2HLI
Solution structure of Crotonaldehyde-Derived N2-[3-Oxo-1(S)-methyl-propyl]-dG DNA Adduct in the 5'-CpG-3' Sequence
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1 mM in 0.25 mL; 10 mM Sodium phosphate buffer; 0.1 M NaCl; 50 uMNa2EDTA | 99.996% D2O | 0.1 M NaCl | 9.3 | 1 atm | 303 | |
2 | DQF-COSY | |||||||
3 | E-COSY |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 800 |
2 | Bruker | AVANCE | 600 |
3 | Bruker | AVANCE | 500 |
NMR Refinement | ||
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Method | Details | Software |
distance geometry simulated annealing molecular dynamics matrix relaxation and torsion angle | 308 distance restraints, 90 sugar pucker restraints, 52 H-bonding restraints | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum |
Conformers Calculated Total Number | 10 |
Conformers Submitted Total Number | 1 |
Representative Model | 10 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear techniques. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 3.5 | Bruker |
2 | processing | NMRPipe | 2.3 | Delaglio F et al. |
3 | data analysis | Felix | 2000 | Accelrys, Inc. |
4 | iterative matrix relaxation | MARDIGRAS | 5.2.1 | Keepers, JW et al. |
5 | refinement | Amber | 8.0 | Case et al |
6 | data analysis | CORMA | 5.2 | Keepers JW et al. |