Effects of functional group changes in the EcoRV recognition site on the cleavage reaction catalyzed by the endonuclease.

Oligodeoxynucleotides have been prepared which contain changes in the functional group pattern present in the EcoRV recognition site d(GATATC). These modifications involve the deletion of specific functional groups or the reversal of the relative positions of functional groups within the canonical six base pair recognition site. The duplex stability of these modified oligodeoxynucleotides has been assessed by determining the thermodynamic parameters characterizing helix formation. Steady-state kinetic parameters have been used to characterize the interaction of the modified oligodeoxynucleotides with the EcoRV endonuclease. The enzyme is very sensitive to the deletion of either of the adenine amino or thymine methyl groups, or the reversal of the relative positions of the adenine amino group and thymine carboxy group which form an interstrand hydrogen bond in the major groove of the B-DNA helix. Conversely, deletion of the guanine amino group had only minimal effects upon the measured kinetic parameters. Deletion of the exocyclic amino group from the "inner" dA-dT base pair resulted in the fragment which interacted with the enzyme on the basis of observed inhibition experiments but was not cleaved. The results suggest that the endonuclease interacts with its recognition sequence via contacts in the major groove of the B-DNA helix and that both hydrogen bonding to the adenine amino groups and also hydrophobic interactions with the thymine methyl groups are involved.