Harvard Catalyst Profiles

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William Shih, Ph.D.

Other Positions

The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01GM131401 (SHIH, WILLIAM M.) Sep 20, 2018 - Aug 31, 2022
    DNA-corralled nanodiscs for study of large membrane proteins and their complexes
    Role: Principal Investigator
  2. 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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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Shrestha P, Yang D, Tomov TE, MacDonald JI, Ward A, Bergal HT, Krieg E, Cabi S, Luo Y, Nathwani B, Johnson-Buck A, Shih WM, Wong WP. Single-molecule mechanical fingerprinting with DNA nanoswitch calipers. Nat Nanotechnol. 2021 Oct 21. PMID: 34675411.
    Citations:    Fields:    
  2. Minev D, Wintersinger CM, Ershova A, Shih WM. Robust nucleation control via crisscross polymerization of highly coordinated DNA slats. Nat Commun. 2021 03 19; 12(1):1741. PMID: 33741912.
    Citations:    Fields:    Translation:Cells
  3. Wickham SFJ, Auer A, Min J, Ponnuswamy N, Woehrstein JB, Schueder F, Strauss MT, Schnitzbauer J, Nathwani B, Zhao Z, Perrault SD, Hahn J, Lee S, Bastings MM, Helmig SW, Kodal AL, Yin P, Jungmann R, Shih WM. Complex multicomponent patterns rendered on a 3D DNA-barrel pegboard. Nat Commun. 2020 11 13; 11(1):5768. PMID: 33188187.
    Citations: 4     Fields:    Translation:Cells
  4. Krieg E, Gupta K, Dahl A, Lesche M, Boye S, Lederer A, Shih WM. A smart polymer for sequence-selective binding, pulldown, and release of DNA targets. Commun Biol. 2020 07 10; 3(1):369. PMID: 32651444.
    Citations: 1     Translation:HumansCells
  5. Padmanabha Das KM, Shih WM, Wagner G, Nasr ML. Large Nanodiscs: A Potential Game Changer in Structural Biology of Membrane Protein Complexes and Virus Entry. Front Bioeng Biotechnol. 2020; 8:539. PMID: 32596222.
    Citations: 4     
  6. Sun W, Shen J, Zhao Z, Arellano N, Rettner C, Tang J, Cao T, Zhou Z, Ta T, Streit JK, Fagan JA, Schaus T, Zheng M, Han SJ, Shih WM, Maune HT, Yin P. Precise pitch-scaling of carbon nanotube arrays within three-dimensional DNA nanotrenches. Science. 2020 05 22; 368(6493):874-877. PMID: 32439790.
    Citations: 8     Fields:    
  7. Anastassacos FM, Zhao Z, Zeng Y, Shih WM. Glutaraldehyde Cross-Linking of Oligolysines Coating DNA Origami Greatly Reduces Susceptibility to Nuclease Degradation. J Am Chem Soc. 2020 02 19; 142(7):3311-3315. PMID: 32011869.
    Citations: 18     Fields:    Translation:HumansCells
  8. Hahn J, Chou LYT, Sørensen RS, Guerra RM, Shih WM. Extrusion of RNA from a DNA-Origami-Based Nanofactory. ACS Nano. 2020 02 25; 14(2):1550-1559. PMID: 31922721.
    Citations:    Fields:    
  9. Minev D, Guerra R, Kishi JY, Smith C, Krieg E, Said K, Hornick A, Sasaki HM, Filsinger G, Beliveau BJ, Yin P, Church GM, Shih WM. Rapid in vitro production of single-stranded DNA. Nucleic Acids Res. 2019 12 16; 47(22):11956-11962. PMID: 31713635.
    Citations: 5     Fields:    Translation:HumansCells
  10. Hahn J, Shih WM. Thermal cycling of DNA devices via associative strand displacement. Nucleic Acids Res. 2019 11 18; 47(20):10968-10975. PMID: 31584082.
    Citations:    Fields:    
  11. Chou LYT, Shih WM. In Vitro Transcriptional Regulation via Nucleic-Acid-Based Transcription Factors. ACS Synth Biol. 2019 11 15; 8(11):2558-2565. PMID: 31574217.
    Citations: 1     Fields:    Translation:Cells
  12. Nathwani B, Shih WM, Wong WP. Force Spectroscopy and Beyond: Innovations and Opportunities. Biophys J. 2018 12 18; 115(12):2279-2285. PMID: 30447991.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  13. Zhao Z, Zhang M, Hogle JM, Shih WM, Wagner G, Nasr ML. DNA-Corralled Nanodiscs for the Structural and Functional Characterization of Membrane Proteins and Viral Entry. J Am Chem Soc. 2018 08 29; 140(34):10639-10643. PMID: 30094995.
    Citations: 11     Fields:    Translation:HumansCells
  14. Bastings MMC, Anastassacos FM, Ponnuswamy N, Leifer FG, Cuneo G, Lin C, Ingber DE, Ryu JH, Shih WM. Modulation of the Cellular Uptake of DNA Origami through Control over Mass and Shape. Nano Lett. 2018 06 13; 18(6):3557-3564. PMID: 29756442.
    Citations: 30     Fields:    Translation:HumansCells
  15. Li J, Johnson-Buck A, Yang YR, Shih WM, Yan H, Walter NG. Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat. Nat Nanotechnol. 2018 08; 13(8):723-729. PMID: 29736034.
    Citations: 12     Fields:    Translation:Cells
  16. 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 01 15; 57(3):714-718. PMID: 29210156.
    Citations: 6     Fields:    Translation:Cells
  17. Johnson-Buck A, Shih WM. Single-Molecule Clocks Controlled by Serial Chemical Reactions. . 2017 12 13; 17(12):7940-7944. PMID: 29090576.
    Citations: 2     
  18. 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 05 31; 8:15654. PMID: 28561045.
    Citations: 62     Fields:    Translation:HumansAnimalsCells
  19. Perrault SD, Shih WM. Lipid Membrane Encapsulation of a 3D DNA Nano Octahedron. Methods Mol Biol. 2017; 1500:165-184. PMID: 27813008.
    Citations: 2     Fields:    
  20. 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.
