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Nucleic Acids Research, 1990, Vol. 18, No. 9 2599-2606
© 1990

Molecular Biology

The tertiary sturcture of the four-way DNA junction affords protection against DNase I Cleavage

Alastair I.H. Murchie, Wendy A. Carter, Josè Portugal+ and David M.J. Lilley*

Department of Biochemistry, The University Dundee DD1 4HN, UK

*To whom correspondence should be addressed

Received March 6, 1990. Accepted April 5, 1990.

The accessibility of phosphodiester bonds in the DNA of four-way helical junctions has been probed with the nuclease DNase I. Regions of protection were observed on all four strands of the junctions, that tended to be longer on the strands that are exchanged between the coaxially stacked pairs of helices. The protected regions on the continuous strands of the stacked helices were not located exactly at the junction, but were displaced towards the 3' side of the strand. This is the region of backbone that becomes located in the major groove of the opposed helix in the non-crossed, right-handed structure for the junction, and might therefore be predicted to be protected against cleavage by an enzyme. However, the major grooves of the structure remain accessible to the much smaller probe dimethyl sulphate.

+Present addresses Departamento de Baoquimica , Fracultad de Quimica, Universidad de Barcelona, Av Diagonal 647, 08028 Barcelona, Sapin


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