1C2Q
SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH* 6.6, D2O | 6.6 | AMBIENT | 298 | |||
2 | DQF-COSY | 0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH* 6.6, D2O | 6.6 | AMBIENT | 298 | |||
3 | 31P-1H CORRELATION SPECTROSCOPY | 0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH* 6.6, D2O | 6.6 | AMBIENT | 298 | |||
4 | 2D NOESY | 0.89 MM HYBRID, 50 MM NACL, 10 MM PHOSPHATE BUFFER, 0.5 MM EDTA, PH 6.7, 90% H2O/10% D2O | 6.7 | AMBIENT | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AMX | 600 |
NMR Refinement | ||
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Method | Details | Software |
SIMULATED ANNEALING/MOLECULAR DYNAMICS | THE STRUCTURE IS BASED ON A TOTAL OF 405 RESTRAINTS: 268 RANDMARDI DERIVED INTERPROTON DISTANCE RESTRAINTS (NON-EXCHANGEABLE: 246; EXCHANGEABLE: 22); 45 DEOXYRIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS DERIVED FROM PSEUDOROTATION ANALYSIS; 45 RIBOSE ENDOCYCLIC TORSION ANGLE RESTRAINTS (BROAD, N-TYPE); 46 WATSON-CRICK DISTANCE AND ANGLE RESTRAINTS. THE FINAL AVERAGE STRUCTURE WAS OBTAINED BY COORDINATE AVERAGING OF THE FINAL ENSEMBLE OF RMD/REM STRUCTURES, FOLLOWED BY RESTRAINED ENERGY MINIMIZATION. ALL STRUCTURE CALCULATIONS WERE PERFORMED USING THE SANDER PROGRAM WITHIN AMBER 4.1, AND THE 1994 ALL ATOM NUCLEIC ACID PARAMETERIZATION. ALL CALCULATIONS WERE CONDUCTED IN VACUO, USING A DISTANCE DEPENDENT DIELECTRIC CONSTANT AND 30 A CUT-OFF FOR NON-BONDED INTERACTIONS. | UXNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | |
Conformers Calculated Total Number | |
Conformers Submitted Total Number | 1 |
Representative Model | 1 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR NMR TECHNIQUES |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | UXNMR | 2.1 | BRUKER |
2 | iterative matrix relaxation | MARDIGRAS | 3.2 | BORGIAS & JAMES, 1989 |
3 | data analysis | CORMA | 5.2 | BORGIAS & JAMES, 1988 |
4 | data analysis | Sparky | 3.33 | UCSF |
5 | refinement | Amber | 4.1 | PEARLMAN ET AL., 1995 |
6 | data analysis | SPHINX/LINSHA | WIDMER & WUTHRICH, 1987 | |
7 | data analysis | Curves | 5.1 | LAVERY & SKLENAR, 1996 |
8 | structure solution | Amber | 4.1 | PEARLMAN ET AL., 1995 |