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3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
NOESY
6.8
288
2
COSY
6.8
288
3
DQF-COSY
6.8
288
4
COSY45
6.8
288
5
TOCSY
6.8
288
6
HETCORR
6.8
288
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
INOVA
500
2
Varian
INOVA
600
NMR Refinement
Method
Details
Software
RESTRAINED MOLECULAR DYNAMICS SIMULATIONS
REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE.
X-PLOR
NMR Ensemble Information
Conformer Selection Criteria
SEE DETAILS
Conformers Calculated Total Number
1
Conformers Submitted Total Number
1
Additional NMR Experimental Information
Details
SEE DETAILS. THE STRUCTURE WAS DETERMINED USING 2D PROTON NMR FOLLOWED BY
DISTANCE RESTRAINED MOLECULAR DYNAMICS SIMULATIONS, AND FURTHER REFINED USING
THE FULL RELAXATION MATRIX BACK CALCULATION APPROACH. 15 STRUCTURES EACH WERE
DETERMINED FROM A- AND B-FORM DNA BY USING DIFFERENT INITIAL TEMPERATURES AND
DIFFERENT LENGTHS OF TIME AT THE HIGH TEMPERATURE STAGE OF THE 30 STRUCTURES
FROM DISTANCE RESTRAINED DYNAMICS, 27 HAD AN RMSD TO THEIR AVERAGE OF LESS
THAN 0.4 A, SO THE AVERAGE OF THESE 27 WAS USED AS THE STARTING STRUCTURE FOR
FULL RELAXATION MATRIX BACK CALCULATIONS. THE MINIMIZED AVERAGE STRUCTURE FROM
THIS LAST STEP IS WHAT HAS BEEN DEPOSITED.