Stephen D. Levene, Ph.D - Publications

Bioengineering University of Texas at Dallas, Richardson, TX, United States 
Biophysical Chemistry of protein-DNA interactions

45 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Shoura MJ, Giovan SM, Vetcher AA, Ziraldo R, Hanke A, Levene SD. Loop-closure kinetics reveal a stable, right-handed DNA intermediate in Cre recombination. Nucleic Acids Research. PMID 32182357 DOI: 10.1093/Nar/Gkaa153  0.76
2019 Ziraldo R, Shoura MJ, Fire AZ, Levene SD. Deconvolution of nucleic-acid length distributions: a gel electrophoresis analysis tool and applications. Nucleic Acids Research. PMID 31226202 DOI: 10.1093/Nar/Gkz534  0.76
2019 Ziraldo R, Hanke A, Levene SD. Kinetic pathways of topology simplification by Type-II topoisomerases in knotted supercoiled DNA. Nucleic Acids Research. 47: 69-84. PMID 30476194 DOI: 10.1093/Nar/Gky1174  0.72
2017 Shoura MJ, Gabdank I, Hansen L, Merker J, Gotlib J, Levene SD, Fire AZ. Intricate and Cell-type-specific Populations of Endogenous Circular DNA (eccDNA) in Caenorhabditis elegans and Homo sapiens. G3 (Bethesda, Md.). PMID 28801508 DOI: 10.1534/G3.117.300141  0.76
2015 Chaires JB, Levene SD. Preface. Biopolymers. 103: 469. PMID 26015222 DOI: 10.1002/bip.22686  1
2015 Giovan SM, Hanke A, Levene SD. DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation. Biopolymers. 103: 528-38. PMID 26014845 DOI: 10.1002/Bip.22683  1
2015 Chaires JB, Levene SD. Preface. Biopolymers. 103: 417. PMID 26010347 DOI: 10.1002/bip.22661  1
2014 Giovan SM, Scharein RG, Hanke A, Levene SD. Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping. The Journal of Chemical Physics. 141: 174902. PMID 25381542 DOI: 10.1063/1.4900657  1
2014 Shoura MJ, Ranatunga RJ, Harris SA, Nielsen SO, Levene SD. Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: a molecular-dynamics study. Biophysical Journal. 107: 700-10. PMID 25099809 DOI: 10.1016/J.Bpj.2014.06.023  1
2013 Levene SD, Giovan SM, Hanke A, Shoura MJ. The thermodynamics of DNA loop formation, from J to Z. Biochemical Society Transactions. 41: 513-8. PMID 23514145 DOI: 10.1042/Bst20120324  1
2012 Shoura MJ, Vetcher AA, Giovan SM, Bardai F, Bharadwaj A, Kesinger MR, Levene SD. Measurements of DNA-loop formation via Cre-mediated recombination. Nucleic Acids Research. 40: 7452-64. PMID 22589415 DOI: 10.1093/Nar/Gks430  1
2011 Neelam S, Kakhniashvili DG, Wilkens S, Levene SD, Goodman SR. Functional 20S proteasomes in mature human red blood cells. Experimental Biology and Medicine (Maywood, N.J.). 236: 580-91. PMID 21508250 DOI: 10.1258/Ebm.2011.010394  1
2011 Hanke A, Giovan S, Levene SD. Evaluating partition functions for multiscale models of DNA Progress of Theoretical Physics Supplement. 109-129. DOI: 10.1143/Ptps.191.109  1
2010 Vetcher AA, McEwen AE, Abujarour R, Hanke A, Levene SD. Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity. Biophysical Chemistry. 148: 104-11. PMID 20346570 DOI: 10.1016/J.Bpc.2010.02.016  1
2009 Levene SD. Analysis of DNA topoisomers, knots, and catenanes by agarose gel electrophoresis. Methods in Molecular Biology (Clifton, N.J.). 582: 11-25. PMID 19763938 DOI: 10.1007/978-1-60761-340-4_2  1
