Advanced search
Publication Cover
Journal of Biomolecular Structure and Dynamics Volume 16, 1998 - Issue 1
Journal homepage
34
Views
10
CrossRef citations to date
0
Altmetric
Original Articles

Ion-RNA Interactions in the RNA Pseudoknot of a Ribosomal Frameshifting Site: Molecular Modeling Studies

Shu-Yun Le Laboratory of Experimental and Computational Biology, DBS, FCRDC, National Cancer Institute, NIH, Frederick, MD, 21701
,
Jih-H. Chen Frederick Biomedical Supercomputing Center, SAIC-NCIIFCRDC, P.O. Box B, Fresderick, MD, 21702
,
N. Pattabiraman Frederick Biomedical Supercomputing Center, SAIC-NCIIFCRDC, P.O. Box B, Fresderick, MD, 21702
&
Jacob V. Maizel Jr. Laboratory of Experimental and Computational Biology, DBS, FCRDC, National Cancer Institute, NIH, Frederick, MD, 21701
Pages 1-11 | Received 11 May 1998, Published online: 21 May 2012

References and Footnotes

  • Brierley , I. , Rolley , N. J. , Jenner , A. J. and Inglis , S. C. 1991 . J. Mol. Biol. , 229 : 889 – 902 .
  • Wills , N. M. , Gesteland , R. F. and Atkins , J. F. 1991 . Proc. Natl. Acad. Sci. USA , 88 : 6991 – 6995 .
  • Tzeng , T.-H. , Tu , C. and Bruenn , J. A. 1992 . J. Virol. , 66 : 999 – 1006 .
  • Chamorro , M. , Parkin , N. and Varmus , H. E. 1992 . Proc. Natl. Acad. Sci. USA , 89 : 713 – 717 .
  • Chen , X. , Chamorro , M. , Lee , S. L. , Shen , L. X. , Hiñes , J. V. , Jr. Tinoco , I. and Varmus , H. E. 1995 . EM BO J. , 14 : 842 – 852 .
  • Morikawa , S. and Bishop , D. H.L. 1992 . Virol. , 186 : 389 – 397 .
  • ten Dam , E. , Brierley , I. , Inglis , S. and Pleij , C. 1994 . Nucl. Acids Res. , 22 : 2304 – 2310 .
  • Puglisi , J. D. , Wyatt , J. R. and Jr. Tinoco , I. 1988 . Nature , 331 : 283 – 286 .
  • Shen , L. X. and Jr. Tinoco , I. 1995 . J. Mol. Biol. , 247 : 963 – 978 .
  • Kang , H. , Hines , J. V. and Jr. Tinoco , I. 1996 . J. Mol. Biol. , 259 : 135 – 147 .
  • Kolk , M. H. , vander Graaf , M. , Wijmenga , S. S. , Pleij , C. W.A. , Heus , H. A. and Hilbers , C. W. 1998 . Science , 280 : 434 – 438 .
  • Cole , P. E. , Yang , S. K. and Crothers , D. M. 1972 . Biochemistry , 11 : 4358 – 4368 .
  • Scott , W. G. , Murray , J. B. , Arnold , J. R.P. , Stoddard , B. L. and Klug , A. 1996 . Science , 274 : 2065 – 2069 .
  • Pyle , A. M. 1993 . Science , 261 : 709 – 714 .
  • Cate , J. H. , Hanna , R. L. and Doudna , J. A. 1997 . Nature Struc. Biol. , 4 : 553 – 558 .
  • Wyatt , J. R. , Puglisi , J. D. and Jr. Tinoco , I. 1990 . J. Mol. Biol. , 214 : 455 – 470 .
  • Shen , L. X. 1994 . Ph.D. Thesis Berkeley, California , , USA : Dept. of Chemistry, University of California .
  • Ferrin , T. E. , Huang , C. C. , Jarvis , L. E. and Langridge , R. 1988 . J. Mol. Graphics , 6 : 13 – 27 . MidasPlus User's Manual, Computer Graphics Laboratory, School of Pharmacy, University of California, San Francisco (1992)
  • Pearl man , D. A. , Case , D. A. , Caldwell , J. C. , Seibel , G. L. , Singh , U. C. , Weiner , P. and Kollman , P. A. 1991 . AMBER 4.0 San Francisco : University of California .
  • Weiner , S. , Kollman , P. A. , Case , D. A. , Singh , U. C. , Ghio , C. , Alagona , G. , Profeta , S. and Weiner , P. 1984 . J. Am. Chem. Soc. , 106 : 765 – 784 .
  • Jorgensen , W. , Chandrasekhar , J. , Madura , J. , Impey , M. and Klein , R. 1983 . J. Chem. Phys. , 79 : 926 – 935 .
  • Saenger , W. 1984 . Principles of Nucleic Acid Structure New York : Springer-Verlag .
  • Westhof , E. and Sundaralingam , M. 1986 . Biochemistry , 25 : 4868 – 4878 .
  • Scott , W. G. , Finch , J. T. and Klug , A. 1995 . Cell , 81 : 991 – 1002 .
  • Gluick , T. C. , Wills , N. M. , Gesteland , R. F. and Draper , D. E. 1997 . Biochemistry , 36 : 16173 – 16186 .
  • Pleij , C. , Rietveld , K. and Bosch , L. 1985 . Nucl. Acids Res. , 13 : 1717 – 731 .
  • Heus , H. A. , Wijmenga , S. S. , Hoppe , H. and Hibers , C. W. 1997 . J. Mol. Biol. , 271 : 147 – 158 .
  • Ojha , R. P. , Dhingra , M. M. , Sarma , M. H. , Myer , Y. P. , Setlik , R. F. , Shibata , M. , Kazim , A. L. , Ornstein , R. L. , Rein , R. , Turner , C. J. and Sarma , R. H. 1997 . J. Biomol. Struct. Dyn. , 15 : 185 – 215 .
  • Michalczyk , R. and Russu , I. M. 1993 . FEBS Letter , 331 : 217 – 222 .
  • Young , M. A. , Srinivasan , J. , Goljer , I. , Kumar , S. , Beveridge , D. L. and Bolton , P. H. 1995 . Methods Enzymol. , 261 : 121 – 144 .
  • Kiran , M. R. and Bansal , M. 1997 . J. Biomol. Struct. Dyn. , 15 : 333 – 345 .
  • Eis , P. S. , Smith , J. A. , Rydzewski , J. M. , Case , D. A. , Boger , D. L. and Chazin , W. J. 1997 . J. Mol. Biol. , 272 : 231 252
  • Du , Z. , Giedroc , D. P. and Hoffman , D. W. 1996 . Biochemistry , 35 : 4187 – 4198 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.