1D6D

SOLUTION DNA STRUCTURE CONTAINING (A-A)-T TRIADS INTERDIGITATED BETWEEN A-T BASE PAIRS AND GGGG TETRADS; NMR, 8 STRUCT.

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	NOESY	5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER		150mM NACL	6.9	1 atm	278
2	TOCSY	5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER		150mM NACL	6.9	1 atm	278
3	DQF-COSY	5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER		150mM NACL	6.9	1 atm	278
4	COSY-45	5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER		150mM NACL	6.9	1 atm	278
5	1H-31P COSY ON ORIGINAL AND SITE-SPECIFIC SUBSTITUTED SAMPLES CONTAINING 8BR-A, 8BR-G,DU,5BR-DU,2,6-DA ANALOGS.	5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER		150mM NACL	6.9	1 atm	278

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	VARIAN UNITY INOVA	600

NMR Refinement
Method	Details	Software
DISTANCE GEOMETRY AND SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT AND RELAXATION MATRIX INTENSITY REFINEMENT	A TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL OF X-PLOR WITH THE DISTANCE RESTRAINTS OBTAINED EXPERIMENTALLY SPECIFIED AS NOE WITH THE "SUM" AVERAGING OPTION.TEN BEST STRUCTURES SELECTED ON THE BASIS OF GOOD COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION AND FAVOURABLE NON-BONDED ENERGY WERE FURTHER OPTIMIZED WITH RESTRAINED MOLECULAR DYNAMICS, MOLECULAR MECHANICS AND RELAXATION MATRIX INTENSITY REFINEMENT.THE PROTOCOLS ARE AS FOLLOWS. THE DYNAMICS WAS INITIATED AT 300K AND THE TEMPERATURE WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS THE FORCE CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN THE PROPORTION 1: 4:8 FOR THREE CLASSES OF NOE: EXCHANGEABLE, NONEXCHANGEABLE AND HYDROGEN BONDS, RESP. THE STRUCTURES WERE THEN SLOWLY COOLED TO 300K IN 2.8 PS AND EQUILIBRATED AT 300K FOR 12 PS. THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST 4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED TO 3000 STEPS OF MINIMIZATION. THE HYDROGEN BONDS OF THE GGGG TETRADS, AND NON- CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE MAINTAINED THROUGHOUT. THE OBTAINED STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSIY VOLUMES WERE USED AS RESTRAINTS. THE RELAXATION PATHWAYS WERE CALCULATED USING CUTOFF 4.5 ANGSTROM AND 7.25 NS ISOTROPIC CORRELATION TIME. THE STRUCTURES EXHIBIT PAIRWISE R.M.S.D. VALUE OF 1.16 A. IN TWO STRUCTURES THE RESIDUES T6 AND T8 DEVIATE FROM TWO CLUSTERS FORMED BY REST OF 8 STRUCTURES, AND THESE TWO STRUCTURES WERE OMITTED FROM DEPOSITION.	X-PLOR

NMR Ensemble Information
Conformer Selection Criteria	BACK CALCULATED DATA AGREE WITH EXPERIMENTAL NOESY SPECTRUM,STRUCTURES WITH ACCEPTABLE COVALENT GEOMETRY,STRUCTURES WITH FAVORABLE NON-BOND ENERGY, STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers Calculated Total Number	100
Conformers Submitted Total Number	8
Representative Model	3 (fewest violations,lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	refinement	X-PLOR	3.1	A.BRUNGER
2	collection	VNMR	5.0	VARIAN
3	data analysis	Felix	97.0	BIOSYM
4	structure solution	X-PLOR	3.1	A.BRUNGER

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.