5OE1
Im polyamide in complex with 5'CGATGTACATCG3'- hairpin polyamides studies
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 | 1.3 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA8 | 90% H2O/10% D2O | 100 phosphate mM | 7.4 | 1 atm | 298 | Bruker AVANCE 600 |
2 | 2D 1H-1H NOESY | 1.3 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA8 | 100% D2O | 100 phosphate mM | 7.4 | 1 atm | 298 | Bruker AVANCE 600 |
3 | 2D DQF-COSY | 1.3 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA8 | 100% D2O | 100 phosphate mM | 7.4 | 1 atm | 298 | Bruker AVANCE 600 |
4 | 2D 1H-1H TOCSY | 1.3 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA8 | 100% D2O | 100 phosphate mM | 7.4 | 1 atm | 298 | Bruker AVANCE 600 |
5 | 2D 1H-13C HSQC | 1.3 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA8 | 100% D2O | 100 phosphate mM | 7.4 | 1 atm | 298 | Bruker AVANCE 600 |
6 | 2D 1H-31P COSY | 1.3 mM DNA (5'-D(*CP*GP*AP*TP*GP*TP*AP*CP*AP*TP*CP*G)-3'), 1.3 mM PA8 | 100% D2O | 100 phosphate mM | 7.4 | 1 atm | 298 | Bruker AVANCE 600 |
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 | Amber | |
matrix relaxation | MARDIGRAS |
NMR Ensemble Information | |
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Conformer Selection Criteria | clustering |
Conformers Calculated Total Number | 2000 |
Conformers Submitted Total Number | 10 |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
2 | structure calculation | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman | |
3 | chemical shift assignment | Sparky | Goddard | |
4 | processing | TopSpin | Bruker Biospin | |
5 | structure calculation | MARDIGRAS | N. Ulyanov |