SOLUTION STRUCTURE OF A PARALLEL-STRANDED G-QUADRUPLEX DNA
Guanine Residues in D(T2Ag3) and D(T2G4) Form Parallel-Stranded Potassium Cation Stabilized G-Quadruplexes with Anti Glycosidic Torsion Angles in Solution
structures with the least restraint violations,structures with the lowest energy
RESTRAINED MOLECULAR DYNAMICS CALCULATIONS WERE DONE ON A MOLECULAR MODEL BUILT TO QUALITATIVELY FIT THE NMR DATA. THE REFINEMENT WAS CONDUCTED IN TWO STAGES. IN THE FIRST STAGE, SEVEN STRUCTURES WERE CALCULATED USING DISTANCE RESTRAINTS (WITH DIFFERENT SEEDS FOR INITIAL VELOCITY ASSIGNMENTS). IN THE SECOND STAGE, FOUR OF THE SEVEN DISTANCE-REFINED STRUCTURES WERE REFINED FURTHER BY NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS CALCULATIONS. THE R(1/6) VALUE WAS USED TO MONITOR THE REFINEMENT DURING THE SECOND STAGE. THE FINAL R(1/6) VALUES FOR THE FOUR AVERAGED MINIMIZED STRUCTURES WERE BETWEEN 0.025 AND 0.033. RMS DEVIATIONS FROM IDEALIZED GEOMETRY FOR THE TWO AVERAGED MINIMIZED STRUCTURES ARE AS FOLLOWS: MODEL1 MODEL2 MODEL3 MODEL4 BOND (ANGSTROMS) 0.013 0.013 0.012 0.011 ANGLES (DEGREES) 2.713 2.634 2.731 2.728 IMPROPERS (DEGREES) 0.476 0.560 0.242 0.280. THE STRUCTURE HAS AN APPROXIMATE FOUR-FOLD SYMMETRY RELATING THE FOUR STRANDS WITH THE SYMMETRY AXIS COINCIDENT WITH THE HELICAL AXIS. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. IT WILL ALSO YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN APPLIED TO CHAIN *B* AND WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *D* WHEN APPLIED TO CHAIN *C*.
DNA, G-QUADRUPLEX, ANTI GLYCOSIDIC TORSION ANGLES