8RW2
Structure of a chair-type antiparallel quadruplex-duplex hybrid at pH 6
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-13C HSQC | 0.9 mM DNA (33-MER), 0.28 mM [U 10%-15N]-Ade DNA (33-MER), 0.2 mM [U 10%-15N]-Gua DNA (33-MER) | 90% H2O/10% D2O | 120 mM | 6.1 | 1 atm | 298 | Bruker AVANCE NEO 600 |
2 | 2D 1H-1H NOESY | 0.9 mM DNA (33-MER), 0.28 mM [U 10%-15N]-Ade DNA (33-MER), 0.2 mM [U 10%-15N]-Gua DNA (33-MER) | 90% H2O/10% D2O | 120 mM | 6.1 | 1 atm | 298 | Bruker AVANCE NEO 600 |
3 | 2D 1H-1H COSY | 0.9 mM DNA (33-MER), 0.28 mM [U 10%-15N]-Ade DNA (33-MER), 0.2 mM [U 10%-15N]-Gua DNA (33-MER) | 90% H2O/10% D2O | 120 mM | 6.1 | 1 atm | 298 | Bruker AVANCE NEO 600 |
4 | 1H-15N HMQC | 0.9 mM DNA (33-MER), 0.28 mM [U 10%-15N]-Ade DNA (33-MER), 0.2 mM [U 10%-15N]-Gua DNA (33-MER) | 90% H2O/10% D2O | 120 mM | 6.1 | 1 atm | 298 | Bruker AVANCE NEO 600 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE NEO | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 10 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | chemical shift assignment | CcpNmr Analysis | 2.4.2 | CCPN |
2 | structure calculation | Amber | 18 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
3 | refinement | Amber | 18 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
4 | peak picking | CcpNmr Analysis | 2.4.2 | CCPN |
5 | processing | TopSpin | 4.0.7 | Bruker Biospin |