1KB1
SOLUTION STRUCTURE OF AN 11-MER DNA DUPLEX CONTAINING 6-THIOGUANINE OPPOSITE CYTOSINE
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA | 100% D2O | 25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA | 6.78 | ambient | 298 | |
2 | COSY | 2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA | 100% D2O | 25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA | 6.78 | ambient | 298 | |
3 | DQF-COSY | 2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA | 100% D2O | 25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA | 6.78 | ambient | 298 | |
4 | COSY45 | 2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA | 100% D2O | 25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA | 6.78 | ambient | 298 | |
5 | TOCSY | 2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA | 100% D2O | 25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA | 6.78 | ambient | 298 | |
6 | HETCO | 2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA | 100% D2O | 25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA | 6.78 | ambient | 298 | |
7 | 2D NOESY | 2.4mM DNA 25mM Phosphate buffer, 50mM NaCl, 0.5mM EDTA | 10 % D2O, 90 % H2O | 25 mM Phosphate, 50 mM NaCl, 0.5 mM EDTA | 6.78 | ambient | 276 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
2 | Varian | INOVA | 500 |
NMR Refinement | ||
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Method | Details | Software |
RESTRAINED MOLECULAR DYNAMICS SIMULATIONS | Felix |
NMR Ensemble Information | |
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Conformer Selection Criteria | |
Conformers Calculated Total Number | |
Conformers Submitted Total Number | 1 |
Additional NMR Experimental Information | |
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Details | THE STRUCTURE WAS DETERMINED USING PROTON NMR FOLLOWED BY DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REFINED BY THE FULL- RELAXATION MATRIX BACK CALCULATION METHOD. 15 STRUCTURES EACH WERE DETERMINED FROM A- AND B-FORM DNA STARTING STRUCTURES. FIVE DIFFERENT STARTING TEMPERATURES AND THREE DIFFERENT LENGTHS OF TIME SPENT AT THE HIGH- TEMPERATURE STEP MAKE UP THE 15 STRUCTURES. 25 OF THE 30 TOTAL STRUCTURES CONVERGED TO AN RMSD OF .59A OR LESS. THE AVERAGE OF THESE 25 STRUCTURES WAS CALCULATED AND UTILIZED IN THE FULL RELAXATION MATRIX BACK CALCULATIONS. THE MINIMIZED AVERAGE STRUCTURE FROM THIS LAST STEP IS THE FORM THAT IS DEPOSITED HERE. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | Felix | 95 AND 98 | BIOSYM TECHNOLOGIES, INC. |
2 | iterative matrix relaxation | X-PLOR | 3.857 | BRUNGER |
3 | refinement | X-PLOR | 3.857 | BRUNGER |