2008 Hanke A, Hu W, Levene SD, Liu JP. Microarray-based hybridization technology for biosensors 2008 8th Ieee Conference On Nanotechnology, Ieee-Nano. 675-676. DOI: 10.1109/NANO.2008.204  1
2007 Metzler R, Ambjörnsson T, Hanke A, Zhang Y, Levene S. Single DNA conformations and biological function Journal of Computational and Theoretical Nanoscience. 4: 1-49. DOI: 10.1166/Jctn.2007.001  1
2007 Vetcher AA, Fan JH, Vetcher IA, Lin T, Abramov SM, Draper R, Kozlov ME, Baughman RH, Levene SD. Electrophoretic fractionation of carbon nanotube dispersions on agarose gels International Journal of Nanoscience. 6: 1-7. DOI: 10.1142/S0219581X07004304  1
2006 Vetcher AA, Srinivasan S, Vetcher IA, Abramov SM, Kozlov M, Baughman RH, Levene SD. Fractionation of SWNT/nucleic acid complexes by agarose gel electrophoresis. Nanotechnology. 17: 4263-9. PMID 21727569 DOI: 10.1088/0957-4484/17/16/043  1
2006 Zhang Y, McEwen AE, Crothers DM, Levene SD. Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping. Plos One. 1: e136. PMID 17205140 DOI: 10.1371/Journal.Pone.0000136  1
2006 Vetcher AA, Lushnikov AY, Navarra-Madsen J, Scharein RG, Lyubchenko YL, Darcy IK, Levene SD. DNA topology and geometry in Flp and Cre recombination. Journal of Molecular Biology. 357: 1089-104. PMID 16483600 DOI: 10.1016/J.Jmb.2006.01.037  1
2006 Zhang Y, McEwen AE, Crothers DM, Levene SD. Statistical-mechanical theory of DNA looping. Biophysical Journal. 90: 1903-12. PMID 16361335 DOI: 10.1529/Biophysj.105.070490  1
2005 You L, Levene SD. Bulge defects do not destabilize negatively supercoiled DNA. Biophysical Journal. 89: L43-5. PMID 16199502 DOI: 10.1529/Biophysj.105.070847  1
2005 Zein SS, Levene SD. Structural aspects of RecA-dependent homologous strand exchange involving human telomeric DNA. Biochemistry. 44: 4817-28. PMID 15779908 DOI: 10.1021/Bi047735R  1
2005 Zein SS, Vetcher AA, Levene SD. PCR-based synthesis of repetitive single-stranded DNA for applications to nanobiotechnology International Journal of Nanoscience. 4: 287-294. DOI: 10.1142/S0219581X05003140  1
2004 Tsen H, Levene SD. Analysis of chemical and enzymatic cleavage frequencies in supercoiled DNA. Journal of Molecular Biology. 336: 1087-102. PMID 15037071 DOI: 10.1016/J.Jmb.2003.12.079  1
2000 Huffman KE, Levene SD, Tesmer VM, Shay JW, Wright WE. Telomere shortening is proportional to the size of the G-rich telomeric 3'-overhang. The Journal of Biological Chemistry. 275: 19719-22. PMID 10787419 DOI: 10.1074/Jbc.M002843200  1
1999 Levene SD, Tsen H. Analysis of DNA knots and catenanes by agarose-gel electrophoresis. Methods in Molecular Biology (Clifton, N.J.). 94: 75-85. PMID 12844864 DOI: 10.1385/1-59259-259-7:75  1
1999 Huffman KE, Levene SD. DNA-sequence asymmetry directs the alignment of recombination sites in the FLP synaptic complex. Journal of Molecular Biology. 286: 1-13. PMID 9931245 DOI: 10.1006/Jmbi.1998.2468  1
1997 Wright WE, Tesmer VM, Huffman KE, Levene SD, Shay JW. Normal human chromosomes have long G-rich telomeric overhangs at one end. Genes & Development. 11: 2801-9. PMID 9353250 DOI: 10.1101/Gad.11.21.2801  1
