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SOLUTION STRUCTURE OF A DNA DUPLEX CONTAINING AN ALPHA-ANOMERIC ADENOSINE: INSIGHTS INTO SUBSTRATE RECOGNITION BY ENDONUCLEASE IV
SOLUTION NMR
NMR Experiment
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
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AMX
600
2
Bruker
AVANCE
500
NMR Refinement
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
Conformer Selection Criteria
Conformers Calculated Total Number
10
Conformers Submitted Total Number
1
Representative Model
1 (minimized average structure)
Additional NMR Experimental Information
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.