title: Triple helix formation at distant sites: hybrid oligonucleotides containing a polymeric linker.
abstract: 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.
authors.affiliation: Center for Biotechnology, Baylor College of Medicine, The Woodlands, TX 77381.
authors.forename: D J
authors.initials: DJ
authors.lastname: Kessler
authors.forename: B M
authors.initials: BM
authors.lastname: Pettitt
authors.forename: Y K
authors.initials: YK
authors.lastname: Cheng
authors.forename: S R
authors.initials: SR
authors.lastname: Smith
authors.forename: K
authors.initials: K
authors.lastname: Jayaraman
authors.forename: H M
authors.initials: HM
authors.lastname: Vu
authors.forename: M E
authors.initials: ME
authors.lastname: Hogan
mesh_terms: D001483:Base Sequence; D001704:Biopolymers; D003196:Computer Graphics; D003850:Deoxyribonuclease I / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D011401:Promoter Regions, Genetic; D014759:Viral Envelope Proteins / Q000235:genetics
chemical_list: D001704:Biopolymers; D009838:Oligodeoxyribonucleotides; D014759:Viral Envelope Proteins; C039447:glycoprotein D, Human herpesvirus 1; D003850:Deoxyribonuclease I