5-Nitroindole oligonucleotides with alkynyl side chains: universal base pairing, triple bond hydration and properties of pyrene ``click'' adducts

Autor(en): Ingale, Sachin A.
Leonard, Peter
Yang, Haozhe
Seela, Frank
Stichwörter: 5-SUBSTITUTED INDOLES; CHARGE-TRANSFER; Chemistry; Chemistry, Organic; DNA DUPLEXES; DUPLEX STABILITY; ELECTRON-TRANSFER; GLYCOSYLATION POSITION; HYBRIDIZATION PROBES; NUCLEIC-ACIDS; QUENCHING EFFICIENCIES; TERMINAL ALKYNES
Erscheinungsdatum: 2014
Herausgeber: ROYAL SOC CHEMISTRY
Journal: ORGANIC & BIOMOLECULAR CHEMISTRY
Volumen: 12
Ausgabe: 42
Startseite: 8519
Seitenende: 8532
Zusammenfassung: 
Oligonucleotides with 3-ethynyl-5-nitroindole and 3-octadiynyl-5-nitroindole 2'-deoxyribonucleosides were prepared by solid-phase synthesis. To this end, nucleoside phosphoramidites with clickable side chains were synthesized. The 3-ethynylated 5-nitroindole nucleoside was hydrated during automatized DNA synthesis to 3-acetyl-5-nitroindole 2'-deoxyribonucleoside. Side product formation was circumvented by triisopropylsltyl protection of the ethynyl side chain and was removed with TBAF after oligonucleotide synthesis. ALL compounds with a clickable 5-nitroindole skeleton show universal base pairing and can be functionalized with almost any azide in any position of the DNA chain. Functionalization of the side chain with 1-azidomethylpyrene afforded click adducts in which the fluorescence was quenched by the 5-nitroindole moieties. However, fluorescence was slightly recovered during duplex formation. Oligonucleotides with a pyrene residue and a long tinker arm are stabilized over those with non-functionalized side chains. From the UV red shift of the pyrene residue in oligonucleotides and modelling studies, pyrene intercalation was established for the tong linker adduct showing increased duplex stability over those with a short side chain.
ISSN: 14770520
DOI: 10.1039/c4ob01478b

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