Allowance for heterogeneous stacking in the DNA helix-coil transition theory

Journal of Biomolecular Structure & Dynamics
A V VologodskiiM D Frank-Kamenetskii

Abstract

Melting profiles of eight DNA molecules with lengths ranging from 849 to 4362 bp have been measured in an SSC buffer where the melting is an equilibrium process up to complete strand separation. A theoretical analysis shows that the melting profiles depend on only eight invariants that are linear combinations of 10 original stacking parameters. As a result it is impossible to determine the 10 parameters from the melting profiles. The 8 variants have been determined by fitting theoretical profiles to experimental ones for two fragments. Then theoretical and experimental profiles are compared for those 6 fragments that were not used in the fitting procedure. This comparison demonstrates that allowance for heterogeneous stacking considerably improves the agreement between theory and experiment. The values of invariants have proved to be small. This confirms the previous conclusion that heterogeneous stacking interactions produce only small corrections to the major effect of the difference in the mean stabilities of AT and GC pairs. Some discrepancy between theory and experiment that remains after the allowance for heterogeneous stacking is probably due to even finer effects of long-range interactions.

References

Apr 1, 1978·Nucleic Acids Research·D G KnorreE A Sheshogova
Jan 1, 1979·Cold Spring Harbor Symposia on Quantitative Biology·J G Sutcliffe
Dec 1, 1977·Biopolymers·M Fixman, J J Freire
Jul 1, 1978·Nucleic Acids Research·A V Vologodskii, M D Frank-Kamenetskii
Sep 21, 1978·Nature·D L VizardA T Ansevin
Dec 1, 1978·Nucleic Acids Research·E BeckM Takanami
Aug 15, 1974·Biochimica Et Biophysica Acta·J Bearden
Sep 25, 1980·Nucleic Acids Research·A S BorovikE I Golovanov
May 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·M YamadaA Nakazawa
Oct 24, 1981·Nucleic Acids Research·B R Amirikyan Lyubchenko YuL
Aug 25, 1981·Nucleic Acids Research·M P PerelroyzenA V Vologodskii
Jun 5, 1981·Journal of Molecular Biology·J J Dunn, F W Studier

❮ Previous
Next ❯

Citations

Jan 1, 1986·Progress in Biophysics and Molecular Biology·A Wada, A Suyama
Aug 13, 2010·Proceedings of the National Academy of Sciences of the United States of America·Stephanie Geggier, Alexander Vologodskii
Mar 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SantaLucia
Aug 1, 1997·Journal of Biomolecular Structure & Dynamics·D Y Lando
Oct 27, 2004·Bioinformatics·Alejandro Panjkovich, Francisco Melo
May 25, 1988·Nucleic Acids Research·M P Perelroyzen, A V Vologodskii
May 21, 1998·Nucleic Acids Research·H T Allawi, J SantaLucia
Feb 13, 2003·Nucleic Acids Research·Wenonah A VercoutereMark Akeson
Feb 2, 2006·Nucleic Acids Research·Peter YakovchukMaxim D Frank-Kamenetskii
Feb 26, 2010·BMC Bioinformatics·Dan TulpanSerge Leger
Feb 25, 2014·Physics of Life Reviews·Maxim D Frank-Kamenetskii, Shikha Prakash
Jan 1, 1991·Critical Reviews in Biochemistry and Molecular Biology·G Yagil
Jun 29, 2012·Biochimie·Raffaele SaladinoErnesto Di Mauro
Dec 27, 2011·Physics of Life Reviews·Raffaele SaladinoErnesto Di Mauro
Feb 28, 2006·Biophysical Journal·Andrew KruegerMaxim D Frank-Kamenetskii
Sep 3, 2004·Journal of Molecular Biology·Ekaterina ProtozanovaMaxim D Frank-Kamenetskii
Apr 16, 2013·Journal of Biomolecular Structure & Dynamics·Ernesto Di MauroEdward N Trifonov
May 3, 2011·The Journal of Chemical Physics·Juan C AraqueMarc A Robert
Apr 23, 2017·International Journal of Biological Macromolecules·Chun-Ling ChangDmitri Y Lando
Jan 1, 1997·Biopolymers·J SantaLucia, D H Turner
Nov 28, 2017·Nucleic Acids Research·Josep Maria HuguetFelix Ritort
Feb 3, 2004·Biopolymers·David N Dubins, Robert B Macgregor
Jan 1, 1994·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·Y Z Chen, E W Prohofsky
Aug 13, 2004·Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences·A A Travers
Jan 1, 1986·Annals of the New York Academy of Sciences·W K Olson, J Cicariello
May 21, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Vassili IvanovGiovanni Zocchi
May 16, 2007·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ralf EveraersChristian Simm
Jan 15, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Vera CherepinskyBud Mishra
Aug 1, 1987·Journal of Biomolecular Structure & Dynamics·S M MirkinA V Vologodskii
Aug 1, 1987·Journal of Biomolecular Structure & Dynamics·S A KozyavkinB R Amirikyan
Jun 12, 2012·Chemical Society Reviews·Raffaele SaladinoErnesto Di Mauro
Nov 28, 2013·Molecular BioSystems·Sattar SoltaniRosa Aghdam

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cajal Bodies & Gems

Cajal bodies or coiled bodies are dense foci of coilin protein. Gemini of Cajal bodies, or gems, are microscopically similar to Cajal bodies. It is believed that Cajal bodies play important roles in RNA processing while gems assist the Cajal bodies. Find the latest research on Cajal bodies and gems here.