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For: Krueger A, Protozanova E, Frank-Kamenetskii MD. Sequence-dependent base pair opening in DNA double helix. Biophys J 2006;90:3091-9. [PMID: 16500982 PMCID: PMC1432109 DOI: 10.1529/biophysj.105.078774] [Citation(s) in RCA: 138] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Banerjee A, Anand M, Kalita S, Ganji M. Single-molecule analysis of DNA base-stacking energetics using patterned DNA nanostructures. NATURE NANOTECHNOLOGY 2023;18:1474-1482. [PMID: 37591937 PMCID: PMC10716042 DOI: 10.1038/s41565-023-01485-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 07/10/2023] [Indexed: 08/19/2023]
2
Genthon A, Dvirnas A, Ambjörnsson T. Equilibrium melting probabilities of a DNA molecule with a defect: An exact solution of the Poland-Scheraga model. J Chem Phys 2023;159:145102. [PMID: 37815110 DOI: 10.1063/5.0168915] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 09/20/2023] [Indexed: 10/11/2023]  Open
3
Nicy, Chakraborty D, Wales DJ. Energy Landscapes for Base-Flipping in a Model DNA Duplex. J Phys Chem B 2022;126:3012-3028. [PMID: 35427136 PMCID: PMC9098180 DOI: 10.1021/acs.jpcb.2c00340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 03/24/2022] [Indexed: 12/31/2022]
4
Pant P, Aggarwal L. Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations. Biophys Chem 2022;282:106758. [DOI: 10.1016/j.bpc.2021.106758] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/09/2021] [Accepted: 12/30/2021] [Indexed: 01/17/2023]
5
Dutta N, Deb I, Sarzynska J, Lahiri A. Inosine and its methyl derivatives: Occurrence, biogenesis, and function in RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022;169-170:21-52. [PMID: 35065168 DOI: 10.1016/j.pbiomolbio.2022.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 12/11/2021] [Accepted: 01/11/2022] [Indexed: 05/21/2023]
6
Jeong J, Kim HD. Determinants of cyclization-decyclization kinetics of short DNA with sticky ends. Nucleic Acids Res 2020;48:5147-5156. [PMID: 32282905 PMCID: PMC7229855 DOI: 10.1093/nar/gkaa207] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 03/17/2020] [Accepted: 03/25/2020] [Indexed: 12/16/2022]  Open
7
Basov A, Drobotenko M, Svidlov A, Gerasimenko E, Malyshko V, Elkina A, Baryshev M, Dzhimak S. Inequality in the Frequency of the Open States Occurrence Depends on Single 2H/1H Replacement in DNA. Molecules 2020;25:E3753. [PMID: 32824686 PMCID: PMC7463606 DOI: 10.3390/molecules25163753] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/04/2020] [Accepted: 08/15/2020] [Indexed: 12/15/2022]  Open
8
Sarkar S, Rajdev P, Singh PC. Hydrogen bonding of ionic liquids in the groove region of DNA controls the extent of its stabilization: synthesis, spectroscopic and simulation studies. Phys Chem Chem Phys 2020;22:15582-15591. [PMID: 32613973 DOI: 10.1039/d0cp01548b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
9
Zoli M. Stretching DNA in hard-wall potential channels. ACTA ACUST UNITED AC 2020. [DOI: 10.1209/0295-5075/130/28002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
10
Liebl K, Zacharias M. How global DNA unwinding causes non-uniform stress distribution and melting of DNA. PLoS One 2020;15:e0232976. [PMID: 32413048 PMCID: PMC7228070 DOI: 10.1371/journal.pone.0232976] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/24/2020] [Indexed: 12/31/2022]  Open
11
Oh KI, Kim J, Park CJ, Lee JH. Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy. Int J Mol Sci 2020;21:E2673. [PMID: 32290457 PMCID: PMC7216225 DOI: 10.3390/ijms21082673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022]  Open
12
Buckle AM, Buckle M. Ribosome Evolution and Structural Capacitance. Front Mol Biosci 2019;6:123. [PMID: 31803754 PMCID: PMC6872460 DOI: 10.3389/fmolb.2019.00123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/24/2019] [Indexed: 11/13/2022]  Open
13
Discovery of Cisplatin Binding to Thymine and Cytosine on a Single-Stranded Oligodeoxynucleotide by High Resolution FT-ICR Mass Spectrometry. Molecules 2019;24:molecules24101852. [PMID: 31091778 PMCID: PMC6571787 DOI: 10.3390/molecules24101852] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/09/2019] [Accepted: 05/13/2019] [Indexed: 11/16/2022]  Open
14
Zoli M. DNA size in confined environments. Phys Chem Chem Phys 2019;21:12566-12575. [DOI: 10.1039/c9cp01098j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
15
Kingsland A, Maibaum L. DNA Base Pair Mismatches Induce Structural Changes and Alter the Free-Energy Landscape of Base Flip. J Phys Chem B 2018;122:12251-12259. [DOI: 10.1021/acs.jpcb.8b06007] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
