Theoretical analysis of competing conformational transitions in superhelical DNA.

PLoS Computational Biology
Dina Zhabinskaya, C J Benham

Abstract

We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence. Since DNA superhelicity topologically couples together the transition behaviors of all base pairs, a unified model is required to analyze all the transitions to which the DNA sequence is susceptible. Here we present a first model of this type. Our numerical approach generalizes the strategy of previously developed algorithms, which studied superhelical transitions to a single alternate conformation. We apply our multi-state model to study the competition between strand separation and B-Z transitions in superhelical DNA. We show this competition to be highly sensitive to temperature and to the imposed level of supercoiling. Comparison of our results with experimental data shows that, when the energetics appropriate to the experimental conditions are used, the competition between these two transitions is accurately captured by our algorithm. We analyze the superhelical competition between B-Z transitions and denaturation around the c-myc oncogene, where both transitions are known to occur when this gene is transcrib...Continue Reading

References

Nov 1, 1979·Biopolymers·V V AnshelevichM D Frank-Kamenetskii
Nov 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·D E Depew, J C Wang
Aug 1, 1979·Proceedings of the National Academy of Sciences of the United States of America·C J Benham
Nov 1, 1975·Proceedings of the National Academy of Sciences of the United States of America·D E PulleyblankH P Vosberg
Jun 5, 1992·Journal of Molecular Biology·C J Benham
Mar 15, 1991·Proceedings of the National Academy of Sciences of the United States of America·B WittigA Rich
May 28, 1991·Biochemistry·B H JohnstonA Rich
Oct 20, 1989·Science·A R Rahmouni, R D Wells
Oct 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·L F Liu, J C Wang
Dec 3, 1987·Nature·S M MirkinM D Frank-Kamenetskii
Dec 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·D KowalskiM J Eddy
Nov 6, 1987·Science·A JaworskiR D Wells
Jun 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·K J BreslauerL A Marky
Sep 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·R J KelleherA Rich
Dec 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·M J EllisonA Rich
Nov 1, 1980·Proceedings of the National Academy of Sciences of the United States of America·D M Lilley
Apr 5, 1982·Journal of Molecular Biology·K MizuuchiM Gellert
Jun 1, 1984·Journal of Biomolecular Structure & Dynamics·A V Vologodskii, M D Frank-Kamenetskii
Dec 1, 1983·Journal of Biomolecular Structure & Dynamics·D B Haniford, D E Pulleyblank
Jan 1, 1983·Cold Spring Harbor Symposia on Quantitative Biology·C J Benham
Oct 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·L J Peck, J C Wang
Feb 2, 1984·Nature·M D Frank-Kamenetskii, A V Vologodskii
Aug 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·L J PeckJ C Wang
Feb 5, 1981·Nature·N Panayotatos, R D Wells
Sep 27, 1994·Proceedings of the National Academy of Sciences of the United States of America·P S Ho
Dec 20, 1993·Journal of Molecular Biology·W R Bauer, C J Benham
Apr 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·C J Benham
Dec 27, 1995·Biochimica Et Biophysica Acta·S WölflA Rich
Feb 12, 1998·Journal of Molecular Biology·C BenhamJ Bode
Mar 13, 1999·The Journal of Biological Chemistry·S D SheridanG W Hatfield
Sep 14, 2000·Proceedings of the National Academy of Sciences of the United States of America·B P LeblancD J Clark
Feb 19, 2003·Journal of Molecular Biology·Vladimir N PotamanRichard R Sinden

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Citations

Dec 18, 2012·Nucleic Acids Research·Elizabeth D Howe, Jun S Song
Sep 5, 2014·PLoS Computational Biology·Sam Meyer, Guillaume Beslon
Oct 16, 2016·Biophysics Reviews·Samuel Corless, Nick Gilbert
May 17, 2017·Biophysics Reviews·David LevensFedor Kouzine
Feb 29, 2020·The Journal of Biological Chemistry·Frederic Chedin, Craig J Benham
Dec 31, 2016·Biophysics Reviews·Samuel Corless, Nick Gilbert
May 17, 2017·Biophysics Reviews·David LevensFedor Kouzine
Apr 24, 2018·Nucleic Acids Research·Shane ScottSabrina R Leslie
Jul 8, 2018·Biology Direct·Irina Sorokina, Arcady Mushegian
Aug 28, 2019·Computational and Structural Biotechnology Journal·Shiny Martis BSam Meyer
Aug 28, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Alan Herbert

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Methods Mentioned

BETA
electrophoresis

Software Mentioned

BDZ
SIBZ
SIDD
BDZ trans

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