2M3P
DNA containing a cluster of 8-oxo-guanine and abasic site lesion: alpha anomer
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H TOCSY | 0.55 mM DNA (5'-D(*CP*GP*CP*TP*CP*ORP*CP*AP*CP*GP*C)-3'), 0.55 mM DNA (5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*(8OG)P*CP*G)-3') | 100% D2O | 120 | 6 | ambient | 283 | |
2 | 2D 1H-1H NOESY | 0.55 mM DNA (5'-D(*CP*GP*CP*TP*CP*ORP*CP*AP*CP*GP*C)-3'), 0.55 mM DNA (5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*(8OG)P*CP*G)-3') | 100% D2O | 120 | 6 | ambient | 283 | |
3 | 2D DQF-COSY | 0.55 mM DNA (5'-D(*CP*GP*CP*TP*CP*ORP*CP*AP*CP*GP*C)-3'), 0.55 mM DNA (5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*(8OG)P*CP*G)-3') | 100% D2O | 120 | 6 | ambient | 283 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | UNITYPLUS | 500 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing, molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 500 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman | |
2 | refinement | Amber | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman |