Structure and Dynamics of Thioguanine-modified Duplex DNA in Comparison with Unmodified DNA; Structure of Unmodified Duplex DNA

SOLUTION NMR Experimental Data

Experimental Details
Sample Conditions
Sample ContentsSingle-stranded oligodeoxyribonucleotides, d(5-GCTAAGGAAAGCC-3) and the complementary strand d(5-GGCTTTCCTTAGC-3), were synthesized using standard phosphoramidite chemistry. Single-stranded DNA molecules were purified using anion exchange chromatography (MonoQ HR 5/5, Pharmacia Biotech). Purity was confirmed by UV spectroscopy, analytical anion exchange chromatography, and mass spectrometry. The GC and thioGC DNA duplexes were each prepared by annealing either equimolar amounts of complimentary strands or a 1.2 molar excess of the unmodified strand to the modified strand in Buffer A (10 mM sodium phosphate, 50 mM NaCl, pH 7.0) at 70 C for 5 min., followed by slow cooling over 12 hours to room temperature. DNA duplexes were purified using gel filtration chromatography (Superdex Peptide HR 10/30, Pharmacia Biotech) in Buffer A.
SolventBuffer A (10 mM sodium phosphate, 50 mM NaCl, pH 7.0)
Ionic Strengthapprox. 65 mM
Temperature (K)293
Experiment(s):2D NOESY, 2D TOCSY, DQF-COSY
Spectrometer Information
Manufacturer Model Field Strength
Varian INOVA 800.0
Varian INOVA 600.0
NMR Refinement
Method restrained molecular dynamics, relaxation matrix analysis
Details Restrained molecular dynamics (rMD) structure refinement of B-DNA starting structures was performed using an XPLOR 3.1 (26) simulated annealing protocol employing the Cheatham, et al. (19), force field. This force field was modified to include parameterization of thioG, as described above. Starting structures were energy minimized by 160 steps of Powells conjugate gradient minimization followed by rMD while heating to 600 K at 50 K sec-1, cooling to 300 K at 25 K sec-1, and equilibrating at 293 K over 250 ps.
NMR Ensemble Information
Conformer Selection Criteria back calculated data agree with experimental NOESY spectrum
Conformers Calculated Total Number 200
Conformers Submitted Total Number 20
Computation: NMR Software
# Classification Software Name Author
1 refinement X-PLOR 3.1 Brunger, A.
2 iterative matrix relaxation X-PLOR 3.1 Brunger, A.