1DB6
SOLUTION STRUCTURE OF THE DNA APTAMER 5'-CGACCAACGTGTCGCCTGGTCG-3' COMPLEXED WITH ARGININAMIDE
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide | 99.99% D2O | 0-25 mM NaCl | 6.2 | ambient | 293 | |
2 | DQF-COSY | 1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide | 99.99% D2O | 0-25 mM NaCl | 6.2 | ambient | 293 | |
3 | TOCSY | 1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide | 99.99% D2O | 0-25 mM NaCl | 6.2 | ambient | 293 | |
4 | 2D NOESY | 1.44 mM DNA, 10 mM sodium phosphate buffer, pH 6.2, 0.05 mM EDTA, 0-25 mM NaCl, 8-10 equivalents argininamide | 90% H2O/10% D2O | 0-25 mM NaCl | 6.2 | ambient | 278 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | GE | OMEGA | 500 |
2 | Bruker | AMX | 600 |
NMR Refinement | ||
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Method | Details | Software |
Distance restraints were obtained from relaxation rate matrix calculations. Structures were calculated using simulated annealing and molecular dynamics | Felix |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with acceptable covalent geometry,structures with favorable non- bond energy,structures with the least restraint violations,structures with the lowest energy |
Conformers Calculated Total Number | 30 |
Conformers Submitted Total Number | 10 |
Representative Model | 6 (fewest violations) |
Additional NMR Experimental Information | |
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Details | Data were also collected for sequences containing 5-methyl cytosine substituted independently at positions 15 and 16, and for the sequence with inosine substituted at postion 14. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | data analysis | Felix | 950 | Molecular Simulations, Inc |
2 | iterative matrix relaxation | MARDIGRAS | 3.2 | Brandan A. Borgias, Paul D. Thomas, He Liu, Anil Kumar, Marco Tonelli |
3 | refinement | Discover | 2.97 | Molecular Simulations, Inc |