2N4Y

Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome

SOLUTION NMR

---

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 1H-1H NOESY	0.1-1 mM DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')-1	90% H2O/10% D2O	90	7.0	ambient	298
2	2D 1H-1H TOCSY	0.1-1 mM DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')-1	90% H2O/10% D2O	90	7.0	ambient	298
3	2D 1H-13C HSQC aliphatic	0.1-1 mM DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')-1	90% H2O/10% D2O	90	7.0	ambient	298
4	1D JR-HMQC	0.1-1 mM DNA (5'-D(*CP*TP*GP*GP*GP*CP*GP*GP*GP*AP*CP*TP*GP*GP*GP*GP*AP*GP*TP*GP*GP*T)-3')-1	90% H2O/10% D2O	90	7.0	ambient	298

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	600
2	Bruker	AVANCE	700

NMR Refinement
Method	Details	Software
distance geometry, DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics		Sparky

NMR Ensemble Information
Conformer Selection Criteria	structures with the lowest energy
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	chemical shift assignment	Sparky		Goddard
2	data analysis	Sparky		Goddard
3	peak picking	Sparky		Goddard
4	collection	TopSpin		Bruker Biospin
5	geometry optimization	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
6	structure solution	X-PLOR NIH		Schwieters, Kuszewski, Tjandra and Clore
7	refinement	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
8	structure solution	Amber		Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
9	refinement	X-PLOR NIH