Does the restriction endonuclease EcoRV employ a two-metal-Ion mechanism for DNA cleavage?

Two models for the catalytic mechanism of the restriction endonuclease EcoRV exist which differ in the number and function of metal ions proposed to be directly involved in catalysis. In one model, two metal ions bound by Glu45, Asp74, and Asp90 are assumed to have a direct catalytic function; in the other, only one metal ion bound by Asp74 and Asp90. We show here that in the presence of Mn2+, the catalytic activity of an EcoRV-E45A mutant is only slightly reduced (1.

EcoRV-T94V: a mutant restriction endonuclease with an altered substrate specificity towards modified oligodeoxynucleotides.

Synthetic oligodeoxynucleotides with single methyl phosphonate (mp) substitutions were used for an analysis of the contribution of phosphate contacts to the recognition of the cleavage site by the restriction endonuclease EcoRV. Only in the last position within the recognition sequence, is the methyl phosphonate substitution tolerated by the enzyme. The wild-type enzyme cleaves the Sp diastereomer of the oligodeoxynucleotide GACGATATmpCGTC and the unmodified sequence with equal rates, whereas the Rp diastereomer is cleaved much more slowly.

Engineering novel restriction endonucleases: principles and applications.

Restriction endonucleases cleave DNA with remarkable sequence specificity. In this review, we summarize the status of, and prospects for, engineering restriction endonucleases with new specificities. Such variants could be of considerable commercial value because restriction enzymes are among the most frequently used enzymes in molecular biology, and not all the desirable specificities are available.

Accuracy of the EcoRV restriction endonuclease: binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences.

In order to investigate the accuracy of the EcoRV restriction endonuclease, we have synthesized a set of double-stranded oligodeoxynucleotides comprising the canonical recognition sequence, the 9 star sequences (i.e., sequences deviating by one base pair from the canonical sequence), and the 18 mismatch sequences (i.

Evidence for substrate-assisted catalysis in the DNA cleavage of several restriction endonucleases.

Substrate-assisted catalysis was suggested to be involved in the DNA cleavage reaction of the restriction endonucleases (ENases) EcoRI and EcoRV, because experimental evidence exists that the phosphate group 3' to the scissile bond serves to deprotonate the attacking water. Here, we have addressed the question whether this is a general mechanistic feature of the reactions catalyzed by ENases. For this purpose, the cleavage rates of modified and unmodified oligodeoxyribonucleotides (oligos), in which the phosphate group 3' to the scissile bond is substituted by a methyl phosphonate, were measured for 17 enzymes.