Structure and dynamics of a DNA duplex containing single alpha-anomeric deoxyadenosine residue
Bielecki, L.; Adamiak, R.W.
Acta Biochimica Polonica 48(1): 103-111
2001
ISSN/ISBN: 0001-527X PMID: 11440159 Document Number: 528305
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.