7NEJ

Solution structure of DNA:RNA hybrid duplex


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-1H NOESY0.5 M DNA (5'-D(*CP*TP*AP*CP*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 100 mM sodium chloride, 25 mM sodium phosphate, 0.5 % v/v DSS90% H2O/10% D2O125 mM71 atm278Bruker AVANCE 600
22D 1H-1H TOCSY0.5 M DNA (5'-D(*CP*TP*AP*CP*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 100 mM sodium chloride, 25 mM sodium phosphate, 0.5 % v/v DSS90% H2O/10% D2O125 mM71 atm278Bruker AVANCE 600
32D 1H-1H COSY0.5 M DNA (5'-D(*CP*TP*AP*CP*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 100 mM sodium chloride, 25 mM sodium phosphate, 0.5 % v/v DSS100% D2O125 mM71 atm298Bruker AVANCE 600
42D 1H-1H NOESY0.5 M DNA (5'-D(*CP*TP*AP*CP*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 100 mM sodium chloride, 25 mM sodium phosphate, 0.5 % v/v DSS100% D2O125 mM71 atm298Bruker AVANCE 600
52D 1H-1H TOCSY0.5 M DNA (5'-D(*CP*TP*AP*CP*AP*CP*GP*G)-3'), 0.5 M RNA (5'-R(*CP*CP*GP*UP*GP*UP*AP*G)-3'), 100 mM sodium chloride, 25 mM sodium phosphate, 0.5 % v/v DSS100% D2O125 mM71 atm298Bruker AVANCE 600
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE600
NMR Refinement
MethodDetailsSoftware
molecular dynamicsAmber
NMR Ensemble Information
Conformer Selection Criteriaall calculated structures submitted
Conformers Calculated Total Number10
Conformers Submitted Total Number10
Representative Model1 (fewest violations)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1collectionTopSpinBruker Biospin
2processingTopSpinBruker Biospin
3chemical shift assignmentNMRFAM-SPARKYGoddard & Kneller
4structure calculationAmber18Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
5refinementAmber18Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
6data analysisMOLMOLKoradi, Billeter and Wuthrich
7data analysis3DNALu & Olson