Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: a quantum-chemical study
نویسندگان
چکیده
منابع مشابه
DNA electrochemistry as a probe of base pair stacking in A-, B-, and Z-form DNA.
DNA-mediated charge transport (CT) chemistry is sensitive to DNA structure and base pair stacking. In an electrochemical assay based upon DNA CT, DNA-modified electrode surfaces are used to examine the electrochemical reduction of methylene blue (MB), a small molecule that binds to the DNA film by intercalation. Here electrochemically we probe CT in the three primary conformations of double-str...
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An elastic model for double-stranded polymers is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle w), bending deformations of sugar-phosphate backbones, steric effects of nucleotide base pairs, and base-stacking interactions are considered. The comprehe...
متن کاملStretching single-stranded DNA: interplay of electrostatic, base-pairing, and base-pair stacking interactions.
Recent single-macromolecule observations revealed that the force/extension characteristics of single-stranded DNA (ssDNA) are closely related to solution ionic concentration and DNA sequence composition. To understand this, we studied the elastic property of ssDNA through the Monte Carlo implementation of a modified freely jointed chain (FJC), with electrostatic, base-pairing, and base-pair sta...
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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.
متن کاملIR study of base stacking interactions
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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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 1997
ISSN: 0006-3495
DOI: 10.1016/s0006-3495(97)78049-4