1DB6 | pdb_00001db6

SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide	99.99% D2O	0-25 mM NaCl	6.2	ambient	293
2	DQF-COSY	1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide	99.99% D2O	0-25 mM NaCl	6.2	ambient	293
3	TOCSY	1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide	99.99% D2O	0-25 mM NaCl	6.2	ambient	293
4	2D NOESY	1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide	90% H2O/10% D2O	0-25 mM NaCl	6.2	ambient	278

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	GE	OMEGA	500
2	Bruker	AMX	600

NMR Refinement
Method	Details	Software
Distance restraints were obtained from relaxation rate matrix calculations. Structures were calculated using simulated annealing and molecular dynamics		Felix

NMR Ensemble Information
Conformer Selection Criteria	structures with acceptable covalent geometry,structures with favorable non- bond energy,structures with the least restraint violations,structures with the lowest energy
Conformers Calculated Total Number	30
Conformers Submitted Total Number	10
Representative Model	6 (fewest violations)

Additional NMR Experimental Information
Details	Data were also collected for sequences containing 5-methyl cytosine substituted independently at positions 15 and 16, and for the sequence with inosine substituted at postion 14.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	data analysis	Felix	950	Molecular Simulations, Inc
2	iterative matrix relaxation	MARDIGRAS	3.2	Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar, Marco Tonelli
3	refinement	Discover	2.97	Molecular Simulations, Inc

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.