Structure and dynamics of a DNA duplex containing single alpha-anomeric deoxyadenosine residue.

L Bielecki; R W Adamiak

doi:10.18388/abp.2001_5116

Structure and dynamics of a DNA duplex containing single alpha-anomeric deoxyadenosine residue.

L Bielecki Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań.;
R W Adamiak

DOI: https://doi.org/10.18388/abp.2001_5116

Abstract

Structure and dynamics of an undecamer DNA duplex containing a single alpha-anomeric deoxyadenosine residue placed in opposition to a thymidine unit have been studied using simulation of molecular dynamics in aqueous solution. Despite several noticeable deviations from the B-DNA duplex structure caused by the anomerisation, such as: West type puckering of the alpha-anomeric sugar, disrupted base stacking pattern and unstable duplex bending, the formation of a non-classical alpha-dA-T pair was observed. A novel way of visual presentation of trajectory data allowing high throughput screening of the conformational parameters is presented.

Published

2001-03-31

Issue

Vol. 48 No. 1 (2001)

Section

Articles

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