2K3Z
NMR structure of adenosine bulged RNA duplex with C:G-A triple
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 | 1 mM RNA (5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3'), 1 mM RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3') | 100% D2O | 60 | 6.8 | ambient | 298 | |
2 | 2D DQF-COSY | 1 mM RNA (5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3'), 1 mM RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3') | 100% D2O | 60 | 6.8 | ambient | 298 | |
3 | 2D 1H-1H TOCSY | 1 mM RNA (5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3'), 1 mM RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3') | 100% D2O | 60 | 6.8 | ambient | 298 | |
4 | 2D 1H-13C HSQC | 1 mM RNA (5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3'), 1 mM RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3') | 100% D2O | 60 | 6.8 | ambient | 298 | |
5 | 2D 1H-31P HSQC | 1 mM RNA (5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3'), 1 mM RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3') | 100% D2O | 60 | 6.8 | ambient | 298 | |
6 | 2D 1H-1H NOESY | 1 mM RNA (5'-R(*GP*UP*CP*GP*AP*GP*CP*UP*G)-3'), 1 mM RNA (5'-R(*CP*AP*GP*CP*CP*GP*AP*C)-3') | 90% H2O/10% D2O | 60 | 6.8 | ambient | 283 |
NMR Spectrometer Information | |||
---|---|---|---|
Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
NMR Refinement | ||
---|---|---|
Method | Details | Software |
torsion angle dynamics | Felix |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (lowest energy) |
Computation: NMR Software | ||||
---|---|---|---|---|
# | Classification | Version | Software Name | Author |
1 | peak picking | Felix | Accelrys Software Inc. | |
2 | chemical shift assignment | Felix | Accelrys Software Inc. | |
3 | collection | TopSpin | Bruker Biospin | |
4 | processing | TopSpin | Bruker Biospin | |
5 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
6 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
7 | data analysis | Curves | Lavery and Sklenar |