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Nucleic Acids Research, 1993, Vol. 21, No. 20 4810-4815
© 1993

MOLECULAR BIOLOGY

Triple helix formation at distant sites: hybrid oligonucleotides containing a polymeric linker

Donald J. Kessler, B.Montgomery Pettitt1, Yuen-Kit Cheng1, Sean R. Smith, Krishna Jayaraman2, Huynh M. Muv2 and Michael E. Hogan*

The Center for Biotechnology, Baylor College of Medicine, 4000 Research Forest Drive The Woodlands, TX 77381 1department of Chemistry, The University of Houston Houston,TX 77204-5641 2Triplex Pharmaceutical Corporation The Woodlands, TX 77381, USA

*To whom correspondence should be addressed.

Received June 3, 1993. Revised August 12, 1993. Accepted August 12, 1993.

An oligonucleotide hybrid is described which possesses two triple helix forming oligonucleotides which have been connected by a flexible polymeric linker chain. As a prototype, binding of this class of oligonucleotide to duplex DNA has been studied using a segment of the HSV-1 D-glycoprotein promoter, which possesses a pair of 12bp target sites for stable triple helix formation, separated by a duplex spacer region which is one helical turn long. Band shift and footprinting analysis show that such hybrids can bind to both 12bp elements simultaneously, if flexible linkers are included which are longer than 20-25 rotatable bonds. Molecular modeling confirms that a flexible polymeric linker as short as 22 rotatable bonds is enough to link the two distant segments of triple helix, providing that the linker element travels a path which is external to the helix grooves and parallel to the long helix axis.


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