1G5D
NMR STRUCTURE OF AN OLIGONUCLEOTIDE CONTAINING AN ABASIC SITE: ALPHA ANOMER
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | NOESY | 2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer | D2O | 10 mM sodium phosphate buffer | 6.8 | ambient | 293 | |
2 | PE-COSY | 2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer | D2O | 10 mM sodium phosphate buffer | 6.8 | ambient | 293 | |
3 | watergate-NOESY | 2.5 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer | 10% D2O, 90% H2O | 10 mM sodium phosphate buffer | 6.8 | ambient | 278 | |
4 | 31P-HCOSY | 3 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer | D2O | 10 mM sodium phosphate buffer | 6.8 | ambient | 298 | |
5 | 31P-decoupled-PE-COSY | 3 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer | D2O | 10 mM sodium phosphate buffer | 6.8 | ambient | 298 | |
6 | 31P-decoupled-J-scaled-DQCOSY | 3 mM abasic site containing duplex oligonucleotide; 10 mM sodium phosphate buffer | D2O | 10 mM sodium phosphate buffer | 6.8 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Home-built | home-built | 750 |
2 | Home-built | home-built | 600 |
NMR Refinement | ||
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Method | Details | Software |
molecular dynamics | The structure is based on 475 NOE-derived distance constraints and 101 dihedral angle restraints. | X-PLOR |
NMR Ensemble Information | |
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Conformer Selection Criteria | all calculated structures submitted |
Conformers Calculated Total Number | 10 |
Conformers Submitted Total Number | 10 |
Additional NMR Experimental Information | |
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Details | The abasic site deoxyribose 1H-1H coupling constants and the DNA 31P-H3' coupling constants were experimentally determined. This information was used in the modeling protocol. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | structure solution | X-PLOR | 3.851 | Brunger |
2 | processing | Felix | 95.0 | MSI |
3 | data analysis | Felix | 95.0 | MSI |
4 | refinement | X-PLOR | 3.851 | Brunger |