1P96
Solution Structure of a Wedge-Shaped Synthetic Molecule at a Two-Base Bulge Site in DNA
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20 | 90% H20/10% D20; 99.96% D20 | 0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA | 6.5 | ambient | 298 | |
2 | 2D TOCSY | 1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20 | 90% H20/10% D20; 99.96% D20 | 0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA | 6.5 | ambient | 298 | |
3 | DQF-COSY | 1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20 | 90% H20/10% D20; 99.96% D20 | 0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA | 6.5 | ambient | 298 | |
4 | H-P COSY | 1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20 | 90% H20/10% D20; 99.96% D20 | 0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA | 6.5 | ambient | 298 | |
5 | COSY-45 | 1.8mM DDI-bulged DNA complex, 0.1M NaCl, 10mM sodium phosphate and 0.1mM EDTA buffer,90% H20/10% D20; 99.96% D20 | 90% H20/10% D20; 99.96% D20 | 0.1M NaCl, 10mM sodium phosphate, 0.1mM EDTA | 6.5 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
2 | Varian | INOVA | 750 |
3 | Varian | INOVA | 500 |
NMR Refinement | ||
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Method | Details | Software |
distance geometry sinulated annealing | The structures are based on a total of 694 NOE restranints and 166 dihedral angle restraints. | NMRPipe |
NMR Ensemble Information | |
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Conformer Selection Criteria | all calculated structures submitted |
Conformers Calculated Total Number | 10 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (all calculated structures submited have the least restraint violation and the lowst energy.) |
Additional NMR Experimental Information | |
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Details | This structure was determined using 2D homonuclear and heteronuclear techniques. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | processing | NMRPipe | 2002.044.17.08 | Delaglio, F. |
2 | data analysis | Sparky | 3.106 | Goddard, T.D. and Kneller, D.G. |
3 | refinement | CNS | 1.0 | Brunger, A.T. et al |