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NMR Structure of N2-IQ-dG at the G3 position in the NarI recognition sequence
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D 1H-1H NOESY
0.560 uM DNA (5'-D(*CP*TP*CP*GP*GP*CP*IQGP*CP*CP*AP*TP*C)-3'), 0.560 uM DNA (5'-D(*GP*AP*TP*GP*GP*CP*GP*CP*CP*GP*AP*G)-3'), 0.560 uM N2-2-amino-3-methylimidazo[4,5-f]quinoline-deoxyguanosine
100% D2O
0.1
7
ambient
288
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DRX
800
NMR Refinement
Method
Details
Software
simulated annealing, molecular dynamics
TopSpin
NMR Ensemble Information
Conformer Selection Criteria
back calculated data agree with experimental NOESY spectrum
Conformers Calculated Total Number
10
Conformers Submitted Total Number
10
Representative Model
1 (minimized average structure)
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
processing
TopSpin
3.2
Bruker Biospin
2
collection
TopSpin
3.2
Bruker Biospin
3
chemical shift assignment
Sparky
3.115
Goddard
4
data analysis
Sparky
3.115
Goddard
5
peak picking
Sparky
3.115
Goddard
6
structure solution
Amber
10
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
7
refinement
Amber
10
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
8
refinement
CORMA
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman
9
data analysis
MARDIGRAS
Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman