7B4Z
Synthetic DNA duplex dodecamer
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 | 1.1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1.1 mM NA-H DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 200 mM EDTA | 90% H2O/10% D2O | 510 M | 7.2 | 1 atm | 288.4 | Bruker AVIII 600 |
2 | 2D 1H-1H NOESY | 1.1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1.1 mM NA-H DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 200 mM EDTA | 100% D2O | 510 M | 7.2 | 1 atm | 306.5 | Bruker AVIII 600 |
3 | 2D 1H-1H TOCSY | 1.1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1.1 mM NA-H DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 200 mM EDTA | 100% D2O | 510 M | 7.2 | 1 atm | 306.5 | Bruker AVIII 600 |
4 | 2D 1H-1H TOCSY | 1.1 mM NA-H DNA (5'-D(*CP*AP*CP*GP*CP*CP*GP*CP*TP*G)-3'), 1.1 mM NA-H DNA (5'-D(*CP*AP*GP*CP*GP*GP*CP*GP*TP*G)-3'), 10 mM sodium phosphate, 100 mM sodium chloride, 200 mM EDTA | 100% D2O | 510 M | 7.2 | 1 atm | 288.4 | Bruker AVIII 600 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVIII | 600 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | Amber |
NMR Ensemble Information | |
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Conformer Selection Criteria | all calculated structures submitted |
Conformers Calculated Total Number | 10 |
Conformers Submitted Total Number | 10 |
Representative Model | 1 (minimized average structure) |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | Amber | 14 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
2 | structure calculation | Amber | 14 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
3 | chemical shift assignment | CcpNmr Analysis | 2.3.1 | Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides and Ernest D. Laue |
4 | peak picking | CcpNmr Analysis | 2.3.1 | Wim F. Vranken, Wayne Boucher, Tim J. Stevens, Rasmus H. Fogh, Anne Pajon, Miguel Llinas, Eldon L. Ulrich, John L. Markley, John Ionides and Ernest D. Laue |