2GVO
Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O | 10mM | 6.8 | ambient | 274 | |
2 | 2D NOESY | 1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O | 10mM | 6.8 | ambient | 298 | |
3 | 3D HCCH-COSY | 1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O | 10mM | 6.8 | ambient | 298 | |
4 | 2D 1H-13C HSQC | 1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O | 10mM | 6.8 | ambient | 298 | |
5 | DQF-COSY | 1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O | 10mM | 6.8 | ambient | 298 | |
6 | HNN COSY | 1mM 18mer mRNA uniformly 13C/15N labeled, 10 mM Sodium phosphate buffer, 90% H2O, 10% D2O | 90% H2O/10% D2O | 10mM | 6.8 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 500 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | the structures are based on a total of 187 restraints, 84 are sequential and long range internucleotide distances, 85 dihedral angle restraints, 18 sugar puckers restraints and 15 distance restaints from hydrogen bonds. | NMRPipe |
NMR Ensemble Information | |
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Conformer Selection Criteria | all calculated structures submitted, back calculated data agree with experimental NOESY spectrum, structures with acceptable covalent geometry, structures with favorable non-bond energy,structures with the least restraint violations, structures with the lowest energy |
Conformers Calculated Total Number | 30 |
Conformers Submitted Total Number | 21 |
Representative Model | 1 (n/a) |
Additional NMR Experimental Information | |
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Details | The structure was determined using triple-resonance NMR spectroscopy |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | data analysis | NMRPipe | 2.2 | Delaglio, F. et al. |
2 | data analysis | Sparky | 3.110 | Goddard, T.D., Kneller, G.D. |
3 | data analysis | Felix | 97.0 | |
4 | structure solution | Amber | 7.0 | Case, D.A. et al.' |
5 | structure solution | JUMNA | 12 | Lavery, R., Zakrzewska, K., Sklenar, H |
6 | refinement | Amber | 7 | CASE, D.A. et al. |