1S74
SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING AN ALPHA-ANOMERIC ADENOSINE: INSIGHTS INTO SUBSTRATE RECOGNITION BY ENDONUCLEASE IV
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1.0 MM ALPHAA DUPLEX, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.1 MM EDTA, PH 6.6 | 100% D2O | 50 mM NACL | 6.6 | AMBIENT | 293 | |
2 | DQF-COSY | 1.0 MM ALPHAA DUPLEX, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.1 MM EDTA, PH 6.6 | 100% D2O | 50 mM NACL | 6.6 | AMBIENT | 293 | |
3 | 2D TOCSY | 1.0 MM ALPHAA DUPLEX, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.1 MM EDTA, PH 6.6 | 100% D2O | 50 mM NACL | 6.6 | AMBIENT | 293 | |
4 | 2D 31P,1H correlation | 1.0 MM ALPHAA DUPLEX, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.1 MM EDTA, PH 6.6 | 100% D2O | 50 mM NACL | 6.6 | AMBIENT | 293 | |
5 | 1H,13C-HSQC | 1.0 MM ALPHAA DUPLEX, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.1 MM EDTA, PH 6.6 | 100% D2O | 50 mM NACL | 6.6 | AMBIENT | 293 | |
6 | 1.0 MM ALPHAA DUPLEX, 10 MM PHOSPHATE BUFFER, 50 MM NACL, 0.1 MM EDTA, PH 6.6 | 100% D2O | 50 mM NACL | 6.6 | AMBIENT | 293 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AMX | 600 |
2 | Bruker | AVANCE | 500 |
NMR Refinement | ||
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Method | Details | Software |
TORSION ANGLE DYNAMICS MOLECULAR DYNAMICS | THE STRUCTURE IS BASED ON A TOTAL OF 502 RESTRAINTS: 284 DISTANCE RESTRAINTS, 80 ENDOCYCLIC TORSION ANGLE RESTRAINTS, 50 WATSON-CRICK DISTANCE AND ANGLE RESTRAINTS, AND 88 BACKBONE TORSION ANGLE RESTRAINTS. THE ALPHAA DUPLEX STRUCTURE WAS ELUCIDATED BY A COMBINATION OF DYANA AND RMD/REM IN AMBER. ALL CALCULATIONS WERE PERFORMED IN VACUO. THE FINAL STRUCTURE DEPOSITED HERE WAS OBTAINED BY COORDINATE AVERAGING THE FINAL ENSEMBLE OF 10 RMD/REM STRUCTURES FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. THIS STRUCTURE WAS FURTHER REFINED BY RMD IN VACUO WITH AN ADDITIONAL 25 C-H RESIDUAL DIPOLAR COUPLINGS, FOLLOWED BY REM. | DYANA |
NMR Ensemble Information | |
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Conformer Selection Criteria | |
Conformers Calculated Total Number | 10 |
Conformers Submitted Total Number | 1 |
Representative Model | 1 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | FOR NON-EXCHANGEABLE PROTONS, NOESY EXPERIMENTS IN D2O WERE PERFORMED WITH 10S RELAXATION DELAYS AND MIXING TIMES OF 75MS, 150MS AND 250 MS. FOR EXCHANGEABLE PROTONS, A WATERGATE NOESY WAS PERFORMED WITH A RELAXATION DELAY OF 4S AND 150MS MIXING TIME. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | DYANA | 1.5 | Guntert et al. |
2 | structure solution | MARDIGRAS | 3.2 | Borgias et al. |
3 | structure solution | CORMA | 5.2 | Keepers and James |
4 | structure solution | Curves | 5.1 | Lavery and Sklenar |
5 | structure solution | MOLMOL | 2.0 | Koradi et al. |
6 | refinement | Amber | 6.1 | Case et al. |