8OR8
Solution structure of the 8-17 DNAzyme in presence of Zn2+
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 | 2.2 mM 8-17 DNAzyme, 10 mM cacodylate, 4 mM zinc chloride, 200 mM sodium chloride | 100% D2O | 200 mM | 6.0 | 1 atm | 308 | Bruker AVANCE III 700 |
2 | 2D 1H-31P COSY | 2.2 mM 8-17 DNAzyme, 10 mM cacodylate, 4 mM zinc chloride, 200 mM sodium chloride | 100% D2O | 200 mM | 6.0 | 1 atm | 308 | Bruker AVANCE III 700 |
3 | 2D 1H-1H TOCSY | 2.2 mM 8-17 DNAzyme, 10 mM cacodylate, 4 mM zinc chloride, 200 mM sodium chloride | 100% D2O | 200 mM | 6.0 | 1 atm | 308 | Bruker AVANCE III 700 |
4 | 2D 1H-13C HSQC | 2.2 mM 8-17 DNAzyme, 10 mM cacodylate, 4 mM zinc chloride, 200 mM sodium chloride | 100% D2O | 200 mM | 6.0 | 1 atm | 308 | Bruker AVANCE III 700 |
5 | 2D 1H-1H NOESY | 2.2 mM 8-17 DNAzyme, 10 mM cacodylate, 4 mM zinc chloride, 200 mM sodium chloride | 90% H2O/10% D2O | 200 mM | 6.0 | 1 atm | 293 | Bruker AVANCE III 700 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE III | 700 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 200 |
Conformers Submitted Total Number | 20 |
Representative Model | 1 (target function) |
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 | NMRFAM-SPARKY | NMRFAM | |
4 | peak picking | NMRFAM-SPARKY | NMRFAM |