Structure and dynamics of a DNA duplex containing single alpha-anomeric deoxyadenosine residue.
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.
Bielecki
L
L
Laboratory of Structural Chemistry of Nucleic Acids, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań.
Adamiak
R W
RW
D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D003839:Deoxyadenosines / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D013997:Time Factors
D003839:Deoxyadenosines; D009692:Nucleic Acid Heteroduplexes; D004247:DNA