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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