Mung bean nuclease cleavage pattern at a polypurine.polypyrimidine sequence upstream from the mouse metallothionein-I gene

Abstract

Mung bean nuclease, an enzyme specific for single-stranded DNA, was used to probe a non-B DNA structure present in the mouse metallothionein-I gene. The region sensitive to the enzyme was constituted by a 128 base-pair long polypurine.polypyrimidine sequence located at 1.2-kb from the start of transcription. A detailed analysis of the mung bean nuclease cleavage pattern revealed that: (i) under conditions of supercoiling and low pH a triplex structure was formed, (ii) the triplex was flanked by a sequence with the potential of forming a Z-DNA structure, (iii) most of the enzymatic activity was localized at some of the junctions between double-stranded and triple-stranded DNA and at mismatches in the triplex, (iv) no unpaired bases were observed in the loop or outside the triplex, and (v) the triplex was present in more than one configuration.