STRUCTURE OF A DNA DUPLEX CONTAINING A BISTRAND ABASIC SITE LESION STAGGERED IN A 5'-ORIENTATION.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 2mM duplex in 20 mM phosphate buffer, pH 7.6; 50 mM NaCl; 1 mM EDTA. | 99.96% D2O | not determined | 7.6 | ambient | 298 | |
| 2 | COSY, COSY45, TOCSY, DQFCOSY, HETCOR | 2mM duplex in 20 mM phosphate buffer, pH 7.6; 50 mM NaCl; 1 mM EDTA. | 99.96% D2O | not determined | 7.6 | ambient | 298 | |
| 3 | 2D NOESY | 2mM duplex in 20 mM phosphate buffer, pH 7.6; 50 mM NaCl; 1 mM EDTA. | 90% H2O/10% D2O (v/v) | not determined | 7.6 | ambient | 276 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 500 |
| 2 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Restrained molecular dynamics | 1) Heating stage: from 100 to 500 K in 4ps. Introduction of experimental restraints at the end of this stage. 2) High temperature stage: 80 ps dynamics at 500K 3) Cooling stage: From 500 to 300K in 40ps. 4) Equilibration stage: 140ps dynamics at 300K. | Felix |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 30 |
| Conformers Submitted Total Number | 6 |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | Felix | 98 | MSI |
| 2 | data analysis | MARDIGRAS | 5 | Borgia & James |
| 3 | refinement | X-PLOR | 3.1 | A. Brunger |
| 4 | data analysis | Insight | 95 | MSI |
| 5 | data analysis | Midas | Plus | UCSF |
| 6 | data analysis | Curves | 5 | Sklenar & Lavery |
