Atomic detail investigation of the structure and dynamics of DNA-RNA hybrids: a molecular dynamics study

Article Abstract:

A molecular dynamics study was used to explore the relationship between structures, energetics, solvation and RNase H activity of hybrid duplexes in comparison with pure DNA and RNA duplexes. The findings suggest that the differential RNase H activity toward hybrids containing purine versus pyrimidine rich RNA strands is due to sampling of values of the phosphodiester backbone dihedrals in the DNA strands.

Molecular dynamics, Mechanical properties, X-ray analysis

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Impact on pyrophosphate and O-ethyl-substituted pyrophosphate groups on DNA structure

Article Abstract:

The influence of the pyrophosphate (PP) and O-ethyl-substituted pyrophosphate (SPP) internucleotide groups on the helical parameters and geometry of a double-stranded DNA is explored. The results have indicated that subtle perturbations of the DNA backbone conformation affect the processing of base lesions.

Pyrophosphates, Ethyl compounds

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Fluorescence measurements of duplex DNA oligomers under conditions conducive for forming M-DNA (a metal-DNA complex)

Article Abstract:

A metal complex of DNA (M-DNA) with millimolar concentrations of [Zn.sup.2+], [Co.sup.2+] or [Ni.sup.2+] and basic pH is formed by using the ethidium assay. The results have provided insights into the structure of DNA under the high [Zn.sup.2+] concentrations.

Hydrogen-ion concentration, Zinc compounds, pH

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