-
1
-
-
84986898390
-
Applications of CRISPR technologies in research and beyond
-
Barrangou R, Doudna JA (2016) Applications of CRISPR technologies in research and beyond. Nat Biotechnol 34: 933-941.
-
(2016)
Nat Biotechnol
, vol.34
, pp. 933-941
-
-
Barrangou, R.1
Doudna, J.A.2
-
2
-
-
84913594397
-
Genome editing. The new frontier of genome engineering with CRISPR-Cas9
-
Doudna JA, Charpentier E (2014) Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346: 1258096.
-
(2014)
Science
, vol.346
, pp. 1258096
-
-
Doudna, J.A.1
Charpentier, E.2
-
3
-
-
84865070369
-
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
-
Jinek M, et al. (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816-821.
-
(2012)
Science
, vol.337
, pp. 816-821
-
-
Jinek, M.1
-
4
-
-
84895871173
-
DNA interrogation by the CRISPR RNA-guided endonuclease cas9
-
Sternberg SH, Redding S, Jinek M, Greene EC, Doudna JA (2014) DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507: 62-67.
-
(2014)
Nature
, vol.507
, pp. 62-67
-
-
Sternberg, S.H.1
Redding, S.2
Jinek, M.3
Greene, E.C.4
Doudna, J.A.5
-
5
-
-
85019742802
-
CRISPR-cas9 structures and mechanisms
-
Jiang F, Doudna JA (2017) CRISPR-Cas9 structures and mechanisms. Annu Rev Biophys 46: 505-529.
-
(2017)
Annu Rev Biophys
, vol.46
, pp. 505-529
-
-
Jiang, F.1
Doudna, J.A.2
-
6
-
-
84893157352
-
Structures of cas9 endonucleases reveal RNA-mediated conformational activation
-
Jinek M, et al. (2014) Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343: 1247997.
-
(2014)
Science
, vol.343
, pp. 1247997
-
-
Jinek, M.1
-
7
-
-
84933574487
-
Structural biology. A cas9-guide RNA complex preorganized for target DNA recognition
-
Jiang F, Zhou K, Ma L, Gressel S, Doudna JA (2015) Structural biology. A Cas9-guide RNA complex preorganized for target DNA recognition. Science 348: 1477-1481.
-
(2015)
Science
, vol.348
, pp. 1477-1481
-
-
Jiang, F.1
Zhou, K.2
Ma, L.3
Gressel, S.4
Doudna, J.A.5
-
8
-
-
84908508061
-
Structural basis of PAM-dependent target DNA recognition by the cas9 endonuclease
-
Anders C, Niewoehner O, Duerst A, Jinek M (2014) Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513: 569-573.
-
(2014)
Nature
, vol.513
, pp. 569-573
-
-
Anders, C.1
Niewoehner, O.2
Duerst, A.3
Jinek, M.4
-
9
-
-
84896733529
-
Crystal structure of cas9 in complex with guide RNA and target DNA
-
Nishimasu H, et al. (2014) Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156: 935-949.
-
(2014)
Cell
, vol.156
, pp. 935-949
-
-
Nishimasu, H.1
-
10
-
-
84958953000
-
Structures of a CRISPR-cas9 R-loop complex primed for DNA cleavage
-
Jiang F, et al. (2016) Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Science 351: 867-871.
-
(2016)
Science
, vol.351
, pp. 867-871
-
-
Jiang, F.1
-
11
-
-
84946215320
-
Conformational control of DNA target cleavage by CRISPR-Cas9
-
Sternberg SH, LaFrance B, Kaplan M, Doudna JA (2015) Conformational control of DNA target cleavage by CRISPR-Cas9. Nature 527: 110-113.
-
(2015)
Nature
, vol.527
, pp. 110-113
-
-
Sternberg, S.H.1
LaFrance, B.2
Kaplan, M.3
Doudna, J.A.4
-
12
-
-
85023209749
-
A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9
-
Dagdas YS, Chen JS, Sternberg SH, Doudna JA, Yildiz A (2017) A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9. bioRxiv. doi: biorxiv.org/lookup/doi/10.1101/122242.
-
(2017)
BioRxiv
-
-
Dagdas, Y.S.1
Chen, J.S.2
Sternberg, S.H.3
Doudna, J.A.4
Yildiz, A.5
-
13
-
-
85016604142
-
Striking plasticity of CRISPR-Cas9 and key role of non-target DNA, as revealed by molecular simulations
-
Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA (2016) Striking plasticity of CRISPR-Cas9 and key role of non-target DNA, as revealed by molecular simulations. ACS Cent Sci 2: 756-763.
