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Nucleic Acids Research, 1989, Vol. 17, No. 18 7417-7426
© 1989

MOLECULAR BIOLOGY

DNA tertiary structures formed in vitro by misaligned hybridization of multiple tandem repeat sequences

Lesley W. Coggins* and Margaret O'Prey

Beatson Institute for Cancer Research Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK

*To whom correspondence should be addressed

Received July 6, 1989. Revised August 18, 1989. Accepted August 18, 1989.

DNA tertiary structures are shown to be formed by denaturation and reannealing in vitro of molecularly-cloned DNA containing multiple tandem repeat sequences. Electron microscopy of homoduplex DNA molecules containing the human c-Harvey-ras gene revealed knot-like structures which mapped to the position of the 812 bp variable tandem repeat (VTR) sequence. We propose that the structures result from slipped-strand mispairing within the VTR and hybridisation of homologous repetitive sequences in the single-stranded loops so produced. Similar structures were also found in freshly-linearised supercoiled plasmids. More complex knot-like structures were found in homoduplexes of a 4 kb tandem array from the hypervariable region 3' to the human {alpha}-globin locus. Formation of such DNA tertiary structures in vitro also provides a practical method for identifying and mapping direct tandem repeat arrays that are at least 800 bp long.


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