EcoRI* Specificity and Hydrogen Bonding

Abstract

Under standard conditions, Eco RI endonuclease uniquely recognizes the inverted repeat GAATTC. However, this specificity breaks down under non-standard conditions into what has been termed Eco RI* specificity, wherein many other sequences are recognized. We show here that the hydrolysis rates at all known Eco RI* sites can be summarized by the hierarchies: G > > A > T > > C at the first position, A > > [G, C] > > T at the second and third position, and the corresponding complements at the last three positions. This is consistent with a recognition model which assumes that there are two specific hydrogen bonds per base pair under standard conditions. One or more of these are randomly replaced by water under Eco RI* conditions and the position of a sequence within the appropriate hierarchy is primarily determined by the number of retained hydrogen bonds. These retained hydrogen bonds are common recognition features that can be identified by examining the DNA. The recognition points thereby identified for Eco RI all fall within the major groove of the DNA.