Solution structure of the DNA Decamer Duplex Containing Double TG Mismatches of Cis-syn Cyclobutane Pyrimidine Dimer
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 1mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl | 90% H2O, 10% D20 | 100mM NaCl | 7.0 | ambient | 274 | |
| 2 | 2D TOCSY | 1mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl | 100% D2O | 100mM NaCl | 7.0 | ambient | 290 | |
| 3 | DQF-COSY | 1mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl | 100% D2O | 100mM NaCl | 7.0 | ambient | 290 | |
| 4 | 2D NOESY | 1mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl | 90% H2O, 10% D20 | 100mM NaCl | 7.0 | ambient | 290 | |
| 5 | Natural Abundance 1H-13C HSQC | 1mM CPD/GG duplex, nonlabeled, 20mM phosphate buffer, 100mM NaCl | 100% D2O | 100mM NaCl | 7.0 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| 2 | Bruker | DRX | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | the structures are based on a 500 NOE-derived distance constraints, 112 dihedral angle restraints, 13 residual dipolar coupling restraints | NMRPipe |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations, structures with the lowest energy |
| Conformers Calculated Total Number | 40 |
| Conformers Submitted Total Number | 12 |
| Representative Model | 4 (fewest violations) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | NMRPipe | 2.1 | F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Bax |
| 2 | collection | VNMR | 6.1 | Varian, Inc. |
| 3 | refinement | XPLOR-NIH | 2.9.4a | G. Marius Clore , John Kuszewski, Charles D. Schwieters, and Nico Tjandra |
| 4 | structure solution | X-PLOR | 3.1 | Brunger |
