5LIG

G-Quadruplex formed at the 5'-end of NHEIII_1 Element in human c-MYC promoter bound to triangulenium based fluorescence probe DAOTA-M2


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D 1H-1H TOCSY0.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M2100% D2O140 mM7.01 atm298Varian Uniform NMR System 800
22D 1H-1H TOCSY0.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M2100% D2O145 mM7.01 atm278Varian Uniform NMR System 800
32D 1H-1H NOESY0.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M290% H2O/10% D2O140 mM7.01 atm298Varian Uniform NMR System 600
42D 1H-1H NOESY0.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 10 mM LITHIUM CACODYLATE, 0.4 mM DAOTA-M290% H2O/10% D2O145 mM7.01 atm278Varian Uniform NMR System 800
52D 1H-1H DQF_COSY0.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M2100% D2O140 mM7.01 atm298Varian Uniform NMR System 600
62D 1H-31P COSY0.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M2100% D2O140 mM7.01 atm298Varian Uniform NMR System 600
713C HSQC0.2 mM U-8% 15N, U-8 %13C DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M290% H2O/10% D2O140 mM7.01 atm298Varian Uniform NMR System 600
815N HSQC0.2 mM U-8% 15N, U-8 %13C DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 20 mM potassium phosphate, 0.4 mM DAOTA-M290% H2O/10% D2O140 mM7.01 atm298Varian Uniform NMR System 600
92D 1H-13C HSQC0.2 mM DNA (5'-D(*TP*AP*GP*GP*GP*AP*GP*GP*GP*TP*AP*GP*GP*GP*AP*GP*GP*GP*T)-3'), 100 mM potassium chloride, 10 mM LITHIUM CACODYLATE, 0.4 mM DAOTA-M290% H2O/10% D2O140 mM7.01 atm298Varian Uniform NMR System 600
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1VarianUniform NMR System600
2VarianUniform NMR System800
NMR Refinement
MethodDetailsSoftware
simulated annealingAmber
NMR Ensemble Information
Conformer Selection Criteriastructures with the least restraint violations
Conformers Calculated Total Number100
Conformers Submitted Total Number10
Representative Model1 (lowest energy)
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1refinementAmber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
2structure calculationAmber14Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman
3chemical shift assignmentSparkyGoddard
4peak pickingSparkyGoddard
5collectionVNMRVarian
6processingVNMRVarian