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For: Kielkopf CL, Ding S, Kuhn P, Rees DC. Conformational flexibility of B-DNA at 0.74 A resolution: d(CCAGTACTGG)(2). J Mol Biol 2000;296:787-801. [PMID: 10677281 DOI: 10.1006/jmbi.1999.3478] [Citation(s) in RCA: 94] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Number Cited by Other Article(s)
1
Li K, Yatsunyk LA, Neidle S. Machine learning shows torsion angle preferences in left-handed and right-handed quadruplex DNAs. Biophys J 2022;121:4874-4881. [PMID: 35999813 PMCID: PMC9808593 DOI: 10.1016/j.bpj.2022.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/21/2022] [Accepted: 08/18/2022] [Indexed: 01/07/2023]  Open
2
Oh J, Jia T, Xu J, Chong J, Dervan PB, Wang D. RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder. Proc Natl Acad Sci U S A 2022;119:e2114065119. [PMID: 35022237 PMCID: PMC8784135 DOI: 10.1073/pnas.2114065119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023]  Open
3
Sequence-dependent structural properties of B-DNA: what have we learned in 40 years? Biophys Rev 2021;13:995-1005. [DOI: 10.1007/s12551-021-00893-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 11/01/2021] [Indexed: 11/27/2022]  Open
4
Battistini F, Dans PD, Terrazas M, Castellazzi CL, Portella G, Labrador M, Villegas N, Brun-Heath I, González C, Orozco M. The Impact of the HydroxyMethylCytosine epigenetic signature on DNA structure and function. PLoS Comput Biol 2021;17:e1009547. [PMID: 34748533 PMCID: PMC8601608 DOI: 10.1371/journal.pcbi.1009547] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/18/2021] [Accepted: 10/10/2021] [Indexed: 12/30/2022]  Open
5
Balaceanu A, Buitrago D, Walther J, Hospital A, Dans PD, Orozco M. Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond. Nucleic Acids Res 2019;47:4418-4430. [PMID: 30957854 PMCID: PMC6511876 DOI: 10.1093/nar/gkz255] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 03/23/2019] [Accepted: 03/30/2019] [Indexed: 12/21/2022]  Open
6
Gilski M, Zhao J, Kowiel M, Brzezinski D, Turner DH, Jaskolski M. Accurate geometrical restraints for Watson-Crick base pairs. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2019;75:235-245. [PMID: 32830749 PMCID: PMC6457083 DOI: 10.1107/s2052520619002002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 02/05/2019] [Indexed: 05/30/2023]
7
Sunami T, Chatake T, Kono H. DNA conformational transitions inferred from re-evaluation of m|Fo| - D|Fc| electron-density maps. Acta Crystallogr D Struct Biol 2017;73:600-608. [PMID: 28695860 PMCID: PMC5505156 DOI: 10.1107/s2059798317007707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 05/24/2017] [Indexed: 11/30/2022]  Open
8
Zgarbová M, Jurečka P, Lankaš F, Cheatham TE, Šponer J, Otyepka M. Influence of BII Backbone Substates on DNA Twist: A Unified View and Comparison of Simulation and Experiment for All 136 Distinct Tetranucleotide Sequences. J Chem Inf Model 2017;57:275-287. [PMID: 28059516 DOI: 10.1021/acs.jcim.6b00621] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
9
Fromm M, Boulanouar O. Low energy electrons and ultra-soft X-rays irradiation of plasmid DNA. Technical innovations. Radiat Phys Chem Oxf Engl 1993 2016. [DOI: 10.1016/j.radphyschem.2016.05.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
10
Rohner M, Medina-Molner A, Spingler B. N,N,O and N,O,N Meridional cis Coordination of Two Guanines to Copper(II) by d(CGCGCG)2. Inorg Chem 2016;55:6130-40. [DOI: 10.1021/acs.inorgchem.6b00672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
11
Ammar FF, Hobaika Z, Abdel-Azeim S, Zargarian L, Maroun RG, Fermandjian S. A targeted DNA substrate mechanism for the inhibition of HIV-1 integrase by inhibitors with antiretroviral activity. FEBS Open Bio 2016;6:234-50. [PMID: 27239438 PMCID: PMC4821353 DOI: 10.1002/2211-5463.12025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 11/25/2015] [Accepted: 12/16/2015] [Indexed: 12/21/2022]  Open
