title: Synthesis of a new intercalating nucleic acid 6H-INDOLO[2,3-b] quinoxaline oligonucleotides to improve thermal stability of Hoogsteen-type triplexes.
abstract: A new intercalating nucleic acid monomer X was obtained in high yield starting from alkylation of 4-iodophenol with (S)-(+)-2-(2,2-dimethyl-1,3-dioxolan-4-yl)ethanol under Mitsunobu conditions followed by hydrolysis with 80% aqueous acetic acid to give a diol which was coupled under Sonogashira conditions with trimethylsilylacetylene (TMSA) to achieve the TMS protected (S)-4-(4-((trimethylsilyl)ethynyl)phenoxy)butane-1,2-diol. Tetrabutylammonium flouride was used to remove the silyl protecting group to obtain (S)-4-(4-ethynylphenoxy)butane-1,2-diol which was coupled under Sonogashira conditions with 2-(9-bromo-6H-indolo[2,3-b]quinoxalin-6-yl)-N,N-dimethylethanamine to achieve (S)-4-(4-((6-(2-(dimethylamino)ethyl)-6H-indolo[2,3-b]quinoxalin-9-yl)ethynyl)phenoxy)butane-1,2-diol. This compound was tritylated with 4,4'-dimethoxytrityl chloride followed by treatment with 2-cyanoethyltetraisopropylphosphordiamidite in the presence of N,N'-diisopropyl ammonium tetrazolide to afford the corresponding phosphoramidite. This phosphoramidite was used to insert the monomer X into an oligonucleotide which was used for thermal denaturation studies of a corresponding parallel triplex.
authors: Department of Physics, Nucleic Acid Center, University of Southern Denmark, Odense, Denmark.
authors: Amany M A
authors: AM
authors: Osman
authors: Erik B
authors: EB
authors: Pedersen
authors: Jan
authors: J
authors: Bergman
mesh_terms: D000478:Alkylation; D001483:Base Sequence; D060326:Chemistry Techniques, Synthetic; D006868:Hydrolysis; D007211:Indoles / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D007364:Intercalating Agents / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D009690:Nucleic Acid Conformation / Q000187:drug effects; D009691:Nucleic Acid Denaturation / Q000187:drug effects; D009696:Nucleic Acids / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D011810:Quinoxalines / Q000138:chemical synthesis / Q000737:chemistry* / Q000494:pharmacology; D013696:Temperature
chemical_list: D007211:Indoles; D007364:Intercalating Agents; D009696:Nucleic Acids; D009841:Oligonucleotides; D011810:Quinoxalines