NMR OBSERVATION OF T-TETRADS IN A PARALLEL STRANDED DNA QUADRUPLEX FORMED BY SACCHAROMYCES CEREVISIAE TELOMERE REPEATS
This sequence is two repeats of Saccharomyces cerevisiae telomere sequence
0-70 C Temperature dependent one dimensional spectra. pH dependent spectra.
A total of 234 NOEs constarint. 20 hydrogen bonds constraints. 8 convergant structure after IRMA refinement. R1 factor = 0.31-0.33. r.m.s.d.s from average structure 0.2-0.4. Nil violation exceeding 0.2 A.
An initial model of quadruplex was generated on a IRIS workastation.Energy minimization by steepest descent followed by conjugate gradients methods was done using AMBER force field. Conformational search for the cquadruplex was performed by simulated annealing-reastarined molecular dynamics using AMBER forcefield. Relaxation matrix refinement was performed.
1-2 mM DNA in 0.6 ml(90%H20/10%D2O) having 10 mM potassium phosphate, 0.2 mM EDTA, pH 7.0 and 100 mM KCl
1-2 mM DNA in 0.6 ml(D2O) having 10 mM potassium phosphate, 0.2 mM EDTA, pH 7.0 and 100 mM KCl
T-tetrad, G-quadruplex, Telomere, Yeast, Saccharomyces cerevisiae, DNA