12
Thirugnanasambandam A, Karthik S, Artheswari G, Gautham N. DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC). ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2016;72:780-8. [PMID: 27303798 DOI: 10.1107/s2059798316006306] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 04/14/2016] [Indexed: 11/11/2022]
13
Ramazanov RR, Maksimov DA, Kononov AI. Noncanonical Stacking Geometries of Nucleobases as a Preferred Target for Solar Radiation. J Am Chem Soc 2015;137:11656-65. [DOI: 10.1021/jacs.5b05140] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
14
Acosta-Reyes FJ, Subirana JA, Pous J, Sánchez-Giraldo R, Condom N, Baldini R, Malinina L, Campos JL. Polymorphic crystal structures of an all-AT DNA dodecamer. Biopolymers 2014;103:123-33. [DOI: 10.1002/bip.22565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/12/2022]
15
Dans PD, Faustino I, Battistini F, Zakrzewska K, Lavery R, Orozco M. Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA. Nucleic Acids Res 2014;42:11304-20. [PMID: 25223784 PMCID: PMC4191396 DOI: 10.1093/nar/gku809] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/25/2014] [Accepted: 08/26/2014] [Indexed: 11/12/2022]  Open
16
Zubatiuk TA, Shishkin OV, Gorb L, Hovorun DM, Leszczynski J. B-DNA characteristics are preserved in double stranded d(A)3·d(T)3 and d(G)3·d(C)3 mini-helixes: conclusions from DFT/M06-2X study. Phys Chem Chem Phys 2014;15:18155-66. [PMID: 24065071 DOI: 10.1039/c3cp51584b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
17
Xiao S, Zhu H, Wang L, Liang H. DNA conformational flexibility study using phosphate backbone neutralization model. SOFT MATTER 2014;10:1045-1055. [PMID: 24983118 DOI: 10.1039/c3sm52345d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
18
Szulik MW, Voehler MW, Ganguly M, Gold B, Stone MP. Site-specific stabilization of DNA by a tethered major groove amine, 7-aminomethyl-7-deaza-2'-deoxyguanosine. Biochemistry 2013;52:7659-68. [PMID: 24131376 PMCID: PMC3812902 DOI: 10.1021/bi400695r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
19
Robbins TJ, Wang Y. Effect of initial ion positions on the interactions of monovalent and divalent ions with a DNA duplex as revealed with atomistic molecular dynamics simulations. J Biomol Struct Dyn 2012;31:1311-23. [PMID: 23153112 DOI: 10.1080/07391102.2012.732344] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
20
Chenoweth DM, Meier JL, Dervan PB. Pyrrole-imidazole polyamides distinguish between double-helical DNA and RNA. Angew Chem Int Ed Engl 2012;52:415-8. [PMID: 22987334 DOI: 10.1002/anie.201205775] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Indexed: 12/14/2022]
21
Chenoweth DM, Meier JL, Dervan PB. Pyrrole-Imidazole Polyamides Distinguish Between Double-Helical DNA and RNA. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201205775] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
22
Guéroult M, Boittin O, Mauffret O, Etchebest C, Hartmann B. Mg2+ in the major groove modulates B-DNA structure and dynamics. PLoS One 2012;7:e41704. [PMID: 22844516 PMCID: PMC3402463 DOI: 10.1371/journal.pone.0041704] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/25/2012] [Indexed: 12/12/2022]  Open
23
Krepl M, Zgarbová M, Stadlbauer P, Otyepka M, Banáš P, Koča J, Cheatham TE, Jurečka P, Šponer J. Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA. J Chem Theory Comput 2012;8:2506-2520. [PMID: 23197943 PMCID: PMC3506181 DOI: 10.1021/ct300275s] [Citation(s) in RCA: 200] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
24
Mandal PK, Venkadesh S, Gautham N. Structure of the tetradecanucleotide d(CCCCGGTACCGGGG)2 as an A-DNA duplex. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012;68:393-9. [PMID: 22505405 PMCID: PMC3325805 DOI: 10.1107/s174430911200869x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 02/27/2012] [Indexed: 11/10/2022]
