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SOLUTION NMR STRUCTURE OF A DODECAMERIC dsDNA COMPLEXED WITH A NIR FLUORESCENT PROBE QCy-DT
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 300 uM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 300 uM QCY | 90% H2O/10% D2O | 10mM NaCl mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 700 |
2 | 2D 1H-1H TOCSY | 300 uM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 300 uM QCY | 90% H2O/10% D2O | 10mM NaCl mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 700 |
3 | 2D DQF-COSY | 300 uM DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 300 uM QCY | 90% H2O/10% D2O | 10mM NaCl mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 700 |
4 | 2D 1H-1H NOESY | 300 uM [U-2H] DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 300 uM [U-2H] QCY | 100% D2O | 10mM NaCl mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 700 |
5 | 2D 1H-1H TOCSY | 300 uM [U-2H] DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 300 uM [U-2H] QCY | 100% D2O | 10mM NaCl mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 700 |
6 | 2D DQF-COSY | 300 uM [U-2H] DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'), 300 uM [U-2H] QCY | 100% D2O | 10mM NaCl mM | 7.0 | 1 atm | 298 | Bruker AVANCE III 700 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 700 |
NMR Refinement | ||
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Method | Details | Software |
torsion angle dynamics | CYANA |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 20 |
Conformers Submitted Total Number | 4 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | collection | TopSpin | Bruker Biospin | |
2 | peak picking | TopSpin | Bruker Biospin | |
3 | chemical shift assignment | Sparky | Goddard | |
5 | structure calculation | CYANA | 2.1 | Guntert, Mumenthaler and Wuthrich |
6 | geometry optimization | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |