Fluorescent alpha-anomeric 1,N(6)etheno-deoxyadenosine in DNA duplexes. The alpha-epsilondA / dG pair.
Structural properties of the fluorescent alpha-anomeric 1,N(6)ethenodeoxyadenosine residue placed in opposition to all four canonical deoxynucleotide units within 11-mer DNA duplexes have been studied. The duplex with alpha-epsilondA / dG pairing is most thermodynamically stable while the alpha-epsilondA / dC one is the least stable. Fluorescence measurements confirm the thermodynamic data and indicate base-pair dependent stacking properties of alpha-epsilondA within duplex structures. Results of molecular dynamics (MD) simulations in aqueous solution for the most stable duplex point to the presence of different conformational states of the alpha-1,N(6)etheno-deoxyadenosine residue, including formation of a hydrogen bonded pair with the dG and possible occurrence of severe kinking in the duplex.
Bielecki
L
L
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznañ.
Skalski
B
B
Zagórowska
I
I
Verrall
R E
RE
Adamiak
R W
RW
D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D003839:Deoxyadenosines / Q000737:chemistry*; D005453:Fluorescence; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
D003839:Deoxyadenosines; C032221:1,N(6)-ethenodeoxyadenosine; D004247:DNA