1EMQ

NMR OBSERVATION OF T-TETRADS IN A PARALLEL STRANDED DNA QUADRUPLEX FORMED BY SACCHAROMYCES CEREVISIAE TELOMERE REPEATS


SOLUTION NMR Experimental Data


Experimental Details
Sample Conditions
Sample Contents1-2 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
Solvent90 % H2o +10 % D2O
Ionic Strengthn/a
pH7.0
Pressure1 atm
Temperature (K)293
Experiment(s):2D NOESY, E-COSY, 2D-TOCSY
Spectrometer Information
Manufacturer Model Field Strength
Bruker AMX 500.0
Varian UNITYplus 600.0
NMR Refinement
Method 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.
Details 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.
NMR Ensemble Information
Conformer Selection Criteria structures with the lowest energy
Conformers Calculated Total Number 8
Conformers Submitted Total Number 1
Representative Model Choice Rationale
1 minimized average structure
Additional NMR Experimental Information
1 0-70 C Temperature dependent one dimensional spectra. pH dependent spectra.
Computation: NMR Software
# Classification Software Name Author
1 refinement IRMA 2.3 MSI
2 structure solution DISCOVER 3.1 MSI
3 collection VNMR 6.1 Varian
4 processing FELIX 230 MSI