6ALS
Solution structure of a DNA dodecamer with 5-methylcytosine at the 3rd and 9th position and 8-oxoguanine at the 4th position
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*(DC5)P*GP*(DMC)P*(8OG)P*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-3') | 100% D2O | 120 mM | 6.8 | ambient | 298 | Bruker AVANCE III 600 |
2 | 2D 1H-1H NOESY | 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*(DC5)P*GP*(DMC)P*(8OG)P*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-3') | 100% D2O | 120 mM | 6.8 | ambient | 279 | Bruker AVANCE III 600 |
3 | 2D 1H-1H TOCSY | 50 mM sodium chloride, 10 mM potassium phosphate, 0.1 mM EDTA, 1 mM DNA (5'-D(*(DC5)P*GP*(DMC)P*(8OG)P*AP*AP*TP*TP*(DMC)P*GP*CP*(DG3))-3') | 100% D2O | 120 mM | 6.8 | ambient | 298 | Bruker AVANCE III 600 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing | Amber |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 18 |
Conformers Submitted Total Number | 11 |
Representative Model | 1 (minimized average structure) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
3 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
4 | peak picking | NMRView | Johnson, One Moon Scientific | |
5 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
6 | data analysis | CYANA | Guntert, Mumenthaler and Wuthrich |