SOLUTION NMR Experimental Data


Experimental Details
Sample Conditions
Sample Contents80 OD of d(ACATCAFBGATCT)d(AGATAGATGT) solution in NMR Buffer
SolventFor observation of nonexchangeable protons, the sample was dissolved in 0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O. For observation of exchangeable protons, the sample was dissolved in 9:1 H2O:D2O. Most experiments were performed at 5 C. Spectra of exchangeable protons were obtained at 0 C.
Ionic Strength0.5 mL of 0.01 M sodium phosphate containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.4. The sample was dissolved in 99.96% D2O
pH7.4
PressureATM
Temperature (K)278
Experiment(s):2D NOESY, 2D TOCSY, DQF-COSY, P-COSY, T1
Spectrometer Information
Manufacturer Model Field Strength
Bruker DRX 600.0
Bruker DRX 800.0
Bruker DRX 500.0
NMR Refinement
Method distance geometry : MardiGras; simulated annealing molecular dynamics : XPLOR; Average structure Calculation Addition of Solvent, and Counterions : AMBER; simulated annealing and Molecular Dynamics matrix relaxation : CORMA;
Details There were 329 experimental distance restraints derived from nonexchangeable 1H NOEs by MARDIGRAS. These consisted of 181 intranucleotide restraints, 110 internucleotide restraints, and 38 adduct-DNA restraints
NMR Ensemble Information
Conformer Selection Criteria Final Calculated Structure is Being Submitted. Back Calculated Structure is in Agreement with NOESY data. The calculation was performed in Presence of solvent and counterions. Solvent, and Counterion co-ordinates are NOT being reported, only the Duplex DNA. Before Solvating and Addition of Counter IONS, 20 final structures were calculated using XPLOR. The final averaged energy minimized structure was solvated, and the counter Ions were added to it. Then MD was ran for 1.4 ns time scale to obtain final structure.
Conformers Calculated Total Number 20
Conformers Submitted Total Number 1
Representative Model Choice Rationale
1 n/a
Additional NMR Experimental Information
1 40 Structures were calculated starting from B and A form DNA. 20 closely convergent from both was averaged, and RMSD value was checked. The final averaged structure was calculated by averaging Final A and Final B, and after energy Minimization. This energy minimized structure was solvated, and explicit counterions were added. In all, 17 Na+ ions were added to neutralize the system using the Leap module in AMBER 6.0. The SHAKE algorithm constrained bonds involving protons to a tolerance of 0.0005 . A 1 fs time step was used. The rMD calculations were run for 1.4 ns, and coordinates were captured every 200 ps. The emergent structure from AMBER is Being reported
Computation: NMR Software
# Classification Software Name Author
1 processing GAUSSIAN 98 1998 Frisch, M. J., Trucks, G. W., et al. (1998) Gaussian 98, Gaussian Inc., Pittsburgh, PA.
2 structure solution INSIGHTII 2000 Accelyris, Inc., San Diego, CA
3 data analysis CORMA 4.0 Keepers, J. W., and James, T. L. (1984) J. Magn. Reson. 57, 404-426.
4 structure solution AMBER 6.0 Bayly, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. (1993) J. Phys. Chem. 40, 10269-10280
5 refinement X-PLOR 3.1 A.T.Brunger
6 data analysis MARDIGRAS 3.2 Borgias, B. A., and James, T. L. (1990) J. Magn. Reson. 87, 475-487
7 collection XWINNMR 4.0 Bruker
8 processing FELIX 97, 2000 Accelyris, Inc., San Diego, CA