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For: Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M. Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA. J Mol Biol 2007;369:722-34. [PMID: 17445830 DOI: 10.1016/j.jmb.2007.03.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2007] [Revised: 03/01/2007] [Accepted: 03/06/2007] [Indexed: 11/20/2022]
Number Cited by Other Article(s)
1
Liu Y, Xu C, Zhou H, Wang W, Liu B, Li Y, Hu X, Yu F, He J. The crystal structures of Sau3AI with and without bound DNA suggest a self-activation-based DNA cleavage mechanism. Structure 2023;31:1463-1472.e2. [PMID: 37652002 DOI: 10.1016/j.str.2023.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 06/12/2023] [Accepted: 08/04/2023] [Indexed: 09/02/2023]
2
Kisiala M, Kowalska M, Pastor M, Korza HJ, Czapinska H, Bochtler M. Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation. Nucleic Acids Res 2020;48:6954-6969. [PMID: 32459314 PMCID: PMC7337904 DOI: 10.1093/nar/gkaa403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 04/30/2020] [Accepted: 05/18/2020] [Indexed: 11/13/2022]  Open
3
Horton JR, Yang J, Zhang X, Petronzio T, Fomenkov A, Wilson GG, Roberts RJ, Cheng X. Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å. Nucleic Acids Res 2020;48:1466-1478. [PMID: 31879785 PMCID: PMC7026639 DOI: 10.1093/nar/gkz1195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/08/2019] [Accepted: 12/11/2019] [Indexed: 11/19/2022]  Open
4
Poddar S, Chakravarty D, Chakrabarti P. Structural changes in DNA-binding proteins on complexation. Nucleic Acids Res 2019. [PMID: 29534202 PMCID: PMC6283420 DOI: 10.1093/nar/gky170] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
5
Czapinska H, Siwek W, Szczepanowski RH, Bujnicki JM, Bochtler M, Skowronek KJ. Crystal Structure and Directed Evolution of Specificity of NlaIV Restriction Endonuclease. J Mol Biol 2019;431:2082-2094. [DOI: 10.1016/j.jmb.2019.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/14/2019] [Accepted: 04/07/2019] [Indexed: 12/14/2022]
6
Lussi C, Sauter KS, Schweizer M. Homodimerisation-independent cleavage of dsRNA by a pestiviral nicking endoribonuclease. Sci Rep 2018;8:8226. [PMID: 29844335 PMCID: PMC5974291 DOI: 10.1038/s41598-018-26557-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/09/2018] [Indexed: 12/12/2022]  Open
7
Claeys Bouuaert C, Chalmers R. A single active site in the mariner transposase cleaves DNA strands of opposite polarity. Nucleic Acids Res 2017;45:11467-11478. [PMID: 29036477 PMCID: PMC5714172 DOI: 10.1093/nar/gkx826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 09/08/2017] [Indexed: 01/01/2023]  Open
8
Kostiuk G, Dikic J, Schwarz FW, Sasnauskas G, Seidel R, Siksnys V. The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA. Nucleic Acids Res 2017;45:5968-5979. [PMID: 28453854 PMCID: PMC5449598 DOI: 10.1093/nar/gkx294] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 04/13/2017] [Indexed: 11/24/2022]  Open
9
Sasnauskas G, Tamulaitienė G, Tamulaitis G, Čalyševa J, Laime M, Rimšelienė R, Lubys A, Siksnys V. UbaLAI is a monomeric Type IIE restriction enzyme. Nucleic Acids Res 2017;45:9583-9594. [PMID: 28934493 PMCID: PMC5766183 DOI: 10.1093/nar/gkx634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 01/11/2023]  Open
10
Tamulaitiene G, Jovaisaite V, Tamulaitis G, Songailiene I, Manakova E, Zaremba M, Grazulis S, Xu SY, Siksnys V. Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA. Nucleic Acids Res 2017;45:3547-3558. [PMID: 28039325 PMCID: PMC5389614 DOI: 10.1093/nar/gkw1310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 01/19/2023]  Open
11
On the Dimers Stability of Allicin and Its Derivatives Interacting with AT, GC, and DNA Bridge: DFT Study. J CHEM-NY 2017. [DOI: 10.1155/2017/1428508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
12
Zhang J, Pan X, Bell CE. Crystal structure of λ exonuclease in complex with DNA and Ca(2+). Biochemistry 2014;53:7415-25. [PMID: 25370446 DOI: 10.1021/bi501155q] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
13
Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases--a historical perspective and more. Nucleic Acids Res 2014;42:7489-527. [PMID: 24878924 PMCID: PMC4081073 DOI: 10.1093/nar/gku447] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Revised: 05/02/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022]  Open
14
Ma L, Chen K, Clarke DJ, Nortcliffe CP, Wilson GG, Edwardson JM, Morton AJ, Jones AC, Dryden DTF. Restriction endonuclease TseI cleaves A:A and T:T mismatches in CAG and CTG repeats. Nucleic Acids Res 2013;41:4999-5009. [PMID: 23525471 PMCID: PMC3643589 DOI: 10.1093/nar/gkt176] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