25
Nucleic acid-metal ion interactions in the solid state. Met Ions Life Sci 2012;10:43-102. [PMID: 22210335 DOI: 10.1007/978-94-007-2172-2_2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
26
Maehigashi T, Hsiao C, Woods KK, Moulaei T, Hud NV, Williams LD. B-DNA structure is intrinsically polymorphic: even at the level of base pair positions. Nucleic Acids Res 2011;40:3714-22. [PMID: 22180536 PMCID: PMC3333872 DOI: 10.1093/nar/gkr1168] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
27
Russo Krauss I, Merlino A, Giancola C, Randazzo A, Mazzarella L, Sica F. Thrombin-aptamer recognition: a revealed ambiguity. Nucleic Acids Res 2011;39:7858-67. [PMID: 21715374 PMCID: PMC3177225 DOI: 10.1093/nar/gkr522] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]  Open
28
Shin D, Tor Y. Bifacial nucleoside as a surrogate for both T and A in duplex DNA. J Am Chem Soc 2011;133:6926-9. [PMID: 21495708 PMCID: PMC3093761 DOI: 10.1021/ja201397e] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
29
Brzezinski K, Brzuszkiewicz A, Dauter M, Kubicki M, Jaskolski M, Dauter Z. High regularity of Z-DNA revealed by ultra high-resolution crystal structure at 0.55 A. Nucleic Acids Res 2011;39:6238-48. [PMID: 21459852 PMCID: PMC3152349 DOI: 10.1093/nar/gkr202] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
30
Chenoweth DM, Dervan PB. Structural basis for cyclic Py-Im polyamide allosteric inhibition of nuclear receptor binding. J Am Chem Soc 2011;132:14521-9. [PMID: 20812704 PMCID: PMC2954530 DOI: 10.1021/ja105068b] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
31
Grokhovsky SL, Il'icheva IA, Nechipurenko DY, Golovkin MV, Panchenko LA, Polozov RV, Nechipurenko YD. Sequence-specific ultrasonic cleavage of DNA. Biophys J 2011;100:117-25. [PMID: 21190663 PMCID: PMC3010002 DOI: 10.1016/j.bpj.2010.10.052] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2010] [Revised: 10/15/2010] [Accepted: 10/19/2010] [Indexed: 10/18/2022]  Open
32
Mládek A, Šponer JE, Jurečka P, Banáš P, Otyepka M, Svozil D, Šponer J. Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. J Chem Theory Comput 2010. [DOI: 10.1021/ct1004593] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
33
Wu B, Davey CA. Using soft X-rays for a detailed picture of divalent metal binding in the nucleosome. J Mol Biol 2010;398:633-40. [PMID: 20350553 DOI: 10.1016/j.jmb.2010.03.038] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/04/2010] [Accepted: 03/19/2010] [Indexed: 11/17/2022]
34
Hobaika Z, Zargarian L, Boulard Y, Maroun RG, Mauffret O, Fermandjian S. Specificity of LTR DNA recognition by a peptide mimicking the HIV-1 integrase {alpha}4 helix. Nucleic Acids Res 2010;37:7691-700. [PMID: 19808934 PMCID: PMC2794180 DOI: 10.1093/nar/gkp824] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
35
Hänsel R, Foldynová-Trantírková S, Löhr F, Buck J, Bongartz E, Bamberg E, Schwalbe H, Dötsch V, Trantírek L. Evaluation of parameters critical for observing nucleic acids inside living Xenopus laevis oocytes by in-cell NMR spectroscopy. J Am Chem Soc 2010;131:15761-8. [PMID: 19824671 DOI: 10.1021/ja9052027] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
36
Schnieders MJ, Fenn TD, Pande VS, Brunger AT. Polarizable atomic multipole X-ray refinement: application to peptide crystals. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2009;65:952-65. [PMID: 19690373 PMCID: PMC2733883 DOI: 10.1107/s0907444909022707] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 06/13/2009] [Indexed: 11/26/2022]
37
Khuu P, Ho PS. A rare nucleotide base tautomer in the structure of an asymmetric DNA junction. Biochemistry 2009;48:7824-32. [PMID: 19580331 PMCID: PMC2761035 DOI: 10.1021/bi900829b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
