Stephen D. Levene

Last updated
Stephen Daniel Levene
Born
New York, NY, United States
Alma mater Columbia University
Yale University
Known for Nucleic acid structure and function, physical genomics
Scientific career
Fields Chemistry, Biophysics, Bioengineering
Institutions University of Texas at Dallas
Lawrence Berkeley Laboratory
University of California, San Diego
Thesis Studies of Sequence-directed Bending and Flexibility in DNA  (1985)
Doctoral advisor Donald M. Crothers
Website https://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]

Contents

Early life and education

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

Research interests

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

  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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