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William Shih, PH.D.


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  1. DP2OD004641 (SHIH, WILLIAM M.) Sep 30, 2008 - Aug 31, 2013
    NMR Structure Determination of Membrane Proteins Enabled by DNA Nanotubes
    Role: Principal Investigator

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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  1. Krieg E, Shih WM. Selective Nascent Polymer Catch-and-Release Enables Scalable Isolation of Multi-Kilobase Single-Stranded DNA. Angew Chem Int Ed Engl. 2018 Jan 15; 57(3):714-718. PMID: 29210156.
    View in: PubMed
  2. Johnson-Buck A, Shih WM. Single-Molecule Clocks Controlled by Serial Chemical Reactions. Nano Lett. 2017 Dec 13; 17(12):7940-7944. PMID: 29090576.
    View in: PubMed
  3. Ponnuswamy N, Bastings MMC, Nathwani B, Ryu JH, Chou LYT, Vinther M, Li WA, Anastassacos FM, Mooney DJ, Shih WM. Oligolysine-based coating protects DNA nanostructures from low-salt denaturation and nuclease degradation. Nat Commun. 2017 May 31; 8:15654. PMID: 28561045.
    View in: PubMed
  4. Perrault SD, Shih WM. Lipid Membrane Encapsulation of a 3D DNA Nano Octahedron. Methods Mol Biol. 2017; 1500:165-184. PMID: 27813008.
    View in: PubMed
  5. Min J, Shih WM, Bellot G. Designing DNA Nanotube Liquid Crystals as a Weak-Alignment Medium for NMR Structure Determination of Membrane Proteins. Methods Mol Biol. 2017; 1500:203-215. PMID: 27813010.
    View in: PubMed
  6. Iwaki M, Wickham SF, Ikezaki K, Yanagida T, Shih WM. A programmable DNA origami nanospring that reveals force-induced adjacent binding of myosin VI heads. Nat Commun. 2016 Dec 12; 7:13715. PMID: 27941751.
    View in: PubMed
  7. Wang P, Gaitanaros S, Lee S, Bathe M, Shih WM, Ke Y. Programming Self-Assembly of DNA Origami Honeycomb Two-Dimensional Lattices and Plasmonic Metamaterials. J Am Chem Soc. 2016 06 22; 138(24):7733-40. PMID: 27224641.
    View in: PubMed
  8. Xu W, Nathwani B, Lin C, Wang J, Karatekin E, Pincet F, Shih W, Rothman JE. A Programmable DNA Origami Platform to Organize SNAREs for Membrane Fusion. J Am Chem Soc. 2016 Apr 06; 138(13):4439-47. PMID: 26938705; PMCID: PMC4950518.
  9. Yang Y, Wang J, Shigematsu H, Xu W, Shih WM, Rothman JE, Lin C. Self-assembly of size-controlled liposomes on DNA nanotemplates. Nat Chem. 2016 May; 8(5):476-83. PMID: 27102682; PMCID: PMC5021307 [Available on 11/01/16].
  10. Ke Y, Meyer T, Shih WM, Bellot G. Regulation at a distance of biomolecular interactions using a DNA origami nanoactuator. Nat Commun. 2016 Mar 18; 7:10935. PMID: 26988942; PMCID: PMC4802031.
  11. 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 Commun. 2015 Nov 16; 6:8634. PMID: 26567534; PMCID: PMC4660042.
  12. Raschle T, Lin C, Jungmann R, Shih WM, Wagner G. Controlled Co-reconstitution of Multiple Membrane Proteins in Lipid Bilayer Nanodiscs Using DNA as a Scaffold. ACS Chem Biol. 2015 Nov 20; 10(11):2448-54. PMID: 26356202; PMCID: PMC4769731 [Available on 11/20/16].
