Computer simulation of the ionic atmosphere around Z-DNA

Article Abstract:

A coarse-grained model for Z-DNA that mimics the DNA shape with a small number of repulsive interactions sites is described and the ionic atmosphere around this grooved Z-DNA model is investigated with Monte Carlo simulation after placing negative charges at the phosphate positions. It is noted that the concentration of counterions reaches its absolute maximum at the narrow Z-DNA groove, and at the minor groove of B-DNA, the value of the maximum is higher in the Z conformer.

Models, Usage, Ions, Computer simulation, Computer-generated environments, Monte Carlo method, Monte Carlo methods, Structure, Report

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Conformational change detection of DNA with the fluorogenic reagent of o-phthaladehyde-[beta]-mercaptoethanol

Article Abstract:

The reactions of o-phthalaldehyde-[beta]-mercaptoethanol (OPAME) with single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) are analyzed. A conformation-dependent method is developed that is based on the fact that DNA has different reaction activities with OPAME.

Hybridization, Aldehydes, Chemical properties, Phthalates

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