2HSK
NMR Structure of 13mer Duplex DNA containing an abasic site (Y) in 5'-CCAAAGYACCGGG-3' (10 structures, alpha anomer)
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, 10 mM sodium phosphate, 0.2 mM EDTA | 100% D2O | 10 mM sodium phosphate mM | 6.5 | 1 atm | 298 | |
2 | 2D TOCSY | 2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA | 100% D2O | 10 mM sodium phosphate mM | 6.5 | 1 atm | 298 | |
3 | E-COSY | 2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA | 100% D2O | 10 mM sodium phosphate mM | 6.5 | 1 atm | 298 | |
4 | H-P-selective COSY | 2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA | 100% D2O | 10 mM sodium phosphate mM | 6.5 | 1 atm | 298 | |
5 | 2D NOESY | 2.7 mM duplex DNA, 10 mM sodium phosphate, 0.2 mM EDTA | 90%H2O/10%D2O (v/v) | 10 mM sodium phosphate mM | 6.5 | 1 atm | 277 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Home-built | Custom-built | 750 |
2 | Home-built | Custom-built | 591 |
NMR Refinement | ||
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Method | Details | Software |
Simulated annealing Molecular dynamics | the structures are based on 482 NOE-derived distance constraints, 57 dihedral angle restraints,8 distance restraints from hydrogen bonds. | Amber |
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 | 10 |
Representative Model | 1 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear and HP HSQC techniques |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | 8.0 | Case, D.A. et al. |
2 | data analysis | FELIX | 2000 | |
3 | geometry optimization | MARDIGRAS |