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

Structure and dynamics of an undecamer DNA duplex containing a single α-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 α-anomeric sugar, disrupted base stacking pattern and unstable duplex bending, the formation of a non-classical α-dA-T pair was observed. A novel way of visual presentation of trajectory data allowing high throughput screening of the conformational parameters is presented.