  13. Knudsen JB, Liu L, Bank Kodal AL, Madsen M, Li Q, Song J, Woehrstein JB, Wickham SF, Strauss MT, Schueder F, Vinther J, Krissanaprasit A, Gudnason D, Smith AA, Ogaki R, Zelikin AN, Besenbacher F, Birkedal V, Yin P, Shih WM, Jungmann R, Dong M, Gothelf KV. Routing of individual polymers in designed patterns. Nat Nanotechnol. 2015 Oct; 10(10):892-8. PMID: 26322946.
    View in: PubMed
  14. 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. 2015 Jun; 14(2):146-53. PMID: 26032947.
    View in: PubMed
  15. 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. 2015 Jul; 10(7):637-44. PMID: 26005999.
    View in: PubMed
  16. 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 Commun. 2015 May 12; 6:7147. PMID: 25962338; PMCID: PMC4430122.
  17. Shih WM. Materials Science. Exploiting weak interactions in DNA self-assembly. Science. 2015 Mar 27; 347(6229):1417-8. PMID: 25814568.
    View in: PubMed
  18. 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. 2015; 9(4):3530-9. PMID: 25734977; PMCID: PMC4415451.
  19. Ke Y, Ong LL, Sun W, Song J, Dong M, Shih WM, Yin P. DNA brick crystals with prescribed depths. Nat Chem. 2014 Nov; 6(11):994-1002. PMID: 25343605; PMCID: PMC4238964.
  20. Hahn J, Wickham SF, Shih WM, Perrault SD. Addressing the instability of DNA nanostructures in tissue culture. ACS Nano. 2014 Sep 23; 8(9):8765-75. PMID: 25136758; PMCID: PMC4174095.
  21. Perrault SD, Shih WM. Virus-inspired membrane encapsulation of DNA nanostructures to achieve in vivo stability. ACS Nano. 2014 May 27; 8(5):5132-40. PMID: 24694301; PMCID: PMC4046785.
  22. 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. 2014 May 14; 10(9):1765-9. PMID: 24532395.
    View in: PubMed
  23. Jungmann R, Avendaño MS, Woehrstein JB, Dai M, Shih WM, Yin P. Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. Nat Methods. 2014 Mar; 11(3):313-8. PMID: 24487583; PMCID: PMC4153392.
  24. 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. 2014 Mar 06; 426(5):1095-108. PMID: 24075869; PMCID: PMC3934758.
  25. Pfitzner E, Wachauf C, Kilchherr F, Pelz B, Shih WM, Rief M, Dietz H. Rigid DNA beams for high-resolution single-molecule mechanics. Angew Chem Int Ed Engl. 2013 Jul 22; 52(30):7766-71. PMID: 23794413; PMCID: PMC3749440.
  26. Ducani C, Kaul C, Moche M, Shih WM, Högberg B. Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides. Nat Methods. 2013 Jul; 10(7):647-52. PMID: 23727986; PMCID: PMC3843646.
  27. Bellot G, McClintock MA, Chou JJ, Shih WM. DNA nanotubes for NMR structure determination of membrane proteins. Nat Protoc. 2013 Apr; 8(4):755-70. PMID: 23518667; PMCID: PMC3843643.
  28. Ke Y, Ong LL, Shih WM, Yin P. Three-dimensional structures self-assembled from DNA bricks. Science. 2012 Nov 30; 338(6111):1177-83. PMID: 23197527; PMCID: PMC3843647.
  29. Lin C, Perrault SD, Kwak M, Graf F, Shih WM. Purification of DNA-origami nanostructures by rate-zonal centrifugation. Nucleic Acids Res. 2013 Jan; 41(2):e40. PMID: 23155067; PMCID: PMC3553994.
  30. 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. 2012 Nov 02; 338(6107):662-5. PMID: 23065903; PMCID: PMC3840815.
  31. Lin C, Jungmann R, Leifer AM, Li C, Levner D, Church GM, Shih WM, Yin P. Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA. Nat Chem. 2012 Oct; 4(10):832-9. PMID: 23000997; PMCID: PMC3523708.
