2L13
mini-haipin of AT basepairs having a C12-alkyl linker forming the loop region
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D DQF-COSY | 4.2 mM DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-1 | 100% D2O | 0.1 | 7.2 | ambient | 293 | |
2 | 2D 1H-1H TOCSY | 4.2 mM DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-1 | 100% D2O | 0.1 | 7.2 | ambient | 293 | |
3 | 2D 1H-1H NOESY | 4.2 mM DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-1 | 100% D2O | 0.1 | 7.2 | ambient | 293 | |
4 | 2D DQF-COSY | 4.2 mM DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-2 | 90% H2O/10% D2O | 0.1 | 7.2 | ambient | 293 | |
5 | 2D 1H-1H TOCSY | 4.2 mM DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-2 | 90% H2O/10% D2O | 0.1 | 7.2 | ambient | 293 | |
6 | 2D 1H-1H NOESY | 4.2 mM DNA (5'-D(*TP*AP*TP*TP*AP*TP*((CH2)12)P*AP*TP*AP*AP*TP*A)-3')-2 | 90% H2O/10% D2O | 0.1 | 7.2 | ambient | 293 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
simulated annealing, matrix relaxation | CNS |
NMR Ensemble Information | |
---|---|
Conformer Selection Criteria | structures with the lowest energy |
Conformers Calculated Total Number | 80 |
Conformers Submitted Total Number | 11 |
Representative Model | 1 (minimized average) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
2 | refinement | CNS | 1.2 | Brunger, Adams, Clore, Gros, Nilges and Read |
3 | chemical shift assignment | Sparky | 3.113 | Goddard |
4 | data analysis | Sparky | 3.113 | Goddard |
5 | peak picking | Sparky | 3.113 | Goddard |
6 | peak integration | Sparky | 3.113 | Goddard |
7 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax |