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Stephen D. Levene

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Stephen Daniel Levene
Born
New York, NY, United States
Alma materColumbia University
Yale University
Known forNucleic acid structure and function, physical genomics
Scientific career
FieldsChemistry, Biophysics, Bioengineering
InstitutionsUniversity of Texas at Dallas
Lawrence Berkeley Laboratory
University of California, San Diego
Thesis Studies of Sequence-directed Bending and Flexibility in DNA  (1985)
Doctoral advisorDonald M. Crothers
Websitehttps://labs.utdallas.edu/levenelab/

Stephen Levene is an American biophysicist and professor of bioengineering, molecular biology, and physics at the University of Texas at Dallas.[1]

Early life and education

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Levene was born in New York City and attended Horace Mann School and Andrew Hill High School in San Jose, California. He received his A.B. in Chemistry from Columbia University and his Ph.D. in Chemistry from Yale University. His doctoral work demonstrated and quantified the phenomenon of sequence-directed bending in DNA due to adenine-thymine tracts,[2][3] and pioneered the use of Monte Carlo simulation to compute cyclization probabilities of DNA molecules having arbitrary preferred geometries.[4][5][6] Upon leaving Yale, Levene became an American Cancer Society postdoctoral fellow at UC San Diego with Bruno Zimm, where he worked on the physical mechanism of gel electrophoresis.[7][8][9]

Career

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Research interests

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Levene's research interests are broadly in the area of genome architecture and its maintenance by enzyme mechanisms and protein-DNA interactions. His work in this area began from the time he was a Staff Scientist at the Human Genome Center at Lawrence Berkeley National Laboratory, when he collaborated with Nicholas Cozzarelli's group on the structure and properties of supercoiled DNA[10] and DNA catenanes.[11] Levene's group has made both experimental and theoretical/computational contributions to understanding DNA topology and its relationship to local DNA structures,[12][13][14] DNA-loop formation,[15][16][17] site-specific DNA recombination,[18][19] the structure of human telomeres,[20][21] and extrachromosomal-circular DNA.[22]

References

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  1. ^ UT-Dallas Bioengineering Web Page
  2. ^ Marini, Joan C.; Levene, Stephen D.; Crothers, Donald M.; Englund, Paul T. (1982). "Bent helical structure in kinetoplast DNA". Proceedings of the National Academy of Sciences. 79 (24): 7664–7668. Bibcode:1982PNAS...79.7664M. doi:10.1073/pnas.79.24.7664. PMC 347408. PMID 16593261.
  3. ^ Levene, Stephen D.; Ming Wu, Hen; Crothers, Donald M. (1986). "Bending and flexibility of kinetoplast DNA". Biochemistry. 25 (14): 3988–3995. doi:10.1021/bi00362a003. PMID 3017412.
  4. ^ Levene, Stephen D.; Crothers, Donald M. (1986). "Ring closure probabilities for DNA fragments by Monte Carlo simulation". Journal of Molecular Biology. 189 (1): 61–72. doi:10.1016/0022-2836(86)90381-5. PMID 3783680.
  5. ^ Levene, Stephen D.; Crothers, Donald M. (1986). "Topological distributions and the torsional rigidity of DNA". Journal of Molecular Biology. 189 (1): 73–83. doi:10.1016/0022-2836(86)90382-7. PMID 3783681.
  6. ^ Crothers, Donald M.; Drak, Jacqueline; Kahn, Jason D.; Levene, Stephen D. (1992). "[1] DNA bending, flexibility, and helical repeat by cyclization kinetics". DNA Structures Part B: Chemical and Electrophoretic Analysis of DNA. Methods in Enzymology. Vol. 212. pp. 3–29. doi:10.1016/0076-6879(92)12003-9. ISBN 9780121821135. PMID 1518450.
  7. ^ Levene, SD; Zimm, BH (1987). "Separations of open-circular DNA using pulsed-field electrophoresis". Proceedings of the National Academy of Sciences. 84 (12): 4054–7. Bibcode:1987PNAS...84.4054L. doi:10.1073/pnas.84.12.4054. PMC 305020. PMID 3295875.
  8. ^ Levene, Stephen D.; Zimm, Bruno H. (1989). "Understanding the Anomalous Electrophoresis of Bent DNA Molecules: A Reptation Model". Science. 245 (4916): 396–399. Bibcode:1989Sci...245..396L. doi:10.1126/science.2756426. PMID 2756426.
  9. ^ Zimm, BH; Levene, SD (1992). "Problems and prospects in the theory of gel electrophoresis of DNA". Quarterly Reviews of Biophysics. 25 (2): 171–204. doi:10.1017/s0033583500004662. PMID 1518924. S2CID 27976751.
  10. ^ Vologodskii, AV; Levene, SD; Klenin, KV; Frank-Kamenetskii, M; Cozzarelli, NR (1992). "Conformational and thermodynamic properties of supercoiled DNA". Journal of Molecular Biology. 227 (4): 1224–43. doi:10.1016/0022-2836(92)90533-p. PMID 1433295.
  11. ^ Levene, SD; Donahue, C; Boles, TC; Cozzarelli, NR (1995). "Analysis of the structure of dimeric DNA catenanes by electron microscopy". Biophysical Journal. 69 (3): 1036–45. Bibcode:1995BpJ....69.1036L. doi:10.1016/S0006-3495(95)79978-7. PMC 1236332. PMID 8519958.
  12. ^ Tsen, H; Levene, SD (1997). "Supercoiling-dependent flexibility of adenosine-tract-containing DNA detected by a topological method". Proceedings of the National Academy of Sciences. 94 (7): 2817–22. Bibcode:1997PNAS...94.2817T. doi:10.1073/pnas.94.7.2817. PMC 20279. PMID 9096303.
  13. ^ Tsen, H; Levene, SD (2004). "Analysis of chemical and enzymatic cleavage frequencies in supercoiled DNA". Journal of Molecular Biology. 336 (5): 1087–102. doi:10.1016/j.jmb.2003.12.079. PMID 15037071.
  14. ^ Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D. (2014). "Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping". The Journal of Chemical Physics. 141 (17): 174902. Bibcode:2014JChPh.141q4902G. doi:10.1063/1.4900657. PMC 4241824. PMID 25381542.
  15. ^ Zhang, Yongli; McEwen, Abbye E.; Crothers, Donald M.; Levene, Stephen D. (2006). "Statistical-Mechanical Theory of DNA Looping". Biophysical Journal. 90 (6): 1903–1912. Bibcode:2006BpJ....90.1903Z. doi:10.1529/biophysj.105.070490. PMC 1386771. PMID 16361335.
  16. ^ Zhang, Yongli; McEwen, Abbye E.; Crothers, Donald M.; Levene, Stephen D. (2006). "Analysis of In-Vivo LacR-Mediated Gene Repression Based on the Mechanics of DNA Looping". PLOS ONE. 1 (1): e136. Bibcode:2006PLoSO...1..136Z. doi:10.1371/journal.pone.0000136. PMC 1762422. PMID 17205140.
  17. ^ Giovan, Stefan M.; Hanke, Andreas; Levene, Stephen D. (2015). "DNA cyclization and looping in the wormlike limit: Normal modes and the validity of the harmonic approximation". Biopolymers. 103 (9): 528–538. doi:10.1002/bip.22683. PMC 6815668. PMID 26014845.
  18. ^ Huffman, Kenneth E.; Levene, Stephen D. (1999). "DNA-sequence asymmetry directs the alignment of recombination sites in the FLP synaptic complex". Journal of Molecular Biology. 286 (1): 1–13. doi:10.1006/jmbi.1998.2468. PMID 9931245.
  19. ^ Vetcher, Alexandre A.; Lushnikov, Alexander Y.; Navarra-Madsen, Junalyn; Scharein, Robert G.; Lyubchenko, Yuri L.; Darcy, Isabel K.; Levene, Stephen D. (2006). "DNA Topology and Geometry in FLP and Cre Recombination". Journal of Molecular Biology. 357 (4): 1089–1104. doi:10.1016/j.jmb.2006.01.037. PMID 16483600.
  20. ^ Wright, WE; Tesmer, VM; Huffman, KE; Levene, SD; Shay, JW (November 1997). "Normal human chromosomes have long G-rich telomeric overhangs at one end". Genes & Development. 11 (21): 2801–9. doi:10.1101/gad.11.21.2801. PMC 316649. PMID 9353250.
  21. ^ Huffman, KE; Levene, SD; Tesmer, VM; Shay, JW; Wright, WE (2000). "Telomere shortening is proportional to the size of the G-rich telomeric 3'-overhang". The Journal of Biological Chemistry. 275 (26): 19719–22. doi:10.1074/jbc.M002843200. PMID 10787419.
  22. ^ Shoura, Massa J.; Gabdank, Idan; Hansen, Loren; Merker, Jason; Gotlib, Jason; Levene, Stephen D.; Fire, Andrew Z. (2017). "Intricate and Cell Type-Specific Populations of Endogenous Circular DNA (EccDNA) in Caenorhabditis elegans and Homo sapiens". G3: Genes, Genomes, Genetics. 7 (10): 3295–3303. doi:10.1534/g3.117.300141. PMC 5633380. PMID 28801508.
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