2KAZ | pdb_00002kaz

Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the connecting loop

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D DQF-COSY	2 mM DNA (5'-D(DGPDGPDGPDAPDCPDGPDTPDAPDGPDTPDGPDGP*DG)-3'), 10 mM K+, 10 % D2O	90% H2O/10% D2O	10	7.85	ambient	298
2	2D 1H-1H NOESY	2 mM DNA (5'-D(DGPDGPDGPDAPDCPDGPDTPDAPDGPDTPDGPDGP*DG)-3'), 10 mM K+, 10 % D2O	90% H2O/10% D2O	10	7.85	ambient	298
3	2D 1H-1H TOCSY	2 mM DNA (5'-D(DGPDGPDGPDAPDCPDGPDTPDAPDGPDTPDGPDGP*DG)-3'), 10 mM K+, 10 % D2O	90% H2O/10% D2O	10	7.85	ambient	298

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

NMR Refinement
Method	Details	Software
molecular dynamics	Molecular dynamics on selected model. Conformers selected from the last 200ps of rMD. 5 structures selected based on a cluster analysis to group structures by RMSD.	Amber

NMR Ensemble Information
Conformer Selection Criteria	structures with acceptable covalent geometry
Conformers Calculated Total Number	6000
Conformers Submitted Total Number	5
Representative Model	1 (closest to the average)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	Amber	8	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
2	refinement	Amber	8	Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm
3	processing	TopSpin	2.1	Bruker Biospin
4	collection	TopSpin	2.1	Bruker Biospin
5	data analysis	MOLMOL	2k	Koradi, Billeter and Wuthrich
6	chemical shift assignment	CCPNMR	1.16	CCPN

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.