16
Johnson RP, Perera RT, Fleming AM, Burrows CJ, White HS. Energetics of base flipping at a DNA mismatch site confined at the latch constriction of α-hemolysin. Faraday Discuss 2018;193:471-485. [PMID: 27711888 DOI: 10.1039/c6fd00058d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
17
Zoli M. End-to-end distance and contour length distribution functions of DNA helices. J Chem Phys 2018;148:214902. [DOI: 10.1063/1.5021639] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
18
Bergamo A, Dyson PJ, Sava G. The mechanism of tumour cell death by metal-based anticancer drugs is not only a matter of DNA interactions. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.01.009] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
19
Drobotenko MI, Dzhimak SS, Svidlov AA, Basov AA, Lyasota OM, Baryshev MG. A Mathematical Model for Basepair Opening in a DNA Double Helix. Biophysics (Nagoya-shi) 2018. [DOI: 10.1134/s0006350918020069] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]  Open
20
Vologodskii A, Frank-Kamenetskii MD. DNA melting and energetics of the double helix. Phys Life Rev 2017;25:1-21. [PMID: 29170011 DOI: 10.1016/j.plrev.2017.11.012] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/23/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
21
Ma N, van der Vaart A. Free Energy Coupling between DNA Bending and Base Flipping. J Chem Inf Model 2017;57:2020-2026. [PMID: 28696686 DOI: 10.1021/acs.jcim.7b00215] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
22
Andrabi M, Hutchins AP, Miranda-Saavedra D, Kono H, Nussinov R, Mizuguchi K, Ahmad S. Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences. Sci Rep 2017;7:4071. [PMID: 28642456 PMCID: PMC5481346 DOI: 10.1038/s41598-017-03199-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 04/26/2017] [Indexed: 12/24/2022]  Open
23
Zoli M. Twist-stretch profiles of DNA chains. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017;29:225101. [PMID: 28394255 DOI: 10.1088/1361-648x/aa6c50] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
24
Paston SV, Nikolaev AI, Ushkov PA. EDTA, thymidine, and Cu2+ ion complexes from mass spectrometry data. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617020251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
25
Kilchherr F, Wachauf C, Pelz B, Rief M, Zacharias M, Dietz H. Single-molecule dissection of stacking forces in DNA. Science 2017;353:353/6304/aaf5508. [PMID: 27609897 DOI: 10.1126/science.aaf5508] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 07/01/2016] [Indexed: 01/01/2023]
26
Wang Y, Gong S, Wang Z, Zhang W. The thermodynamics and kinetics of a nucleotide base pair. J Chem Phys 2017;144:115101. [PMID: 27004898 DOI: 10.1063/1.4944067] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
27
Tian L, Zhang Z, Wang H, Zhao M, Dong Y, Gong Y. Sequence-Dependent T:G Base Pair Opening in DNA Double Helix Bound by Cren7, a Chromatin Protein Conserved among Crenarchaea. PLoS One 2016;11:e0163361. [PMID: 27685992 PMCID: PMC5042384 DOI: 10.1371/journal.pone.0163361] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/07/2016] [Indexed: 12/26/2022]  Open
28
Zoli M. J-factors of short DNA molecules. J Chem Phys 2016;144:214104. [DOI: 10.1063/1.4952978] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
29
Maity A, Singh A, Singh N. Differential stability of DNA based on salt concentration. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2016;46:33-40. [DOI: 10.1007/s00249-016-1132-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 04/05/2016] [Accepted: 04/11/2016] [Indexed: 01/28/2023]
30
McCarty J, Valsson O, Parrinello M. Bespoke Bias for Obtaining Free Energy Differences within Variationally Enhanced Sampling. J Chem Theory Comput 2016;12:2162-9. [PMID: 27057791 DOI: 10.1021/acs.jctc.6b00125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
31
Zoli M. Flexibility of short DNA helices under mechanical stretching. Phys Chem Chem Phys 2016;18:17666-77. [DOI: 10.1039/c6cp02981g] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
32
Reiter-Schad M, Werner E, Tegenfeldt JO, Mehlig B, Ambjörnsson T. How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model. J Chem Phys 2015;143:115101. [DOI: 10.1063/1.4930220] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
33
Zrimec J, Lapanje A. Fast Prediction of DNA Melting Bubbles Using DNA Thermodynamic Stability. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015;12:1137-1145. [PMID: 26451825 DOI: 10.1109/tcbb.2015.2396057] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
34
