Solution structure of a DNA duplex containing an alpha-anomeric adenosine: insights into substrate recognition by endonuclease IV
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6 | 100% D2O | 50 mM NaCl | 6.6 | ambient | 293 | |
| 2 | DQF-COSY | 1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6 | 100% D2O | 50 mM NaCl | 6.6 | ambient | 293 | |
| 3 | 2D TOCSY | 1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6 | 100% D2O | 50 mM NaCl | 6.6 | ambient | 293 | |
| 4 | 2D 31P,1H correlation | 1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6 | 100% D2O | 50 mM NaCl | 6.6 | ambient | 293 | |
| 5 | HSQC | 1.0 mM alphaA duplex, 10 mM phosphate buffer, 50 mM NaCl, 0.1 mM EDTA, pH 6.6 | 100% D2O | 50 mM NaCl | 6.6 | ambient | 293 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AMX | 600 |
| 2 | Bruker | AVANCE | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| torsion angle dynamics molecular dynamics | The structure is based on a total of 502 restraints: 284 distance restraints, 80 endocyclic torsion angle restraints, 50 Watson-Crick distance and angle restraints, and 88 backbone torsion angle restraints. The alphaA duplex structure was elucidated by a combination of DYANA and rMD/rEM in AMBER. All calculations were performed in vacuo. The final structure deposited here was obtained by coordinate averaging the final ensemble of 10 rMD/rEM structures followed by restrained energy minimization. | DYANA |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | |
| Conformers Calculated Total Number | 10 |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (minimized average structure) |
| Additional NMR Experimental Information | |
|---|---|
| Details | For non-exchangeable protons, NOESY experiments in D2O were performed with 10s relaxation delays and mixing times of 75ms, 150ms and 250 ms. For exchangeable protons, a WATERGATE NOESY was performed with a relaxation delay of 4s and 150ms mixing time. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | DYANA | 1.5 | Guntert et al |
| 2 | refinement | Amber | 6.0 | Case et al. |
| 3 | iterative matrix relaxation | MARDIGRAS | 3.2 | Borgias et al. |
| 4 | structure solution | CORMA | 5.2 | Keepers and James |
| 5 | structure solution | Curves | 5.1 | Lavery and Sklenar |
| 6 | structure solution | MOLMOL | 2.0 | Koradi et al. |