  32. 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. Chem Sci. 2012 Aug 01; 3(8):2587-2597. PMID: 24653832.
    View in: PubMed
  33. Ke Y, Voigt NV, Gothelf KV, Shih WM. Multilayer DNA origami packed on hexagonal and hybrid lattices. J Am Chem Soc. 2012 Jan 25; 134(3):1770-4. PMID: 22187940; PMCID: PMC3336742.
  34. 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. Nat Struct Mol Biol. 2012 Jan 08; 19(2):193-200. PMID: 22231401; PMCID: PMC3272163.
  35. Pinheiro AV, Han D, Shih WM, Yan H. Challenges and opportunities for structural DNA nanotechnology. Nat Nanotechnol. 2011 Nov 06; 6(12):763-72. PMID: 22056726; PMCID: PMC3334823.
  36. Berardi MJ, Shih WM, Harrison SC, Chou JJ. Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching. Nature. 2011 Jul 24; 476(7358):109-13. PMID: 21785437; PMCID: PMC3150631.
  37. Bellot G, McClintock MA, Lin C, Shih WM. Recovery of intact DNA nanostructures after agarose gel-based separation. Nat Methods. 2011 Mar; 8(3):192-4. PMID: 21358621; PMCID: PMC3843644.
  38. Liedl T, Högberg B, Tytell J, Ingber DE, Shih WM. Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nat Nanotechnol. 2010 Jul; 5(7):520-4. PMID: 20562873; PMCID: PMC2898913.
  39. Shih WM, Lin C. Knitting complex weaves with DNA origami. Curr Opin Struct Biol. 2010 Jun; 20(3):276-82. PMID: 20456942; PMCID: PMC2916953.
  40. Ke Y, Douglas SM, Liu M, Sharma J, Cheng A, Leung A, Liu Y, Shih WM, Yan H. Multilayer DNA origami packed on a square lattice. J Am Chem Soc. 2009 Nov 04; 131(43):15903-8. PMID: 19807088; PMCID: PMC2821935.
  41. Dietz H, Douglas SM, Shih WM. Folding DNA into twisted and curved nanoscale shapes. Science. 2009 Aug 07; 325(5941):725-30. PMID: 19661424; PMCID: PMC2737683.
  42. Högberg B, Liedl T, Shih WM. Folding DNA origami from a double-stranded source of scaffold. J Am Chem Soc. 2009 Jul 08; 131(26):9154-5. PMID: 19566089; PMCID: PMC2724999.
  43. Douglas SM, Marblestone AH, Teerapittayanon S, Vazquez A, Church GM, Shih WM. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 2009 Aug; 37(15):5001-6. PMID: 19531737; PMCID: PMC2731887.
  44. Douglas SM, Dietz H, Liedl T, Högberg B, Graf F, Shih WM. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature. 2009 May 21; 459(7245):414-8. PMID: 19458720; PMCID: PMC2688462.
  45. Jungmann R, Liedl T, Sobey TL, Shih W, Simmel FC. Isothermal assembly of DNA origami structures using denaturing agents. J Am Chem Soc. 2008 Aug 06; 130(31):10062-3. PMID: 18613687.
    View in: PubMed
  46. Shih W. Biomolecular assembly: dynamic DNA. Nat Mater. 2008 Feb; 7(2):98-100. PMID: 18219328.
    View in: PubMed
  47. Douglas SM, Chou JJ, Shih WM. DNA-nanotube-induced alignment of membrane proteins for NMR structure determination. Proc Natl Acad Sci U S A. 2007 Apr 17; 104(16):6644-8. PMID: 17404217; PMCID: PMC1871839.
  48. Shih WM, Quispe JD, Joyce GF. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature. 2004 Feb 12; 427(6975):618-21. PMID: 14961116.
    View in: PubMed
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