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.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2006
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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.
Publication Name: Journal of Physical Chemistry B
Subject: Chemicals, plastics and rubber industries
ISSN: 1520-6106
Year: 2008
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