    Citations:    Fields:    
  21. 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 12 12; 7:13715. PMID: 27941751.
    Citations: 14     Fields:    Translation:HumansCells
  22. 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.
    Citations: 17     Fields:    Translation:Cells
  23. 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.
    Citations: 16     Fields:    Translation:Cells
  24. 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 05; 8(5):476-83. PMID: 27102682.
    Citations: 33     Fields:    
  25. 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.
    Citations: 21     Fields:    Translation:Cells
  26. 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.
    Citations: 19     Fields:    Translation:Cells
  27. 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.
    Citations: 8     Fields:    Translation:Cells
  28. 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.
    Citations: 31     Fields:    Translation:Cells
  29. 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.
    Citations: 10     Fields:    Translation:Animals
  30. 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.
    Citations: 34     Fields:    Translation:Cells
  31. 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.
    Citations: 98     Fields:    Translation:AnimalsCells
  32. Shih WM. Materials Science. Exploiting weak interactions in DNA self-assembly. Science. 2015 Mar 27; 347(6229):1417-8. PMID: 25814568.
    Citations:    Fields:    Translation:Cells
  33. 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.
    Citations: 29     Fields:    Translation:Cells
  34. 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.
    Citations: 22     Fields:    Translation:Cells
  35. 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.
    Citations: 63     Fields:    Translation:HumansAnimalsCells
  36. 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.
    Citations: 91     Fields:    Translation:AnimalsCells
  37. 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.
    Citations: 7     Fields:    Translation:Cells
  38. 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.
    Citations: 231     Fields:    
  39. 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.
    Citations: 16     Fields:    Translation:HumansCells
  40. 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.
    Citations: 25     Fields:    
  41. 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.
    Citations: 34     Fields:    Translation:Cells
  42. 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.
    Citations: 11     Fields:    Translation:Cells
  43. 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.
    Citations: 189     Fields:    Translation:Cells
  44. 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.
    Citations: 29     Fields:    
  45. 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.
    Citations: 118     Fields:    Translation:Cells
  46. 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.
    Citations: 51     Fields:    
  47. 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.
    Citations: 17     
  48. 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.
    Citations: 20     Fields:    Translation:Cells
  49. 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.
    Citations: 91     Fields:    Translation:AnimalsCells
  50. 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.
    Citations: 191     Fields:    Translation:HumansCells
  51. 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.
    Citations: 112     Fields:    Translation:AnimalsCells
  52. 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.
    Citations: 16     Fields:    
  53. 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.
    Citations: 63     Fields:    Translation:Cells
  54. Shih WM, Lin C. Knitting complex weaves with DNA origami. Curr Opin Struct Biol. 2010 Jun; 20(3):276-82. PMID: 20456942.
    Citations: 32     Fields:    Translation:Cells
  55. 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.
    Citations: 84     Fields:    Translation:Cells
  56. Dietz H, Douglas SM, Shih WM. Folding DNA into twisted and curved nanoscale shapes. Science. 2009 Aug 07; 325(5941):725-30. PMID: 19661424.
    Citations: 247     Fields:    Translation:Cells
  57. 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.
    Citations: 15     Fields:    Translation:Cells
  58. 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.
    Citations: 215     Fields:    Translation:Cells
  59. 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.
    Citations: 444     Fields:    Translation:Cells
  60. 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.
    Citations: 15     Fields:    Translation:Cells
  61. Shih W. Biomolecular assembly: dynamic DNA. Nat Mater. 2008 Feb; 7(2):98-100. PMID: 18219328.
    Citations: 5     Fields:    Translation:Cells
  62. 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.
    Citations: 110     Fields:    Translation:Cells
  63. 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.
    Citations: 154     Fields:    Translation:Cells
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.