Activation volume of DNA duplex formation

Biochemistry
M C Lin, R B Macgregor

Abstract

The denaturation-renaturation thermal hysteresis was used to investigate the kinetics of the helix-coil equilibrium of four 22-base pair homopurine-homopyrimidine duplex oligonucleotides with fractional G x C base pair content (f(G x C)) between 0.14 and 0.5. In 20 mM NaCl and 20 mM Tris-HCl at pH 7.0 and at hydrostatic pressures up to 200 MPa, a two-state bimolecular reaction mechanism adequately described the observed kinetics. At 1 MPa and 47 degrees C, the rate constant for helix formation, k1, increased by a factor of 210, and the reverse rate constant, k(-1), decreased by a factor of 420 upon increasing f(G x C) from 0.14 to 0.5. The activation energies for formation of the duplexes were negative and relatively insensitive to f(G x C). The pressure-induced change in the rate constants is related to the activation volume of the reaction step. Pressure causes k1 to become larger, and the magnitude of the change in k1 with pressure increases the lower the f(G x C) value. Thus, when f(G x C) = 0.14, the activation volume for forward reaction, delta V++(1), equals -20 mL/mol, while when f(G x C) = 0.5, delta V++(1) = -6.7 mL/mol. The rate constant for strand separation, k(-1), decreases at high pressure. The activation volume ...Continue Reading

References

Aug 15, 1979·Journal of Molecular Biology·C J Alden, S H Kim

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Citations

Nov 18, 1998·Current Opinion in Structural Biology·T V Chalikian, K J Breslauer
Nov 5, 1999·Trends in Microbiology·F AbeK Horikoshi
Aug 1, 2014·Physical Chemistry Chemical Physics : PCCP·Jean Ann WyerSteen Brøndsted Nielsen
Nov 1, 2013·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Shuntaro Takahashi, Naoki Sugimoto
Feb 3, 2004·Biopolymers·David N Dubins, Robert B Macgregor
Mar 4, 2000·Biopolymers·R B Macgregor
Oct 21, 2020·Physical Chemistry Chemical Physics : PCCP·Hsuan-Lei Sung, David J Nesbitt
May 6, 2021·Nanomaterials·Anna V EpanchintsevaDmitrii V Pyshnyi
Jun 30, 2021·The Journal of Physical Chemistry. B·Lutan LiuTigran V Chalikian

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