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 Experimental Data


Experimental Details
Sample Conditions
Sample Contentsthe 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
SolventThe sample was dissolved in 99.96% D2O.
Ionic Strength0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA
pH7.2
Pressureambient
Temperature (K)278
Experiment(s):2D NOESY, DQF-COSY, P-COSY
Sample Contentsthe 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
SolventThe sample was dissolved in 99.96% D2O.
Ionic Strength0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA
pH6.7
Pressureambient
Temperature (K)278
Experiment(s):2D NOESY
Sample Contentsthe 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
Solventthe sample was dissolved in 9:1 H2O:D2O.
Ionic Strength0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA
pH7.2
Pressureambient
Temperature (K)278
Experiment(s):2D NOESY
Spectrometer Information
Manufacturer Model Field Strength
Bruker AVANCE 800.0
Bruker AVANCE 600.0
Bruker AVANCE 500.0
NMR Refinement
Method distance geometry simulated annealing NMR data : Felix 97, 2000 molecular dynamics : XPLOR, AMBER matrix relaxation CORMA torsion angle dynamics Gaussian 98, INSIGHTII (2000)
Details 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.
NMR Ensemble Information
Conformers Calculated Total Number 20
Conformers Submitted Total Number 1
Representative Model Choice Rationale
1 minimized average structure
Additional NMR Experimental Information
1 This structure was determined using standard 2D homonuclear techniques.
Computation: NMR Software
# Classification Software Name Author
1 collection XWINNMR 3 Bruker Inc
2 refinement AMBER 6.0 Case
3 iterative matrix relaxation MARDIGRAS 5.2, 6.2 Borgias, B. A., & James, T. L.
4 data analysis FELIX 97, 2000 Accelaris INC
5 structure solution InsightII 2000 Accelaris Inc
6 refinement X-PLOR 6.5 Brunger