Structural Basis for Bifunctional Zn(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA, Structure of a Thymine bulge
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D DQF-COSY | 1.8 mM DNA (5'-D(*GP*GP*CP*CP*GP*CP*AP*GP*TP*GP*CP*C)-3') | 100% D2O | 0.1 | ambient | 298 | ||
| 2 | 2D 1H-1H TOCSY | 1.8 mM DNA (5'-D(*GP*GP*CP*CP*GP*CP*AP*GP*TP*GP*CP*C)-3') | 100% D2O | 0.1 | ambient | 298 | ||
| 3 | 2D 1H-1H NOESY | 1.8 mM DNA (5'-D(*GP*GP*CP*CP*GP*CP*AP*GP*TP*GP*CP*C)-3') | 100% D2O | 0.1 | ambient | 298 | ||
| 4 | 2D 1H-1H NOESY | 1.8 mM DNA (5'-D(*GP*GP*CP*CP*GP*CP*AP*GP*TP*GP*CP*C)-3') | 100% D2O | 0.1 | ambient | 288 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Varian | INOVA | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| DGSA-distance geometry simulated annealing | CYANA | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 1000 |
| Conformers Submitted Total Number | 18 |
| Representative Model | 1 (fewest violations) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | geometry optimization | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
| 2 | chemical shift assignment | Sparky | 3.14 | Goddard |
| 3 | data analysis | Sparky | 3.14 | Goddard |
| 4 | refinement | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
