Skip Navigation

This Article
Right arrow Print PDF (421K)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (30)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Lustig, B.
Right arrow Articles by Jernigan, R. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lustig, B.
Right arrow Articles by Jernigan, R. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 1995, Vol. 23, No. 22 4707-4711
© 1995

Articles

Consistences of individual DNA base—amino acid interactions in structures and sequences

Brooke Lustig and Robert L. Jernigan*

Laboratory of mathematical Biology, Room B116, Building 12B, MSC-5677, National Cancer Institute, National Institutes of Health Bethesda, MD 20892–5677, USA

*To whom correspondence should be addressed

Received July 10, 1995. Accepted October 14, 1995.

Amino acid-amino acid interaction energies have been derived from crystal structure data for a number of years. Here is reported the first derivation of normalized relative interaction from binding data for each of the four bases interacting with a specific amino acid, utilizing data from combinatorial multiplex ONA binding of zinc finger domains [Desjarlais, J. R. and Berg, J. M. (1994) Proc. Natl. Acad. Sci. USA, 91, 11099–11103]. The five strongest Interactions are observed for lysine-guanine, lysine-thymine, arginine- guanine, aspartic acid-cytosine and asparagineadenine. These rankings for interactions with the four bases appear to be related to base-amino acid partial charges. Also, similar normalized relative interaction energies are derived by using DNA binding data for Cro and X repressors and the R2R3 c-Myb protein domain [Takeda, Y., Sarai, A. and Rivera, V. M. (1989) Proc. Natl. Acad. Sci. USA, 86, 439–443; Sarai, A. and Takeda, Y. (1989) Proc. Natl. Acad. Sci. USA, 86, 6513–6517; Ogata, K. et al. (1995) submitted]. These energies correlate well with the combinatorial multiplex energies, and the strongest cases are similar between the two sets. They also correlate well with similar relative interaction energies derived directly from frequencies of bases in the bacteriophage X operator sequences. These results suggest that such potentials are general and that extensive combinatorial binding studies can be used to derive potential energies for DNA-protein interactions.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 J. Immunol.Home page
P. J. Wettstein, N. D. Borson, J. G. Park, K. T. McNallan, and A. M. Reed
Cysteine-Tailed Class I-Binding Peptides Bind to CpG Adjuvant and Enhance Primary CTL Responses
J. Immunol., September 15, 2005; 175(6): 3681 - 3689.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
M. J. Harley and J. F. Schildbach
Swapping single-stranded DNA sequence specificities of relaxases from conjugative plasmids F and R100
PNAS, September 30, 2003; 100(20): 11243 - 11248.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
F. S. Silbaq, S. E. Ruttenberg, and G. D. Stormo
Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections
Nucleic Acids Res., December 15, 2002; 30(24): 5539 - 5548.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
L. A. Mirny and M. S. Gelfand
Structural analysis of conserved base pairs in protein-DNA complexes
Nucleic Acids Res., April 1, 2002; 30(7): 1704 - 1711.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
I. Artsimovitch, K. Murakami, A. Ishihama, and M. M. Howe
Transcription Activation by the Bacteriophage Mu Mor Protein Requires the C-terminal Regions of Both alpha and sigma 70 Subunits of Escherichia coli RNA Polymerase
J. Biol. Chem., December 13, 1996; 271(50): 32343 - 32348.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.