Center-Authored Papers

Filters: Author is Stoddard, Barry L  [Clear All Filters]
2008
Lambert AR, Sussman D, Shen B, Maunus R, Nix J, Samuelson J, Xu S-Y, Stoddard BL.  2008.  Structures of the rare-cutting restriction endonuclease NotI reveal a unique metal binding fold involved in DNA binding.. Structure (London, England : 1993). 16(4):558-69. Abstract
Nomura N, Nomura Y, Sussman D, Klein D, Stoddard BL.  2008.  Recognition of a common rDNA target site in archaea and eukarya by analogous LAGLIDADG and His-Cys box homing endonucleases.. Nucleic acids research. 36(22):6988-98. Abstract
Shen BW, Spiegel PC, Chang C-H, Huh J-W, Lee J-S, Kim J, Kim Y-H, Stoddard BL.  2008.  The tertiary structure and domain organization of coagulation factor VIII.. Blood. 111(3):1240-7. Abstract
Stolworthy TS, Korkegian AM, Willmon CL, Ardiani A, Cundiff J, Stoddard BL, Black ME.  2008.  Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine.. Journal of molecular biology. 377(3):854-69. Abstract
Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A, Gallaher JL, Betker JL, Tanaka F, Barbas CF et al..  2008.  De novo computational design of retro-aldol enzymes.. Science (New York, N.Y.). 319(5868):1387-91. Abstract
2009
Li H, Pellenz S, Ulge U, Stoddard BL, Monnat RJ.  2009.  Generation of single-chain LAGLIDADG homing endonucleases from native homodimeric precursor proteins.. Nucleic acids research. 37(5):1650-62. Abstract
Takeuchi R, Certo M, Caprara MG, Scharenberg AM, Stoddard BL.  2009.  Optimization of in vivo activity of a bifunctional homing endonuclease and maturase reverses evolutionary degradation.. Nucleic acids research. 37(3):877-90. Abstract
Zhao L, Pellenz S, Stoddard BL.  2009.  Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I.. Journal of molecular biology. 385(5):1498-510. Abstract
Fuchita M, Ardiani A, Zhao L, Serve K, Stoddard BL, Black ME.  2009.  Bacterial cytosine deaminase mutants created by molecular engineering show improved 5-fluorocytosine-mediated cell killing in vitro and in vivo.. Cancer research. 69(11):4791-9. Abstract
Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, Baker D.  2009.  Alteration of enzyme specificity by computational loop remodeling and design.. Proceedings of the National Academy of Sciences of the United States of America. 106(23):9215-20. Abstract
McConnell Smith A, Takeuchi R, Pellenz S, Davis L, Maizels N, Monnat RJ, Stoddard BL.  2009.  Generation of a nicking enzyme that stimulates site-specific gene conversion from the I-AniI LAGLIDADG homing endonuclease.. Proceedings of the National Academy of Sciences of the United States of America. 106(13):5099-104. Abstract
Dassa B, London N, Stoddard BL, Schueler-Furman O, Pietrokovski S.  2009.  Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family.. Nucleic acids research. 37(8):2560-73. Abstract
Jarjour J, West-Foyle H, Certo MT, Hubert CG, Doyle L, Getz MM, Stoddard BL, Scharenberg AM.  2009.  High-resolution profiling of homing endonuclease binding and catalytic specificity using yeast surface display.. Nucleic acids research. 37(20):6871-80. Abstract
Kaiser BK, Clifton MC, Shen BW, Stoddard BL.  2009.  The structure of a bacterial DUF199/WhiA protein: domestication of an invasive endonuclease.. Structure (London, England : 1993). 17(10):1368-76. Abstract
Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, Scharenberg AM, Stoddard BL, Baker D.  2009.  Exploitation of binding energy for catalysis and design.. Nature. 461(7268):1300-4. Abstract
2010
Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL et al..  2010.  Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction.. Science (New York, N.Y.). 329(5989):309-13. Abstract
Shen BW, Heiter DF, Chan S-H, Wang H, Xu S-Y, Morgan RD, Wilson GG, Stoddard BL.  2010.  Unusual target site disruption by the rare-cutting HNH restriction endonuclease PacI.. Structure (London, England : 1993). 18(6):734-43. Abstract
Stoddard BL, Belfort M.  2010.  Social networking between mobile introns and their host genes.. Molecular microbiology. 78(1):1-4. Abstract
Mak AN-S, Lambert AR, Stoddard BL.  2010.  Folding, DNA recognition, and function of GIY-YIG endonucleases: crystal structures of R.Eco29kI.. Structure (London, England : 1993). 18(10):1321-31. Abstract
Ashworth J, Taylor GK, Havranek JJ, Quadri AS, Stoddard BL, Baker D.  2010.  Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs.. Nucleic acids research. 38(16):5601-8. Abstract
2011
Kaiser BK, Stoddard BL.  2011.  DNA recognition and transcriptional regulation by the WhiA sporulation factor.. Scientific reports. 1:156. Abstract
Takeuchi R, Lambert AR, Mak AN-S, Jacoby K, Dickson RJ, Gloor GB, Scharenberg AM, Edgell DR, Stoddard BL.  2011.  Tapping natural reservoirs of homing endonucleases for targeted gene modification.. Proceedings of the National Academy of Sciences of the United States of America. 108(32):13077-82. Abstract
Metzger MJ, McConnell-Smith A, Stoddard BL, Miller AD.  2011.  Single-strand nicks induce homologous recombination with less toxicity than double-strand breaks using an AAV vector template.. Nucleic acids research. 39(3):926-35. Abstract
Chan S-H, Stoddard BL, Xu S-Y.  2011.  Natural and engineered nicking endonucleases--from cleavage mechanism to engineering of strand-specificity.. Nucleic acids research. 39(1):1-18. Abstract
Stoddard BL.  2011.  Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification.. Structure (London, England : 1993). 19(1):7-15. Abstract