2LLJ
Structure of a bis-naphthalene bound to a thymine-thymine DNA mismatch
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H TOCSY | 1.5 mM DNA (5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3'), 1.5 mM DNA (5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3'), 1.5 mM 2,7-bisnaphthalene | 90% H2O/10% D2O | 0.06 | 6 | ambient | 283 | |
2 | 2D DQF-COSY | 1.5 mM DNA (5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3'), 1.5 mM DNA (5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3'), 1.5 mM 2,7-bisnaphthalene | 90% H2O/10% D2O | 0.06 | 6 | ambient | 283 | |
3 | 2D 1H-1H NOESY | 1.5 mM DNA (5'-D(*CP*GP*TP*CP*GP*TP*AP*GP*TP*GP*C)-3'), 1.5 mM DNA (5'-D(*GP*CP*AP*CP*TP*TP*CP*GP*AP*CP*G)-3'), 1.5 mM 2,7-bisnaphthalene | 90% H2O/10% D2O | 0.06 | 6 | ambient | 283 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | UNITYPLUS | 500 |
2 | Varian | UNITY | 800 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing, molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 5 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | Amber | 10.1 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |
2 | refinement | Amber | 10.1 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |