SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE
Structure determination and binding kinetics of a DNA aptamer-argininamide complex.
Identification of Two Novel Arginine Binding DNAs
(DC)(DG)(DA)(DC)(DC)(DA)(DA)(DC)(DG)(DT)(DG)(DT)(DC)(DG)(DC)(DC)(DT)(DG)(DG)(DT) (DC)(DG)
2ARG contains a different DNA aptamer complexed with argininamide
Sequence is derived from in-vitro selection experiments. Sequences were chemically sythethesized.
Data were also collected for sequences containing 5-methyl cytosine substituted independently at positions 15 and 16, and for the sequence with inosine substituted at postion 14.
structures with acceptable covalent geometry,structures with favorable non- bond energy,structures with the least restraint violations,structures with the lowest energy
Distance restraints were obtained from relaxation rate matrix calculations. Structures were calculated using simulated annealing and molecular dynamics
1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide
Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar, Marco Tonelli
APTAMER, ARGININE, ARGININAMIDE, SINGLE-STRAND, HAIRPIN, SELEX, DNA