SOLUTION NMR Experimental Data


Experimental Details
Sample Conditions
Sample Contents5-10 MM DNA (SINGLE STRANDS); 5MM SODIUM PHOSPHATE BUFFER
Solventn/a
Ionic Strength150mM NACL
pH6.9
Pressure1
Temperature (K)278
Experiment(s):NOESY, TOCSY, DQF-COSY, COSY-45, 1H-31P COSY ON ORIGINAL AND SITE-SPECIFIC SUBSTITUTED SAMPLES CONTAINING 8BR-A, 8BR-G,DU,5BR-DU,2,6-DA ANALOGS.
Spectrometer Information
Manufacturer Model Field Strength
Varian VARIAN UNITY INOVA 600.0
NMR Refinement
Method DISTANCE GEOMETRY AND SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT AND RELAXATION MATRIX INTENSITY REFINEMENT
Details 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.
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 Choice Rationale
1 fewest violations,lowest energy
Computation: NMR Software
# Classification Software Name Author
1 refinement version: 3.1 X-PLOR A.BRUNGER
2 collection version: 5.0 VNMR VARIAN
3 data analysis version: 97.0 FELIX BIOSYM
4 structure solution version: 3.1 X-PLOR A.BRUNGER