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Nucleic Acids Research, 1981, Vol. 9, No. 6 1271-1290
© 1981

MOLECULAR BIOLOGY

Hairpin-loop formation by inverted repeats in supercoiled DNA is a local and transmissible property

David M.J. Lilley

Department of Molecular Genetics, Searle Research Laboratories Lane End Road, High Wycombe, HP12 4HL, UK

Received January 21, 1981. Short inverted repeat sequences adopt hairpin stem-loop type structures in supercoiled closed circular DNA molecules, demonstrated by Sl nuclease cleavage. Fine mapping of cleavage frequencies is in good agreement with expected cleavage patterns based upon the interaction between an unpaired loop and a sterically bulky enzyme molecule. Whilst the topological properties of underwound DNA circles depend ultimately upon reduced linkage, necessarily a global molecular property, hairpin loop formation is an essentially local property. Thus molecular size is unimportant for the Sl hypersensitivity of the ColE1 inverted repeat. Furthermore, a 440 bp Sau3AI, EcoRI fragment of ColE1 which contains the inverted repeat has been cloned into pBR322 where-upon it exhibits Sl cleavage similar to ColE1 in the supercoiled recombinant molecule. The effect is therefore both local and transmissible. Direct competition between inverted repeats in the recombinant, coupled with close examination of flanking sequences, enables some simple ‘rules’ for base pairing in hairpin loops to be formulated. Whilst limited G-T and A-C base pairing appears not to be destabilising, A-G, T-C or loop outs are highly destabilising.


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