TRIPLE-HELIX FORMATION AT DISTANT SITES - HYBRID OLIGONUCLEOTIDES CONTAINING A POLYMERIC LINKER

An oligonucleotide hybrid is described which possesses two triple heli x forming oligonucleotides which have been connected by a flexible pol ymeric linker chain. As a prototype, binding of this class of oligonuc leotide 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 wh ich is one helical turn long. Band shift and footprinting analysis sho w 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 segment s of triple helix, providing that the linker element travels a path wh ich is external to the helix grooves and parallel to the long helix ax is.