-
(2016)
ACS Cent Sci
, vol.2
, pp. 756-763
-
-
Palermo, G.1
Miao, Y.2
Walker, R.C.3
Jinek, M.4
McCammon, J.A.5
-
14
-
-
84987837936
-
Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease cas9
-
Singh D, Sternberg SH, Fei J, Doudna JA, Ha T (2016) Real-time observation of DNA recognition and rejection by the RNA-guided endonuclease Cas9. Nat Commun 7: 12778.
-
(2016)
Nat Commun
, vol.7
, pp. 12778
-
-
Singh, D.1
Sternberg, S.H.2
Fei, J.3
Doudna, J.A.4
Ha, T.5
-
15
-
-
84892573703
-
Trapping the dynamic acyl carrier protein in fatty acid biosynthesis
-
Nguyen C, et al. (2014) Trapping the dynamic acyl carrier protein in fatty acid biosynthesis. Nature 505: 427-431.
-
(2014)
Nature
, vol.505
, pp. 427-431
-
-
Nguyen, C.1
-
16
-
-
84866146945
-
Routine access to millisecond time scale events with accelerated molecular dynamics
-
Pierce LCT, Salomon-Ferrer R, Augusto F de Oliveira C, McCammon JA, Walker RC (2012) Routine access to millisecond time scale events with accelerated molecular dynamics. J Chem Theory Comput 8: 2997-3002.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 2997-3002
-
-
Pierce, L.C.T.1
Salomon-Ferrer, R.2
Augusto, F.3
De Oliveira, C.4
McCammon, J.A.5
Walker, R.C.6
-
17
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9: 646-652.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
18
-
-
84938909114
-
Gaussian accelerated molecular dynamics: Unconstrained enhanced sampling and free energy calculation
-
Miao Y, Feher VA, McCammon JA (2015) Gaussian accelerated molecular dynamics: Unconstrained enhanced sampling and free energy calculation. J Chem Theory Comput 11: 3584-3595.
-
(2015)
J Chem Theory Comput
, vol.11
, pp. 3584-3595
-
-
Miao, Y.1
Feher, V.A.2
McCammon, J.A.3
-
19
-
-
84992314140
-
Graded activation and free energy landscapes of a muscarinic G-protein-coupled receptor
-
Miao Y, McCammon JA (2016) Graded activation and free energy landscapes of a muscarinic G-protein-coupled receptor. Proc Natl Acad Sci USA 113: 12162-12167.
-
(2016)
Proc Natl Acad Sci USA
, vol.113
, pp. 12162-12167
-
-
Miao, Y.1
McCammon, J.A.2
-
20
-
-
84977614030
-
Unconstrained enhanced sampling for free energy calculations of biomolecules: A review
-
Miao Y, McCammon JA (2016) Unconstrained enhanced sampling for free energy calculations of biomolecules: A review. Mol Simul 42: 1046-1055.
-
(2016)
Mol Simul
, vol.42
, pp. 1046-1055
-
-
Miao, Y.1
McCammon, J.A.2
-
21
-
-
84924322574
-
Rational design of a split-cas9 enzyme complex
-
Wright AV, et al. (2015) Rational design of a split-Cas9 enzyme complex. Proc Natl Acad Sci USA 112: 2984-2989.
-
(2015)
Proc Natl Acad Sci USA
, vol.112
, pp. 2984-2989
-
-
Wright, A.V.1
-
22
-
-
84952943845
-
Rationally engineered cas9 nucleases with improved specificity
-
Slaymaker IM, et al. (2016) Rationally engineered Cas9 nucleases with improved specificity. Science 351: 84-88.
-
(2016)
Science
, vol.351
, pp. 84-88
-
-
Slaymaker, I.M.1
-
23
-
-
84937908208
-
Engineered CRISPR-Cas9 nucleases with altered PAM specificities
-
Kleinstiver BP, et al. (2015) Engineered CRISPR-Cas9 nucleases with altered PAM specificities. Nature 523: 481-485.
-
(2015)
Nature
, vol.523
, pp. 481-485
-
-
Kleinstiver, B.P.1
-
24
-
-
85008234074
-
Probing the structural dynamics of the CRISPR-cas9 RNA-guided DNA-cleavage system by coarse-grained modeling
-
Zheng W (2017) Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling. Proteins 85: 342-353.
