2HSR
13mer duplex DNA containing an abasic site with beta anomer
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2.7 mM duplex DNA containing an abasic site with beta anomer, 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 containing an abasic site with beta anomer, 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 containing an abasic site with beta anomer, 10 mM sodium phosphate, 0.2 mM EDTA | 100% D2O | 10 mM sodium phosphate mM | 6.5 | 1 atm | 298 | |
4 | HP-selective HSQC | 2.7 mM duplex DNA containing an abasic site with beta anomer, 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 containing an abasic site with beta anomer, 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 | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Home-built | Custom-built | 750 |
2 | Home-built | Custom-built | 591 |
NMR Refinement | ||
---|---|---|
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 | Felix |
NMR Ensemble Information | |
---|---|
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 | |
---|---|
Details | This structure was determined using standard 2D homonuclear techniques and HP-HSQC heteronuclear techniques |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | data analysis | Felix | 2000 | |
2 | geometry optimization | MARDIGRAS | ||
3 | refinement | Amber | 8.0 | Case, et al. |