1B60

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.

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.

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	X-PLOR	3.851	BRUNGER
2	structure solution	Felix
3	structure solution	X-PLOR

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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1B60

3,N4-ETHENO-2'-DEOXYCYTIDINE OPPOSITE CYTIDINE IN AN 11-MER DUPLEX, SOLUTION STRUCTURE FROM NMR AND MOLECULAR DYNAMICS