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SOLUTION STRUCTURE OF A DNA.RNA HYBRID CONTAINING AN ALPHAT-ANOMERIC THYMIDINE AND POLARITY REVERSALS
SOLUTION NMR
NMR Experiment
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
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AMX
600
NMR Refinement
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
Conformer Selection Criteria
Conformers Calculated Total Number
Conformers Submitted Total Number
1
Representative Model
1 (minimized average structure)
Additional NMR Experimental Information
Details
THIS STRUCTURE WAS DETERMINED USING STANDARD 2D HOMONUCLEAR NMR TECHNIQUES