Molecular simulations have boosted knowledge of CRISPR/Cas9: A Review
作者： Angana Ray , Rosa Di Felice
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摘要: Genome editing allows scientists to change an organism's DNA. One promising genome protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic acid complexes. When the CRISPR/Cas approach was first demonstrated 2012, its advantages with respect previously available techniques, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector (TALENs), immediately got attention method has seen a surge of experimental computational investigations since then. However, molecular mechanisms involved target DNA recognition cleavage are still not completely resolved need further attention. The large size complex nature CRISPR/Cas9 complexes been challenge for studies, but some seed results exist illuminating activity. In this review, we present recent progress studying systems by dynamics simulations coarse-grained atomistic descriptions, including enhanced sampling.
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harvard.edu参考文章(59)
Samuel H. Sternberg, Sy Redding, Martin Jinek, Eric C. Greene, Jennifer A. Doudna, DNA interrogation by the CRISPR RNA-guided endonuclease Cas9 Nature. ,vol. 507, pp. 62- 67 ,(2014) , 10.1038/NATURE13011
Peter Z Qin, Ian S Haworth, Qi Cai, Ana K Kusnetzow, Gian Paola G Grant, Eric A Price, Glenna Z Sowa, Anna Popova, Bruno Herreros, Honghang He, Measuring nanometer distances in nucleic acids using a sequence-independent nitroxide probe. Nature Protocols. ,vol. 2, pp. 2354- 2365 ,(2007) , 10.1038/NPROT.2007.308
Wei Yang, Jae Young Lee, Marcin Nowotny, Making and Breaking Nucleic Acids: Two-Mg2+-Ion Catalysis and Substrate Specificity Molecular Cell. ,vol. 22, pp. 5- 13 ,(2006) , 10.1016/J.MOLCEL.2006.03.013
Prashant Mali, Luhan Yang, Kevin M Esvelt, John Aach, Marc Guell, James E DiCarlo, Julie E Norville, George M Church, RNA-Guided Human Genome Engineering via Cas9 Science. ,vol. 339, pp. 823- 826 ,(2013) , 10.1126/SCIENCE.1232033
Devashish Rath, Lina Amlinger, Archana Rath, Magnus Lundgren, The CRISPR-Cas Immune System: Biology, Mechanisms and Applications Biochimie. ,vol. 117, pp. 119- 128 ,(2015) , 10.1016/J.BIOCHI.2015.03.025
Wei Yang, An equivalent metal ion in one- and two-metal-ion catalysis Nature Structural & Molecular Biology. ,vol. 15, pp. 1228- 1231 ,(2008) , 10.1038/NSMB.1502
David E. Shaw, J.P. Grossman, Joseph A. Bank, Brannon Batson, J. Adam Butts, Jack C. Chao, Martin M. Deneroff, Ron O. Dror, Amos Even, Christopher H. Fenton, Anthony Forte, Joseph Gagliardo, Gennette Gill, Brian Greskamp, C. Richard Ho, Douglas J. Ierardi, Lev Iserovich, Jeffrey S. Kuskin, Richard H. Larson, Timothy Layman, Li-Siang Lee, Adam K. Lerer, Chester Li, Daniel Killebrew, Kenneth M. Mackenzie, Shark Yeuk-Hai Mok, Mark A. Moraes, Rolf Mueller, Lawrence J. Nociolo, Jon L. Peticolas, Terry Quan, Daniel Ramot, John K. Salmon, Daniele P. Scarpazza, U. Ben Schafer, Naseer Siddique, Christopher W. Snyder, Jochen Spengler, Ping Tak Peter Tang, Michael Theobald, Horia Toma, Brian Towles, Benjamin Vitale, Stanley C. Wang, Cliff Young, Anton 2: raising the bar for performance and programmability in a special-purpose molecular dynamics supercomputer ieee international conference on high performance computing data and analytics. pp. 41- 53 ,(2014) , 10.1109/SC.2014.9
Fedor V. Karginov, Gregory J. Hannon, The CRISPR System: Small RNA-Guided Defense in Bacteria and Archaea Molecular Cell. ,vol. 37, pp. 7- 19 ,(2010) , 10.1016/J.MOLCEL.2009.12.033
William Humphrey, Andrew Dalke, Klaus Schulten, VMD: Visual molecular dynamics Journal of Molecular Graphics. ,vol. 14, pp. 33- 38 ,(1996) , 10.1016/0263-7855(96)00018-5
David A Scott, Joshua A Weinstein, F Ann Ran, Silvana Konermann, Vineeta Agarwala, Yinqing Li, Eli J Fine, Xuebing Wu, Ophir Shalem, Thomas J Cradick, Luciano A Marraffini, Gang Bao, Feng Zhang, Patrick D Hsu, DNA targeting specificity of RNA-guided Cas9 nucleases Nature Biotechnology. ,vol. 31, pp. 827- 832 ,(2013) , 10.1038/NBT.2647