Solvent Influence on Base Stacking
نویسندگان
چکیده
منابع مشابه
Kinetics of base stacking-aided DNA hybridization.
The association and dissociation rate constants (k(a) and k(d)) of DNA hybridizations involving dual, single or no stacking with different base-pairing sizes were measured, which reveals the advantage of stacking hybridization in both the kinetic and steady state.
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For D2O solutions of 1,3-dimethyluracil, cytidine, caffeine, inosine and 2'-deoxyadenosine the concentration dependence of IR spectra (1800-1400 cm-1) have been found which reflects stacking association of these compounds. A method is proposed to use this data to obtain thermodynamic parameters of association and the molecular spectra in the monomer and associated forms. The homoassociation con...
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A generalization of the recently published quantum-classical approximation [A. A. Neufeld, J. Chem. Phys., 119, 2488 (2003)] for the purposes of reaction dynamics in condensed phase is presented. The obtained kinetic equations treat a solvent influence in a nonphenomenological way, account for the change of the free energy of the surrounding media, allow for different solvent dynamics in each r...
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Simple expressions for the bending and the base-stacking energy of double-stranded semiflexible biopolymers (such as DNA and actin) are derived. The distribution of the folding angle between the two strands is obtained by solving a Schrödinger equation variationally. Theoretical results based on this model on the extension versus force and extension versus degree of supercoiling relations of DN...
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The folding of bacterial tRNAs with disparate sequences has been observed to proceed in distinct folding mechanisms despite their structural similarity. To explore the folding landscapes of tRNA, we performed ion concentration-dependent coarse-grained TIS model MD simulations of several E. coli tRNAs to compare their thermodynamic melting profiles to the classical absorbance spectra of Crothers...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 1998
ISSN: 0006-3495
DOI: 10.1016/s0006-3495(98)77796-3