-
(2017)
Proteins
, vol.85
, pp. 342-353
-
-
Zheng, W.1
-
25
-
-
33846406882
-
A comparison of methods to compute the potential of mean force
-
Trzesniak D, Kunz AP, van Gunsteren WF (2007) A comparison of methods to compute the potential of mean force. ChemPhysChem 8: 162-169.
-
(2007)
ChemPhysChem
, vol.8
, pp. 162-169
-
-
Trzesniak, D.1
Kunz, A.P.2
Van Gunsteren, W.F.3
-
26
-
-
34948885722
-
Crystal structure of T4 endonuclease VII resolving a holliday junction
-
Biertümpfel C, Yang W, Suck D (2007) Crystal structure of T4 endonuclease VII resolving a Holliday junction. Nature 449: 616-620.
-
(2007)
Nature
, vol.449
, pp. 616-620
-
-
Biertümpfel, C.1
Yang, W.2
Suck, D.3
-
27
-
-
0027184481
-
A general two-metal-ion mechanism for catalytic RNA
-
Steitz TA, Steitz JA (1993) A general two-metal-ion mechanism for catalytic RNA. Proc Natl Acad Sci USA 90: 6498-6502.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 6498-6502
-
-
Steitz, T.A.1
Steitz, J.A.2
-
28
-
-
84996524306
-
Cas9-catalyzed DNA cleavage generates staggered ends: Evidence from molecular dynamics simulations
-
Zuo Z, Liu J (2016) Cas9-catalyzed DNA cleavage generates staggered ends: Evidence from molecular dynamics simulations. Sci Rep 5: 37584.
-
(2016)
Sci Rep
, vol.5
, pp. 37584
-
-
Zuo, Z.1
Liu, J.2
-
29
-
-
50249094329
-
Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism
-
De Vivo M, Dal Peraro M, Klein ML (2008) Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism. J Am Chem Soc 130: 10955-10962.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 10955-10962
-
-
De Vivo, M.1
Dal Peraro, M.2
Klein, M.L.3
-
30
-
-
85016334214
-
Development of site-specific Mg(2+)-RNA force field parameters: A dream or reality? Guidelines from combined molecular dynamics and quantum mechanics simulations
-
Casalino L, Palermo G, Abdurakhmonova N, Rothlisberger U, Magistrato A (2017) Development of site-specific Mg(2+)-RNA force field parameters: A dream or reality? Guidelines from combined molecular dynamics and quantum mechanics simulations. J Chem Theory Comput 13: 340-352.
-
(2017)
J Chem Theory Comput
, vol.13
, pp. 340-352
-
-
Casalino, L.1
Palermo, G.2
Abdurakhmonova, N.3
Rothlisberger, U.4
Magistrato, A.5
-
31
-
-
84923092809
-
Catalytic metal ions and enzymatic processing of DNA and RNA
-
Palermo G, et al. (2015) Catalytic metal ions and enzymatic processing of DNA and RNA. Acc Chem Res 48: 220-228.
-
(2015)
Acc Chem Res
, vol.48
, pp. 220-228
-
-
Palermo, G.1
-
32
-
-
34250318638
-
Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers
-
Pérez A, et al. (2007) Refinement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophys J 92: 3817-3829.
-
(2007)
Biophys J
, vol.92
, pp. 3817-3829
-
-
Pérez, A.1
-
33
-
-
78651294111
-
Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins
-
Banas P, et al. (2010) Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins. J Chem Theory Comput 6: 3836-3849.
-
(2010)
J Chem Theory Comput
, vol.6
, pp. 3836-3849
-
-
Banas, P.1
-
34
-
-
80052820313
-
Refinement of the cornell et al. Nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles
-
Zgarbová M, et al. (2011) Refinement of the Cornell et al. nucleic acids force field based on reference quantum chemical calculations of glycosidic torsion profiles. J Chem Theory Comput 7: 2886-2902.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 2886-2902
-
-
Zgarbová, M.1
-
35
-
-
0344796204
-
Ion-water interaction potentials derived from free energy perturbation simulations
-
Aqvist J (1990) Ion-water interaction potentials derived from free energy perturbation simulations. J Phys Chem 94: 8021-8024.
-
(1990)
J Phys Chem
, vol.94
, pp. 8021-8024
-
-
Aqvist, J.1
-
36
-
-
84980364284
-
-
(University of California, San Francisco, San Francisco, CA)
-
Case DA, et al. (2016) AMBER 2016 (University of California, San Francisco, San Francisco, CA).
-
(2016)
AMBER 2016
-
-
Case, D.A.1
-
37
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips JC, et al. (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26: 1781-1802.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
|