1997 Tsen H, Levene SD. Supercoiling-dependent flexibility of adenosine-tract-containing DNA detected by a topological method. Proceedings of the National Academy of Sciences of the United States of America. 94: 2817-22. PMID 9096303 DOI: 10.1073/Pnas.94.7.2817  1
1995 Levene SD, Donahue C, Boles TC, Cozzarelli NR. Analysis of the structure of dimeric DNA catenanes by electron microscopy. Biophysical Journal. 69: 1036-45. PMID 8519958 DOI: 10.1016/S0006-3495(95)79978-7  1
1995 Chastain PD, Eichler EE, Kang S, Nelson DL, Levene SD, Sinden RR. Anomalous rapid electrophoretic mobility of DNA containing triplet repeats associated with human disease genes. Biochemistry. 34: 16125-31. PMID 8519769 DOI: 10.1021/Bi00049A027  1
1992 Zimm BH, Levene SD. Problems and prospects in the theory of gel electrophoresis of DNA. Quarterly Reviews of Biophysics. 25: 171-204. PMID 1518924 DOI: 10.1017/S0033583500004662  1
1992 Crothers DM, Drak J, Kahn JD, Levene SD. DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods in Enzymology. 212: 3-29. PMID 1518450 DOI: 10.1016/0076-6879(92)12003-9  1
1992 Vologodskii AV, Levene SD, Klenin KV, Frank-Kamenetskii M, Cozzarelli NR. Conformational and thermodynamic properties of supercoiled DNA. Journal of Molecular Biology. 227: 1224-43. PMID 1433295 DOI: 10.1016/0022-2836(92)90533-P  1
1989 Lumpkin O, Levene SD, Zimm BH. Exactly solvable reptation model. Physical Review. A. 39: 6557-6566. PMID 9901258 DOI: 10.1103/Physreva.39.6557  1
1989 Levene SD, Zimm BH. Understanding the anomalous electrophoresis of bent DNA molecules: a reptation model. Science (New York, N.Y.). 245: 396-9. PMID 2756426 DOI: 10.1126/Science.2756426  1
1987 Levene SD, Zimm BH. Separations of open-circular DNA using pulsed-field electrophoresis. Proceedings of the National Academy of Sciences of the United States of America. 84: 4054-7. PMID 3295875 DOI: 10.1073/Pnas.84.12.4054  1
1986 Levene SD, Crothers DM. Topological distributions and the torsional rigidity of DNA. A Monte Carlo study of DNA circles. Journal of Molecular Biology. 189: 73-83. PMID 3783681 DOI: 10.1016/0022-2836(86)90382-7  1
1986 Levene SD, Crothers DM. Ring closure probabilities for DNA fragments by Monte Carlo simulation. Journal of Molecular Biology. 189: 61-72. PMID 3783680 DOI: 10.1016/0022-2836(86)90381-5  1
1986 Levene SD, Wu HM, Crothers DM. Bending and flexibility of kinetoplast DNA. Biochemistry. 25: 3988-95. PMID 3017412 DOI: 10.1021/Bi00362A003  1
1983 Marini JC, Levene SD, Crothers DM, Englund PT. A bent helix in kinetoplast DNA. Cold Spring Harbor Symposia On Quantitative Biology. 47: 279-83. PMID 6574847 DOI: 10.1101/Sqb.1983.047.01.033  1
1983 Levene SD, Crothers DM. A computer graphics study of sequence-directed bending in DNA. Journal of Biomolecular Structure & Dynamics. 1: 429-35. PMID 6400882 DOI: 10.1080/07391102.1983.10507452  1
1982 Marini JC, Levene SD, Crothers DM, Englund PT. Bent helical structure in kinetoplast DNA. Proceedings of the National Academy of Sciences of the United States of America. 79: 7664-8. PMID 16593261 DOI: 10.1073/Pnas.79.24.7664  1
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