DNA.RNA HYBRID DUPLEX CONTAINING A 5-PROPYNE DNA STRAND AND PURINE-RICH RNA STRAND, NMR, 4 STRUCTURES


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
1NOESY100% D2O OR 90% H2O, 10% D2O100 mM KCL7.01 atm303
2COSY100% D2O OR 90% H2O, 10% D2O100 mM KCL7.01 atm303
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianUNITY500
2VarianUNITYPLUS600
NMR Refinement
MethodDetailsSoftware
MULTIPLE STARTING CONFORMATIONSDISTANCE CONSTRAINTS FOR GLYCOSIDIC TORSION ANGLES, PENTOSE PSEUDOROTATIONAL PHASE ANGLES/AMPLITUDES AND FRACTION OF SOUTH STATE SUGARS CALCULATED FROM NOE BUILD-UP CURVES AND COUPLING CONSTANTS BY A LEAST-SQUARES/GRID SEARCH METHOD IMPLEMENTED IN NUCFIT AND PFIT (A.N. LANE, NIMR, UK). TEN DIFFERENT SETS OF UNIQUE RESTRAINTS GENERATED 10 STRUCTURES, THE AVERAGE OF WHICH SATISFIED THE EXPERIMENTALLY DERIVED FRACTION OF SOUTH STATE SUGARS BETTER THAN STRUCTURES GENERATED FROM A SINGLE SET OF RESTRAINTS. INTERNUCLEOTIDE DISTANCE CONSTRAINTS CALCULATED FROM NOE-BUILD-UP CURVES. STRUCTURES CALCULATED BY SIMULATED ANNEALING/RMD PROTOCOL WITHIN DISCOVER 95.0 USING AN AMBER FORCE FIELD AND A DISTANCE DIELECTRIC CONSTANT.Amber
NMR Ensemble Information
Conformer Selection Criteriaall calculated structures submitted
Conformers Calculated Total Number4
Conformers Submitted Total Number4
Representative Model1 (minimized average structure)
Additional NMR Experimental Information
DetailsTHE STRUCTURE WAS DETERMINED FROM 2D HOMONUCLEAR NMR EXPERIMENTS USING UNLABELLED SAMPLE
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementAmber7.0CORNELL, W.D., ET AL.
2processingFelix95.0Biosym
3data analysisNUCFITLane, A.N.
4data analysispfitConte, M.R., Bauer, C.J., Lane, A.N.