title: Oligonucleotide-mediated triple helix formation using an N3-protonated deoxycytidine analog exhibiting pH-independent binding within the physiological range.
abstract: Triple helix formation with pyrimidine deoxyoligonucleotides for the sequence-specific recognition of DNA duplex targets suffers from a decrease in affinity as the pH of the medium increases to that of physiological fluids. A solution to this problem has been identified and entails the substitution of N6-methyl-8-oxo-2'-deoxyadenosine (M) for the 5-methyl-deoxycytosine base residues. The triple helix forming ability of an oligonucleotide consisting of thymidine and M residues is pH independent in the physiological range. Furthermore, M has been found to be superior to the previously used 5-methyldeoxycytidine and deoxyguanosine in conferring increased affinity for duplex DNA under physiological salt conditions.
authors.affiliation: Gilead Sciences, Inc., Foster City, CA 94404.
authors.forename: S H
authors.initials: SH
authors.lastname: Krawczyk
authors.forename: J F
authors.initials: JF
authors.lastname: Milligan
authors.forename: S
authors.initials: S
authors.lastname: Wadwani
authors.forename: C
authors.initials: C
authors.lastname: Moulds
authors.forename: B C
authors.initials: BC
authors.lastname: Froehler
authors.forename: M D
authors.initials: MD
authors.lastname: Matteucci
mesh_terms: D001483:Base Sequence; D003841:Deoxycytidine / Q000031:analogs & derivatives; D006860:Hydrogen Bonding; D006863:Hydrogen-Ion Concentration; D066298:In Vitro Techniques; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*
chemical_list: D009838:Oligodeoxyribonucleotides; D003841:Deoxycytidine