5OPH | pdb_00005oph

G-quadruplex structure of DNA oligonucleotide containing GGGGCC repeats linked to ALS and FTD

SOLUTION NMR

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NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	1.0 mM DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate	90% H2O/10% D2O	53 mM	5.8	1 bar	298	Varian VNMRS 800
9	2D 1H-1H NOESY	0.4 mM DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate	100% D2O	53 mM	5.8	1 bar	298	Varian VNMRS 800
2	2D 1H-1H TOCSY	0.4 mM DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate	100% D2O	53 mM	5.8	1 bar	298	Varian VNMRS 800
4	2D DQF-COSY	0.4 mM DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate	100% D2O	53 mM	5.8	1 bar	298	Varian VNMRS 600
5	2D 1H-13C HSQC aliphatic	0.4 mM DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate	100% D2O	53 mM	5.8	1 bar	298	Varian VNMRS 600
6	2D 1H-13C HSQC aromatic	0.4 mM DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate	100% D2O	53 mM	5.8	1 bar	298	Varian VNMRS 600
7	1D 15N-edited HSQC	0.3 mM one guanine in the sequence labeled 5% 15N and 13 C DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate	90% H2O/10% D2O	53 mM	5.8	1 bar	298	Varian VNMRS 600
8	1D 13C-edited HSQC	0.3 mM one guanine in the sequence labeled 5% 15N and 13 C DNA (5'-D(*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*GP*GP*CP*CP*GP*GP*(BGM)P*G)-3'), 30 mM potassium chloride, 20 mM potassium phosphate	90% H2O/10% D2O	53 mM	5.8	1 bar	298	Varian VNMRS 600

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	VNMRS	600
2	Varian	VNMRS	800

NMR Refinement
Method	Details	Software
simulated annealing		Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	Amber	14	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2	structure calculation	Amber	14	Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
3	chemical shift assignment	Sparky		Goddard
4	processing	VNMR		Varian
5	peak picking	Sparky		Goddard