38
Millonig H, Pous J, Gouyette C, Subirana JA, Campos JL. The interaction of manganese ions with DNA. J Inorg Biochem 2009;103:876-80. [DOI: 10.1016/j.jinorgbio.2009.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Revised: 03/10/2009] [Accepted: 03/16/2009] [Indexed: 12/01/2022]
39
Marathe A, Karandur D, Bansal M. Small local variations in B-form DNA lead to a large variety of global geometries which can accommodate most DNA-binding protein motifs. BMC STRUCTURAL BIOLOGY 2009;9:24. [PMID: 19393049 PMCID: PMC2687451 DOI: 10.1186/1472-6807-9-24] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Accepted: 04/24/2009] [Indexed: 01/01/2023]
40
Brownlee C. Sheng Ding: using chemical methods to control cell fate. ACS Chem Biol 2009;4:153-6. [PMID: 19298091 DOI: 10.1021/cb900054a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
41
Kumar TS, Madsen AS, Østergaard ME, Sau SP, Wengel J, Hrdlicka PJ. Functionalized 2'-amino-alpha-L-LNA: directed positioning of intercalators for DNA targeting. J Org Chem 2009;74:1070-81. [PMID: 19108636 PMCID: PMC2853939 DOI: 10.1021/jo802037v] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
42
Narayana N, Weiss MA. Crystallographic analysis of a sex-specific enhancer element: sequence-dependent DNA structure, hydration, and dynamics. J Mol Biol 2008;385:469-90. [PMID: 18992257 DOI: 10.1016/j.jmb.2008.10.041] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2008] [Revised: 10/02/2008] [Accepted: 10/06/2008] [Indexed: 11/29/2022]
43
McCann JAB, Berti PJ. Transition-state analysis of the DNA repair enzyme MutY. J Am Chem Soc 2008;130:5789-97. [PMID: 18393424 DOI: 10.1021/ja711363s] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
44
Solt I, Simon I, Császár AG, Fuxreiter M. Electrostatic versus nonelectrostatic effects in DNA sequence discrimination by divalent ions Mg2+ and Mn2+. J Phys Chem B 2007;111:6272-9. [PMID: 17497910 DOI: 10.1021/jp0668192] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
45
Durbeej B, Eriksson LA. On the Formation of Cyclobutane Pyrimidine Dimers in UV-irradiated DNA: Why are Thymines More Reactive?¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0780159otfocp2.0.co2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Griffiths KK, Russu IM. Specific Interactions of Divalent Metal Ions with a DNA Duplex Containing the d(CA)n/(GT)nTandem Repeat. J Biomol Struct Dyn 2006;23:667-76. [PMID: 16615812 DOI: 10.1080/07391102.2006.10507091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Arai S, Chatake T, Ohhara T, Kurihara K, Tanaka I, Suzuki N, Fujimoto Z, Mizuno H, Niimura N. Complicated water orientations in the minor groove of the B-DNA decamer d(CCATTAATGG)2 observed by neutron diffraction measurements. Nucleic Acids Res 2005;33:3017-24. [PMID: 15914673 PMCID: PMC1140084 DOI: 10.1093/nar/gki616] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]  Open
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Li X, Eriksson LA. Influence of C5-methylation of cytosine on the formation of cyclobutane pyrimidine dimers. Chem Phys Lett 2005. [DOI: 10.1016/j.cplett.2004.11.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Hays FA, Jones ZJR, Ho PS. Influence of minor groove substituents on the structure of DNA Holliday junctions. Biochemistry 2004;43:9813-22. [PMID: 15274635 DOI: 10.1021/bi049461d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Anthony NG, Johnston BF, Khalaf AI, MacKay SP, Parkinson JA, Suckling CJ, Waigh RD. Short Lexitropsin that Recognizes the DNA Minor Groove at 5‘-ACTAGT-3‘:  Understanding the Role of Isopropyl-thiazole. J Am Chem Soc 2004;126:11338-49. [PMID: 15355117 DOI: 10.1021/ja030658n] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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