NMR Structure of a 1:1 Complex of Polyamide (Im-Py-Beta-Im-Beta-Im-Py-Beta-Dp) with the Tridecamer DNA Duplex 5'-CCAAAGAGAAGCG-3'
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 3.67 millimolar polyamide-DNA complex, 10 millimolar sodium phosphate, pH 7.0, 90% H2O, 10% D2O | 90% H2O/10% D2O | 10 Millimolar | 7.0 | ambient | 298 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| restrained molecular dynamics/simulated annealing, matrix relaxation/NOE-derived distance restraints. | The structure calculations used 548 distance restraints. 508 were NOE-derived, and 40 were for Watson-Crick hydrogen bonds. | VNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 40 |
| Conformers Submitted Total Number | 11 |
| Representative Model | 1 (fewest violations) |
| Additional NMR Experimental Information | |
|---|---|
| Details | This structure was determined using standard 2D homonuclear techniques. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | VNMR | 6.1 B | Varian Associates, Inc. |
| 2 | processing | NMRPipe | 1 | Delalgio, grzesiek, Vuister, Zhu, Pfeifer, & Bax |
| 3 | data analysis | NMRView | 4.1.2 | Johnson, & Blevins |
| 4 | iterative matrix relaxation | MARDIGRAS | 3.2 | Borgias, & James |
| 5 | structure solution | Amber | 6.0 | Kollman, Case, Merz, Cheatham, Simmerling, Darden, Pearlman, Caldwell, Ross, Ferguson, Seibel, Singh, & Weiner |
| 6 | refinement | SANDER MODULE OF AMBER 6.0 PACKAGE (2000) | Kollman, Case, Merz, Cheatham, Simmerling, Darden, Pearlman, Caldwell, Ross, Ferguson, Seibel, Singh, & Weiner | |
