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 1EMQ | pdb_00001emq

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


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY1-2 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 KCl90% H2O/10% D2O7.01 atm293
2E-COSY1-2 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 KCl90% H2O/10% D2O7.01 atm293
32D-TOCSY1-2 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 KCl90% H2O/10% D2O7.01 atm293
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianUNITYPLUS600
2BrukerAMX500
NMR Refinement
MethodDetailsSoftware
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.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.Felix
NMR Ensemble Information
Conformer Selection Criteriastructures with the lowest energy
Conformers Calculated Total Number8
Conformers Submitted Total Number1
Representative Model1 (minimized average structure)
Additional NMR Experimental Information
Details0-70 C Temperature dependent one dimensional spectra. pH dependent spectra.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1processingFelix230MSI
2collectionVNMR6.1Varian
3structure solutionDiscover3.1MSI
4refinementIRMA2.3MSI