title: Recognition of base pair inversions in duplex by chimeric (alpha,beta) triplex-forming oligonucleotides.
abstract: DNA recognition by triplex-forming oligonucleotides (TFOs) is usually limited by homopurine-homopyrimidine sequence in duplexes. Modifications of the third strand may overcome this limitation. Chimeric alpha-beta TFOs are expected to form triplex DNA upon binding to non-regular sequence duplexes. In the present study we describe binding properties of chimeric alpha-beta oligodeoxynucleotides in the respect to short DNA duplexes with one, three, and five base pair inversions. Non-natural chimeric TFO's contained alpha-thymidine residues inside (GT) or (GA) core sequences. Modified residues were addressed to AT/TA inversions in duplexes. It was found in the non-denaturing gel-electrophoresis experiments that single or five adjacent base pair inversions in duplexes may be recognized by chimeric alpha-beta TFO's at 10 degrees C and pH 7.8. Three dispersed base pair inversions in the double stranded DNA prevented triplex formation by either (GT) or (GA) chimeras. Estimation of thermal stability of chimeric alpha-beta triplexes showed decrease in T(m) values as compared with unmodified complexes.
authors.affiliation: W.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov St., 119991 Moscow, Russia. edward@eimb.ru
authors.forename: Edward N
authors.initials: EN
authors.lastname: Timofeev
authors.forename: Baira V
authors.initials: BV
authors.lastname: Goryaeva
authors.forename: Vladimir L
authors.initials: VL
authors.lastname: Florentiev
mesh_terms: D020029:Base Pairing / Q000502:physiology*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D006860:Hydrogen Bonding; D009841:Oligonucleotides / Q000737:chemistry* / Q000378:metabolism
chemical_list: D009841:Oligonucleotides; C051802:triplex DNA; D004247:DNA