2KAZ
Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the connecting loop
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D DQF-COSY | 2 mM DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'), 10 mM K+, 10 % D2O | 90% H2O/10% D2O | 10 | 7.85 | ambient | 298 | |
2 | 2D 1H-1H NOESY | 2 mM DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'), 10 mM K+, 10 % D2O | 90% H2O/10% D2O | 10 | 7.85 | ambient | 298 | |
3 | 2D 1H-1H TOCSY | 2 mM DNA (5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3'), 10 mM K+, 10 % D2O | 90% H2O/10% D2O | 10 | 7.85 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | Molecular dynamics on selected model. Conformers selected from the last 200ps of rMD. 5 structures selected based on a cluster analysis to group structures by RMSD. | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with acceptable covalent geometry |
Conformers Calculated Total Number | 6000 |
Conformers Submitted Total Number | 5 |
Representative Model | 1 (closest to the average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | Amber | 8 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm |
2 | refinement | Amber | 8 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm |
3 | processing | TopSpin | 2.1 | Bruker Biospin |
4 | collection | TopSpin | 2.1 | Bruker Biospin |
5 | data analysis | MOLMOL | 2k | Koradi, Billeter and Wuthrich |
6 | chemical shift assignment | CCPNMR | 1.16 | CCPN |