]


Kocabey S, Kempter S, List J, Xing Y, Bae W, Schiffels D, Shih WM, Simmel FC, Liedl T. Membrane-assisted growth of DNA origami nanostructure arrays. ACS Nano 9, 3530–3539, 2015. [journal link] [zip]


Ke Y, Ong LL, Sun W, Song J, Dong M, Shih WM, Yin P. DNA brick crystals with prescribed depths. Nat Chem. 6, 994–1002, 2014. [journal link] [zip]


Hahn J, Wickham SF, Shih WM, Perrault SD. Addressing the instability of DNA nanostructures in tissue culture. ACS Nano 8, 8765–8775, 2014. [journal link] [zip]


Perrault SD, Shih WM. Virus-Inspired Membrane Encapsulation of DNA Nanostructures To Achieve In Vivo Stability. ACS Nano 8, 5132–5140, 2014. [journal link] [zip]


Nickels PC, Ke Y, Jungmann R, Smith DM, Leichsenring M, Shih WM, Liedl T, Högberg B. DNA Origami Structures Directly Assembled from Intact Bacteriophages. Small 10, 1765–1769, 2014. [journal link] [zip]


Jungmann R*, Avendano MS*, Woehrstein JB*, Dai M, Shih WM, Yin P. Multiplexed 3D Cellular Super-Resolution Imaging with DNA-PAINT and Exchange-PAINT. Nature Methods 11, 313–318, 2014. [journal link] [zip]


Sun ZY, Cheng Y, Kim M, Song L, Choi J, Kudahl UJ, Brusic V, Chowdhury B, Yu L, Seaman MS, Bellot G, Shih WM, Wagner G, Reinherz EL. Disruption of Helix-Capping Residues 671 and 674 Reveals a Role in HIV-1 Entry for a Specialized Hinge Segment of the Membrane Proximal External Region of gp41. J Mol Biol. 426, 1095–1108, 2014. [journal link] [zip]


Pfitzner E, Wachauf C, Kilchherr F, Pelz B, Shih WM, Rief M, Dietz H. Rigid DNA Beams for High-Resolution Single-Molecule Mechanics. Angewandte Chemie Intl Ed. 52, 1–7, 2013. [journal link] [zip]


Ducani C, Kaul C, Moche M, Shih WM, Högberg B. Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides. Nat Methods 10, 647–652, 2013. [journal link] [zip]


Bellot G, McClintock MA, Chou JJ, Shih WM. DNA nanotubes for NMR structure determination of membrane proteins. Nat Protoc. 8, 755–770, 2013. [journal link] [zip]


Lin C, Perrault SD, Kwak M, Graf F, Shih WM. Purification of DNA-origami nanostructures by rate-zonal centrifugation. Nucleic Acids Res. 41, e40, 2013. [journal link] [zip]


Ke Y, Ong LL, Shih WM, Yin P. Three-dimensional structures self-assembled from DNA bricks. Science 338, 1177–1183, 2012. (cover) [journal link] [zip]


Derr ND, Goodman BS, Jungmann R, Leschziner AE, Shih WM, Reck-Peterson SL, Tug of War in Motor Protein Ensembles Revealed with a Programmable DNA Origami Scaffold, Science 338, 662–665, 2012. [journal link] [zip]


Lin C, Jungmann R, Leifer AM, Li C, Levner D, Church GM, Shih WM*, Peng Yin*. Sub-micrometer Geometrically Encoded Fluorescent Barcodes Self-Assembled from DNA. Nature Chemistry 4, 832–839, 2012. [journal link] [zip]


Ke Y, Bellot G, Voigt NV, Fradkov E, Shih WM. Two design strategies for enhancement of multilayer–DNA-origami folding: underwinding for specific intercalator rescue and staple-break positioning. Chemical Science 3, 2587–2597, 2012. [journal link] [zip]


Ke Y, Voigt NV, Gothelf K, Shih WM. Multilayer DNA Origami Packed on Hexagonal and Hybrid Lattices. J. Am. Chem. Soc. 134, 1770–1774, 2012. [journal link] [zip]


Qiu W, Derr ND, Goodman BS, Villa E, Wu D, Shih W, Reck-Peterson SL. Dynein achieves processive motion using both stochastic and coordinated stepping. Nature Structural & Molecular Biology 19, 193-200, 2012. [journal link] [zip]


Berardi M, Shih WM, Harrison SC, Chou JJ. Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching. Nature 476, 109–113, 2011. [journal link] [zip]


Bellot G, McClintock MA, Lin CX, Shih WM. Recovery of intact DNA nanostructures after agarose gel-based separation. Nature Methods 8, 192–194, 2011. [journal link] [zip]


Pinheiro AV, Han D, *Shih WM, *Yan H. Challenges and opportunities for structural DNA nanotechnology. Nature Nanotechnology 6, 763–772, 2011. [journal link] [zip]


Liedl T, Högberg B, Tytell J, Ingber DE, Shih WM. Self-assembly of 3D prestressed tensegrity structures from DNA. Nature Nanotechnology 5, 520–524, 2010. [journal link] [zip]


Shih WM, Lin C. Knitting complex weaves with DNA origami. Curr Opin Struct Biol. 20, 276–282, 2010. [journal link] [zip]


Ke Y, Douglas SM, Liu MH, Sharma J, Cheng A, Leung A, Liu Y, Shih W*, Yan H. Multilayer DNA origami packed on a square lattice. J. Am. Chem. Soc. 131, 15903–15908, 2009. [journal link] [zip]


Dietz H, Douglas SM, Shih WM. Folding DNA into twisted and curved nanoscale shapes. Science 325, 725–730, 2009. [journal link] [zip]


Högberg B, Liedl T, Shih WM. Folding DNA origami from a double-stranded source of scaffold. J. Am. Chem. Soc. 131, 9154–9155, 2009. [journal link] [zip]

     

Douglas SM, Marblestone AH, Teerapittayanon S, Vazquez A, Church GM, Shih WM. Rapid prototyping of three-dimensional DNA-origami shapes with caDNAno. Nucleic Acids Research 37, 5001–5006, 2009. [journal link] [zip]


Douglas SM, Dietz H, Liedl T, Högberg B, Graf F, Shih WM. Self-assembly of DNA into nanoscale shapes. Nature 459, 414–418, 2009. [journal link] [zip]


Jungmann R, Liedl T, Sobey TL, Shih W, Simmel FC. Isothermal assembly of DNA origami structures using denaturing agents. J. Am. Chem. Soc. 130, 10062-10063, 2008. [journal link] [zip]


Shih W. Biomolecular self-assembly: dynamic DNA. Nature Materials 7, 98–100, 2008. [journal link] [zip]


Douglas SM, Chou JJ, Shih WM. DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. PNAS 104, 6644–6648, 2007. [journal link] [zip]


Shih WM, Quispe, JD, Joyce GF. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature 427, 618–621, 2004. (cover) [journal link] [zip]







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