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Science 9 November 1990:
Vol. 250. no. 4982, pp. 776 - 786
DOI: 10.1126/science.2237428
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Articles
Science, Vol 250, Issue 4982, 776-786
Copyright © 1990 by American Association for the Advancement of Science
The energetic basis of specificity in the Eco RI endonuclease--DNA interaction
DR Lesser,
MR Kurpiewski,
and
L Jen-Jacobson
Department of Biological Sciences, University of Pittsburgh, PA 15260.
High sequence selectivity in DNA-protein interactions was analyzed by measuring discrimination by Eco RI endonuclease between the recognition site GAATTC and systematically altered DNA sites. Base analogue substitutions that preserve the sequence-dependent conformational motif of the GAATTC site permit deletion of single sites of protein-base contact at a cost of +1 to +2 kcal/mol. However, the introduction of any one incorrect natural base pair costs +6 to +13 kcal/mol in transition state interaction energy, the resultant of the following interdependent factors: deletion of one or two hydrogen bonds between the protein and a purine base; unfavourable steric apposition between a group on the protein and an incorrectly placed functional group on a base; disruption of a pyrimidine contact with the protein; loss of some crucial interactions between protein and DNA phosphates; and an increased energetic cost of attaining the required DNA conformation in the transition state complex. Eco RI endonuclease thus achieves stringent discrimination by both "direct readout" (protein-base contracts) and "indirect readout" (protein-phosphate contacts and DNA conformation) of the DNA sequence.
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