Jump to main content
Jump to site search

Issue 42, 2014
Previous Article Next Article

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

Author affiliations

Abstract

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 triisopropylsilyl 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 linker 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 long linker adduct showing increased duplex stability over those with a short side chain.

Graphical abstract: 5-Nitroindole oligonucleotides with alkynyl side chains: universal base pairing, triple bond hydration and properties of pyrene “click” adducts

Back to tab navigation

Supplementary files

Publication details

The article was received on 14 Jul 2014, accepted on 09 Sep 2014 and first published on 09 Sep 2014


Article type: Paper
DOI: 10.1039/C4OB01478B
Org. Biomol. Chem., 2014,12, 8519-8532

  •   Request permissions

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

    S. A. Ingale, P. Leonard, H. Yang and F. Seela, Org. Biomol. Chem., 2014, 12, 8519
    DOI: 10.1039/C4OB01478B

Search articles by author

Spotlight

Advertisements