title: Triplex-forming twisted intercalating nucleic acids (TINAs): design rules, stabilization of antiparallel DNA triplexes and inhibition of G-quartet-dependent self-association.
abstract: The majority of studies on DNA triple helices have been focused on pH-sensitive parallel triplexes with Hoogsteen CT-containing third strands that require protonation of cytosines. Reverse Hoogsteen GT/GA-containing antiparallel triplex-forming oligonucleotides (TFOs) do not require an acidic pH but their applicability in triplex technology is limited because of their tendency to form undesired highly stable aggregates such as G-quadruplexes. In this study, G-rich oligonucleotides containing 2-4 insertions of twisted intercalating nucleic acid(TINA) monomers are demonstrated to disrupt the formation of G-quadruplexes and form stable antiparallel triplexes with target DNA duplexes. The structure of TINA-incorporated oligonucleotides was optimized, the rules of their design were established and the optimal triplex-forming oligonucleotides were selected. These oligonucleotides show high affinity towards a 16 bp homopurine model sequence from the HIV-1 genome; dissociation constants as low as 160 nM are observed whereas the unmodified TFO does not show any triplex formation and instead forms an intermolecular G-quadruplex with T(m) exceeding 90°C in the presence of 50 mM NaCl. Here we present a set of rules that help to reach the full potential of TINATFOs and demonstrate the effect of TINA on the formation and stability of triple helical DNA.
authors.affiliation: Institute of Fundamental Sciences, Chemistry, Massey University, Private Bag 11-222, Palmerston North 4442, New Zealand.
authors.forename: Osman
authors.initials: O
authors.lastname: Doluca
authors.forename: Alexandre S
authors.initials: AS
authors.lastname: Boutorine
authors.forename: Vyacheslav V
authors.initials: VV
authors.lastname: Filichev
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D054856:G-Quadruplexes; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics; D006801:Humans; D007364:Intercalating Agents / Q000737:chemistry*; D009690:Nucleic Acid Conformation
chemical_list: D004279:DNA, Viral; D007364:Intercalating Agents; C051802:triplex DNA; D004247:DNA