1N1N
Structure of Mispairing of the Deoxycytosine with Deoxyadenosine 5' to the 8,9-Dihydro-8-(N7-guanyl)-9-Hydroxy-Aflatoxin B1 Adduct
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer for NMR containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2 | The sample was dissolved in 99.96% D2O. | 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA | 7.2 | ambient | 278 | |
2 | DQF-COSY | the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer for NMR containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2 | The sample was dissolved in 99.96% D2O. | 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA | 7.2 | ambient | 278 | |
3 | P-COSY | the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer for NMR containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2 | The sample was dissolved in 99.96% D2O. | 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA | 7.2 | ambient | 278 | |
4 | 2D NOESY | the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 6.7 for NMR studies | The sample was dissolved in 99.96% D2O. | 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA | 6.7 | ambient | 278 | |
5 | 2D NOESY | the ample was dissolved in 0.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pH 7.2 for NMR studies | the sample was dissolved in 9:1 H2O:D2O. | 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA | 7.2 | ambient | 278 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 500 |
2 | Bruker | AVANCE | 600 |
3 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
distance geometry simulated annealing NMR data : Felix 97, 2000 molecular dynamics : XPLOR, AMBER matrix relaxation CORMA torsion angle dynamics Gaussian 98, INSIGHTII (2000) | Distance was calculated using RANDMARDI protocol from MARDIGRAS. The 20 structures obtained from molecular dynamics simulation using X-PLOR starting from random, and B-starting structures. The final structure emerged from average of 20 simulated annealing structure from B-form starting structure. The average structure was solvated using X-LEAP protocol in AMBER 6.0, and subjected to 1.4 ns MD simulation using AMBER 6.0 SANDER module, in presence of counter IONs. The final structure was obtained by energy minimization of simulated structure. Solvent, and counter ions were omitted. Back Calculations were performed using CORMA. | X-PLOR |
NMR Ensemble Information | |
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Conformer Selection Criteria | |
Conformers Calculated Total Number | 20 |
Conformers Submitted Total Number | 1 |
Representative Model | 1 (minimized average structure) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear techniques. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR | 6.5 | Brunger |
2 | structure solution | Insight II | 2000 | Accelaris Inc |
3 | data analysis | Felix | 97, 2000 | Accelaris INC |
4 | iterative matrix relaxation | MARDIGRAS | 5.2, 6.2 | Borgias, B. A., & James, T. L. |
5 | refinement | Amber | 6.0 | Case |
6 | collection | XwinNMR | 3 | Bruker Inc |