2O7Y
Duplex DNA containing an abasic site with an opposite T (alpha anomer) in 5'-G_AC-3' (10 structure ensemble and averaged structure)
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2.7 mM duplex DNA | 100% D2O | 10 mM Sodium Phosphate, 0.2 mM EDTA | 6.5 | 1 atm | 298 | |
2 | 2D TOCSY | 2.7 mM duplex DNA | 100% D2O | 10 mM Sodium Phosphate, 0.2 mM EDTA | 6.5 | 1 atm | 298 | |
3 | E-COSY | 2.7 mM duplex DNA | 100% D2O | 10 mM Sodium Phosphate, 0.2 mM EDTA | 6.5 | 1 atm | 298 | |
4 | H-P HSQC | 2.7 mM duplex DNA | 100% D2O | 10 mM Sodium Phosphate, 0.2 mM EDTA | 6.5 | 1 atm | 298 | |
5 | H3'-selective HSQC | 2.7 mM duplex DNA | 100% D2O | 10 mM Sodium Phosphate, 0.2 mM EDTA | 6.5 | 1 atm | 298 | |
6 | watergate-NOESY | 2.7 mM duplex DNA | 90% H2O/10% D2O | 10 mM Sodium Phosphate, 0.2 mM EDTA | 6.5 | 1 atm | 277 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Custom-built | Custom-built | 591 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing molecular dynamics matrix relaxation | the structures are based on 452 NOE-derived distance constraints, 62 dihedral angle restraints. | Felix |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations,structures with the lowest energy |
Conformers Calculated Total Number | 30 |
Conformers Submitted Total Number | 11 |
Representative Model | 11 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear techniques and H-P heteronuclear experiments |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | data analysis | Felix | 2001 | Accelrys Inc. |
2 | iterative matrix relaxation | MARDIGRAS | James | |
3 | structure solution | Amber | 8.0 | Case et al. |
4 | refinement | Amber | 8.0 | Case et al. |