2A5P

Monomeric parallel-stranded DNA tetraplex with snap-back 3+1 3' G-tetrad, single-residue chain reversal loops, GAG triad in the context of GAAG diagonal loop, NMR, 8 struct.


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
11H-1H NOESY70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O90 mM7.01 atm298
21H-1H TOCSY70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O90 mM7.01 atm298
31H-31P COSY70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O90 mM7.01 atm298
41H-1H COSY70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O90 mM7.01 atm298
51H-15N JRHMQC70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O90 mM7.01 atm298
61H-15N HMBC70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O90 mM7.01 atm298
71H-13C JRHM 1H-13C HMBC70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O90 mM7.01 atm298
81H-13C HSQC70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O90 mM7.01 atm298
91H-13C sHMBC70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O90 mM7.01 atm298
101H-31P TOCSY70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O90% H2O/10% D2O90 mM7.01 atm298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianVARIAN UNITY INOVA600
2BrukerAVANCE800
NMR Refinement
MethodDetailsSoftware
DISTANCE GEOMETRY AND SIMULATED ANNEALING, DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT AND RELAXATION MATRIX INTENSITY REFINEMENTXPLOR
NMR Ensemble Information
Conformer Selection Criteriaback calculated data agree with experimental NOESY spectrum
Conformers Calculated Total Number100
Conformers Submitted Total Number8
Representative Model1 (lowest energy)
Additional NMR Experimental Information
DetailsA TOTAL OF 100 INITIAL DNA STRUCTURES WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY PROTOCOL WITH THE EXPERIMENTAL DISTANCE RESTRAINTS SPECIFIED WITH THE R-6 AVERAGING OPTION. EIGHT BEST STRUCTURES SELECTED ON THE BASIS OF GOOD COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION AND FAVOURABLE NON-BONDED ENERGY TERMS 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 14 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 MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS LESS THAN 0.1KCAL/MOL. SOFT PLANARITY RESTRAINTS IMPOSED ON TETRADS AND TRIAD BEFORE HEATING WERE EXCLUDED AT THE EQUILIBRATION STAGE. THE DIHEDRAL AND HYDROGEN-BONDING RESTRAINTS FOR TETRADS, WERE MAINTAINED THROUGHOUT. ALL EIGHT STRUCTURES WERE SUBJECTED TO RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSITY VOLUMES OF NON-EXCHANGEABLE PROTONS WERE USED AS RESTRAINTS WITH EXCHANGEABLE PROTONS REPLACED BY DEUTERONS. DYNAMICS STARTED AT 5K AND THE SYSTEM WAS HEATHED UP TO 300 K IN 0.6 PSEC. THE FORCE CONSTANT FOR NOE INTENSITIES WAS GRADUALLY INCREASED FROM 0 TO 400 KCAL*MOL-1*A-2 WITH SIMULTANEOUS DECREASE OF THE DISTANCE FORCE CONSTANTS FOR NON-EXCHANGEABLE PROTONS FROM 32 to 16. AFTER EQUILIBRATION AT 300 K FOR 3 PSEC THE RESULTING STRUCTURES WERE SUBJECTED TO MINIMIZATION UNTIL THE GRADIENT OF ENERGY WAS LESS THAN 0.1KCAL/MOL. THE DISTANCE RESTRAINTS FOR EXCHANGEABLE PROTONS HYDROGEN BONDS AND DIHEDRAL ANGLE RESTRAINTS WERE MAINTAINED. SOFT PLANARITY RESTRAINTS WEERE SET FOR TETRAD (1 KCAL*MOL-1*A-2) AND TRIAD (0.5 KCAL*MOL-1*A-2).
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementXPLOR3.851AT BRUNGER
2collectionVNMR6.0VARIAN
3processingFelix2000ACCELRYS