1EMQ

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

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	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	90% H2O/10% D2O		7.0	1 atm	293
2	E-COSY	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	90% H2O/10% D2O		7.0	1 atm	293
3	2D-TOCSY	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	90% H2O/10% D2O		7.0	1 atm	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	UNITYPLUS	600
2	Bruker	AMX	500

NMR Refinement
Method	Details	Software
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 Criteria	structures with the lowest energy
Conformers Calculated Total Number	8
Conformers Submitted Total Number	1
Representative Model	1 (minimized average structure)

Additional NMR Experimental Information
Details	0-70 C Temperature dependent one dimensional spectra. pH dependent spectra.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	processing	Felix	230	MSI
2	collection	VNMR	6.1	Varian
3	structure solution	Discover	3.1	MSI
4	refinement	IRMA	2.3	MSI