1N17

Structure and Dynamics of Thioguanine-modified Duplex DNA

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D NOESY	Single-stranded oligodeoxyribonucleotides, d(5-GCTAAGGAAAGCC-3) and the complementary strand d(5-GGCTTTCCTTAGC-3), were synthesized using standard phosphoramidite chemistry. The thioG-modified oligodeoxyribonucleotide, d(5-GCTAAGthioGAAAGCC-3), was commercially synthesized (Trilink Biotechnologies) using 6-thio-deoyxguanosine-cyanoethyl phosphoramidite(Glen Research). 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.	Buffer A (10 mM sodium phosphate, 50 mM NaCl, pH 7.0)	approx. 65 mM	7.0	ambient	293
2	2D TOCSY	Single-stranded oligodeoxyribonucleotides, d(5-GCTAAGGAAAGCC-3) and the complementary strand d(5-GGCTTTCCTTAGC-3), were synthesized using standard phosphoramidite chemistry. The thioG-modified oligodeoxyribonucleotide, d(5-GCTAAGthioGAAAGCC-3), was commercially synthesized (Trilink Biotechnologies) using 6-thio-deoyxguanosine-cyanoethyl phosphoramidite(Glen Research). 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.	Buffer A (10 mM sodium phosphate, 50 mM NaCl, pH 7.0)	approx. 65 mM	7.0	ambient	293
3	DQF-COSY	Single-stranded oligodeoxyribonucleotides, d(5-GCTAAGGAAAGCC-3) and the complementary strand d(5-GGCTTTCCTTAGC-3), were synthesized using standard phosphoramidite chemistry. The thioG-modified oligodeoxyribonucleotide, d(5-GCTAAGthioGAAAGCC-3), was commercially synthesized (Trilink Biotechnologies) using 6-thio-deoyxguanosine-cyanoethyl phosphoramidite(Glen Research). 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.	Buffer A (10 mM sodium phosphate, 50 mM NaCl, pH 7.0)	approx. 65 mM	7.0	ambient	293

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	INOVA	600
2	Varian	INOVA	800

NMR Refinement
Method	Details	Software
restrained molecular dynamics, relaxation matrix analysis	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.	X-PLOR

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	Version	Software Name	Author
1	iterative matrix relaxation	X-PLOR	3.1	Brunger, A.
2	refinement	X-PLOR	3.1	Brunger, A.

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.