2M6W
Solution NMR structure of the d(GGGGTTGGGGTTTTGGGGAAGGGG) quadruplex in sodium conditions
SOLUTION NMR
NMR Experiment | ||||||||
---|---|---|---|---|---|---|---|---|
Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D 1H-1H NOESY | 5 mM DNA (5'-D(*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*AP*AP*GP*GP*GP*G)-3'), 20 mM sodium phosphate | 93% H2O/7% D2O | 25 | 7.8 | ambient | 278 | |
2 | 2D 1H-1H NOESY | 5 mM DNA (5'-D(*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*AP*AP*GP*GP*GP*G)-3'), 20 mM sodium phosphate | 100% D2O | 25 | 7.8 | ambient | 293 | |
3 | 2D 1H-1H TOCSY | 5 mM DNA (5'-D(*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*AP*AP*GP*GP*GP*G)-3'), 20 mM sodium phosphate | 100% D2O | 25 | 7.8 | ambient | 293 | |
4 | 2D DQF-COSY | 5 mM DNA (5'-D(*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*AP*AP*GP*GP*GP*G)-3'), 20 mM sodium phosphate | 100% D2O | 25 | 7.8 | ambient | 293 | |
5 | 2D [1H-13C] H1(C5)H8 JR HMBC | 5 mM DNA (5'-D(*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*AP*AP*GP*GP*GP*G)-3'), 20 mM sodium phosphate | 93% H2O/7% D2O | 25 | 7.8 | ambient | 278 | |
6 | 2D [1H-31P]-HSQC | 5 mM DNA (5'-D(*GP*GP*GP*GP*TP*TP*GP*GP*GP*GP*TP*TP*TP*TP*GP*GP*GP*GP*AP*AP*GP*GP*GP*G)-3'), 20 mM sodium phosphate | 100% D2O | 25 | 7.8 | ambient | 293 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | VNMRS 500 | 500 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
simulated annealing, molecular dynamics | Felix |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 100 |
Conformers Submitted Total Number | 8 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | processing | Felix | Accelrys Software Inc. | |
2 | chemical shift assignment | Sparky | Goddard | |
3 | data analysis | Sparky | Goddard | |
4 | structure solution | X-PLOR | Brunger | |
5 | refinement | X-PLOR | Brunger | |
6 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
7 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
8 | data analysis | MOLMOL | Koradi, Billeter and Wuthrich | |
9 | collection | VnmrJ | Varian |