Freitag C, Noble C, Fritzsche J, Persson F, Reiter-Schad M, Nilsson AN, Granéli A, Ambjörnsson T, Mir KU, Tegenfeldt JO. Visualizing the entire DNA from a chromosome in a single frame. BIOMICROFLUIDICS 2015;9:044114. [PMID: 26392826 PMCID: PMC4570469 DOI: 10.1063/1.4923262] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 06/18/2015] [Indexed: 05/16/2023]
35
Chua EYD, Davey GE, Chin CF, Dröge P, Ang WH, Davey CA. Stereochemical control of nucleosome targeting by platinum-intercalator antitumor agents. Nucleic Acids Res 2015;43:5284-96. [PMID: 25916851 PMCID: PMC4477649 DOI: 10.1093/nar/gkv356] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 04/02/2015] [Indexed: 11/15/2022]  Open
36
Shin J, Lee OC, Sung W. How a short double-stranded DNA bends. J Chem Phys 2015;142:155101. [DOI: 10.1063/1.4916379] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
37
Ding Y, Fleming AM, White HS, Burrows CJ. Internal vs fishhook hairpin DNA: unzipping locations and mechanisms in the α-hemolysin nanopore. J Phys Chem B 2014;118:12873-82. [PMID: 25333648 PMCID: PMC4234443 DOI: 10.1021/jp5101413] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
38
Frank-Kamenetskii MD. DNA breathes Hoogsteen. ARTIFICIAL DNA, PNA & XNA 2014;2:1-3. [PMID: 21686245 DOI: 10.4161/adna.2.1.15509] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 03/17/2011] [Indexed: 11/19/2022]
39
Esguerra M, Nilsson L, Villa A. Triple helical DNA in a duplex context and base pair opening. Nucleic Acids Res 2014;42:11329-38. [PMID: 25228466 PMCID: PMC4191418 DOI: 10.1093/nar/gku848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
40
Zoli M. Twisting and bending stress in DNA minicircles. SOFT MATTER 2014;10:4304-4311. [PMID: 24791278 DOI: 10.1039/c3sm52953c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
41
Ivchenko O, Bachert P, Imhof P. Umbrella sampling of proton transfer in a creatine–water system. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.03.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
42
Talukder S, Sen S, Chakraborti P, Metzler R, Banik SK, Chaudhury P. Breathing dynamics based parameter sensitivity analysis of hetero-polymeric DNA. J Chem Phys 2014;140:125101. [PMID: 24697480 DOI: 10.1063/1.4869112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
43
Fluctuations in the DNA double helix: A critical review. Phys Life Rev 2014;11:153-70. [PMID: 24560595 DOI: 10.1016/j.plrev.2014.01.005] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/27/2013] [Accepted: 12/30/2013] [Indexed: 12/22/2022]
44
Jeon JH, Sung W. An effective mesoscopic model of double-stranded DNA. J Biol Phys 2014;40:1-14. [PMID: 24306264 PMCID: PMC3923960 DOI: 10.1007/s10867-013-9333-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 10/11/2013] [Indexed: 11/26/2022]  Open
45
Mekler V, Severinov K. Cooperativity and interaction energy threshold effects in recognition of the -10 promoter element by bacterial RNA polymerase. Nucleic Acids Res 2013;41:7276-85. [PMID: 23771146 PMCID: PMC3753650 DOI: 10.1093/nar/gkt541] [Citation(s) in RCA: 13] [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
46
Zoli M. Helix untwisting and bubble formation in circular DNA. J Chem Phys 2013;138:205103. [DOI: 10.1063/1.4807381] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]  Open
47
de Oliveira Guerra JC. Calculation of nucleation free energy for duplex oligomers in the context of nearest neighbor models. Biopolymers 2013;99:538-47. [DOI: 10.1002/bip.22214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2012] [Accepted: 01/19/2013] [Indexed: 11/08/2022]
48
Vologodskii A, Frank-Kamenetskii MD. Strong bending of the DNA double helix. Nucleic Acids Res 2013;41:6785-92. [PMID: 23677618 PMCID: PMC3737528 DOI: 10.1093/nar/gkt396] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
49
Oberstrass FC, Fernandes LE, Lebel P, Bryant Z. Torque spectroscopy of DNA: base-pair stability, boundary effects, backbending, and breathing dynamics. PHYSICAL REVIEW LETTERS 2013;110:178103. [PMID: 23679785 PMCID: PMC3696636 DOI: 10.1103/physrevlett.110.178103] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Indexed: 05/16/2023]
50
Moreno PMD, Geny S, Pabon YV, Bergquist H, Zaghloul EM, Rocha CSJ, Oprea II, Bestas B, Andaloussi SE, Jørgensen PT, Pedersen EB, Lundin KE, Zain R, Wengel J, Smith CIE. Development of bis-locked nucleic acid (bisLNA) oligonucleotides for efficient invasion of supercoiled duplex DNA. Nucleic Acids Res 2013;41:3257-73. [PMID: 23345620 PMCID: PMC3597675 DOI: 10.1093/nar/gkt007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
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