Molecular mechanics parameterization of thionucleoside disulfides for modeling cross-linked duplex DNA

Bioorganic and Medicinal Chemistry Letters

Volumn 8, Issue 21, 1998, Pages 3039-3042

  Coleman, Robert S ^a   McCary, Jason L ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; NUCLEOSIDE;

ARTICLE; BASE PAIRING; COVALENT BOND; CROSS LINKING; DISULFIDE BOND; DNA CONFORMATION; DNA HELIX; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; X RAY CRYSTALLOGRAPHY;

EID: 0032212670     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0960-894X(98)00561-7     Document Type: Article

References (11)

1. 1. Coleman, R. S.; McCary, J. L.; Perez, R. J. J. Am. Chem. Soc., submitted for publication.
2. 2. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Chio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765. Weiner, S. J.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 1986, 7, 230.
3. 2. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Chio, C.; Alagona, G.; Profeta, S.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765. Weiner, S. J.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 1986, 7, 230.
4. 3. Snyder, J. P.; Nevins, N.; Tardif, S. L.; Harpp, D. N. J. Am. Chem. Soc. 1997, 119, 12685. Rauk, A. J. Am. Chem. Soc. 1984, 106, 6517. Snyder, J. P.; Carlsen, L. J. Am. Chem. Soc. 1977, 99, 2931. Fraser, R. R.; Boussard, G.; Saunders, J. K.; Lambert, J. B.; Mixan, C. E. J. Am. Chem. Soc. 1971, 93, 3822.
5. 3. Snyder, J. P.; Nevins, N.; Tardif, S. L.; Harpp, D. N. J. Am. Chem. Soc. 1997, 119, 12685. Rauk, A. J. Am. Chem. Soc. 1984, 106, 6517. Snyder, J. P.; Carlsen, L. J. Am. Chem. Soc. 1977, 99, 2931. Fraser, R. R.; Boussard, G.; Saunders, J. K.; Lambert, J. B.; Mixan, C. E. J. Am. Chem. Soc. 1971, 93, 3822.
6. 3. Snyder, J. P.; Nevins, N.; Tardif, S. L.; Harpp, D. N. J. Am. Chem. Soc. 1997, 119, 12685. Rauk, A. J. Am. Chem. Soc. 1984, 106, 6517. Snyder, J. P.; Carlsen, L. J. Am. Chem. Soc. 1977, 99, 2931. Fraser, R. R.; Boussard, G.; Saunders, J. K.; Lambert, J. B.; Mixan, C. E. J. Am. Chem. Soc. 1971, 93, 3822.
7. 3. Snyder, J. P.; Nevins, N.; Tardif, S. L.; Harpp, D. N. J. Am. Chem. Soc. 1997, 119, 12685. Rauk, A. J. Am. Chem. Soc. 1984, 106, 6517. Snyder, J. P.; Carlsen, L. J. Am. Chem. Soc. 1977, 99, 2931. Fraser, R. R.; Boussard, G.; Saunders, J. K.; Lambert, J. B.; Mixan, C. E. J. Am. Chem. Soc. 1971, 93, 3822.
8. 4. Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.; Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem. 1990, 11, 440.
9. 5. Shefter, E.; Kalman, T. I. Biochem. Biophys. Res. Comm. 1968, 32, 878. The ribose ring of 4 does not alter the conformation about the internucleoside S-S bond, so we removed the sugar in ab initio and AMBER calculations.
10. 6. X-ray data for the S-S bond was gathered from proteins in the Brookhaven Protein Data Base.
11. 7. Hopfinger, A. J.; Pearlstein, R. A. J. Comput. Chem. 1984, 5, 486.