15
Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K. Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily. Nucleic Acids Res 2012;40:7016-45. [PMID: 22638584 PMCID: PMC3424549 DOI: 10.1093/nar/gks382] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
16
Siwek W, Czapinska H, Bochtler M, Bujnicki JM, Skowronek K. Crystal structure and mechanism of action of the N6-methyladenine-dependent type IIM restriction endonuclease R.DpnI. Nucleic Acids Res 2012;40:7563-72. [PMID: 22610857 PMCID: PMC3424567 DOI: 10.1093/nar/gks428] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]  Open
17
Sasnauskas G, Kostiuk G, Tamulaitis G, Siksnys V. Target site cleavage by the monomeric restriction enzyme BcnI requires translocation to a random DNA sequence and a switch in enzyme orientation. Nucleic Acids Res 2011;39:8844-56. [PMID: 21771860 PMCID: PMC3203586 DOI: 10.1093/nar/gkr588] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
18
Chen F, Yang Z, Yan M, Alvarado JB, Wang G, Benner SA. Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity. Nucleic Acids Res 2011;39:3949-61. [PMID: 21245035 PMCID: PMC3089450 DOI: 10.1093/nar/gkq1274] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
19
Kostiuk G, Sasnauskas G, Tamulaitiene G, Siksnys V. Degenerate sequence recognition by the monomeric restriction enzyme: single mutation converts BcnI into a strand-specific nicking endonuclease. Nucleic Acids Res 2011;39:3744-53. [PMID: 21227928 PMCID: PMC3089477 DOI: 10.1093/nar/gkq1351] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
20
Nucleases: diversity of structure, function and mechanism. Q Rev Biophys 2010;44:1-93. [PMID: 20854710 DOI: 10.1017/s0033583510000181] [Citation(s) in RCA: 447] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
21
Firczuk M, Wojciechowski M, Czapinska H, Bochtler M. DNA intercalation without flipping in the specific ThaI-DNA complex. Nucleic Acids Res 2010;39:744-54. [PMID: 20861000 PMCID: PMC3025569 DOI: 10.1093/nar/gkq834] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
22
Stier I, Kiss A. The type II restriction endonuclease MvaI has dual specificity. Nucleic Acids Res 2010;38:8231-8. [PMID: 20693529 PMCID: PMC3001055 DOI: 10.1093/nar/gkq676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
23
Raskó T, Dér A, Klement E, Slaska-Kiss K, Pósfai E, Medzihradszky KF, Marshak DR, Roberts RJ, Kiss A. BspRI restriction endonuclease: cloning, expression in Escherichia coli and sequential cleavage mechanism. Nucleic Acids Res 2010;38:7155-66. [PMID: 20587501 PMCID: PMC2978348 DOI: 10.1093/nar/gkq567] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
24
Zaremba M, Owsicka A, Tamulaitis G, Sasnauskas G, Shlyakhtenko LS, Lushnikov AY, Lyubchenko YL, Laurens N, van den Broek B, Wuite GJL, Siksnys V. DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme. Nucleic Acids Res 2010;38:7142-54. [PMID: 20571089 PMCID: PMC2978343 DOI: 10.1093/nar/gkq560] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]  Open
25
Sanders KL, Catto LE, Bellamy SRW, Halford SE. Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands. Nucleic Acids Res 2009;37:2105-15. [PMID: 19223323 PMCID: PMC2673415 DOI: 10.1093/nar/gkp046] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
26
Jakubauskas A, Sasnauskas G, Giedriene J, Janulaitis A. Domain organization and functional analysis of type IIS restriction endonuclease Eco31I. Biochemistry 2008;47:8546-56. [PMID: 18642930 DOI: 10.1021/bi800660u] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
27
Daujotyte D, Liutkeviciūte Z, Tamulaitis G, Klimasauskas S. Chemical mapping of cytosines enzymatically flipped out of the DNA helix. Nucleic Acids Res 2008;36:e57. [PMID: 18450817 PMCID: PMC2425465 DOI: 10.1093/nar/gkn200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
28
Gasiunas G, Sasnauskas G, Tamulaitis G, Urbanke C, Razaniene D, Siksnys V. Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family. Nucleic Acids Res 2007;36:938-49. [PMID: 18086711 PMCID: PMC2241918 DOI: 10.1093/nar/gkm1090] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
29
Strand-specific Contacts and Divalent Metal Ion Regulate Double-strand Break Formation by the GIY-YIG Homing Endonuclease I-BmoI. J Mol Biol 2007;374:306-21. [DOI: 10.1016/j.jmb.2007.09.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2007] [Revised: 09/04/2007] [Accepted: 09/10/2007] [Indexed: 11/22/2022]
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