Jump to main content
Jump to site search

Issue 44, 2017
Previous Article Next Article

Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers

Author affiliations

Abstract

Development of hybridization-based probes that enable recognition of specific mixed-sequence double-stranded DNA (dsDNA) regions is of considerable interest due to their potential applications in molecular biology, biotechnology, and medicine. We have recently demonstrated that nucleic acid duplexes with +1 interstrand zipper arrangements of intercalator-functionalized nucleotides such as 2′-O-(pyren-1-yl)methyl RNA monomers are inherently activated for recognition of mixed-sequence dsDNA targets, including chromosomal DNA. In the present work, we follow up on our previous structure–activity relationship studies and explore if the dsDNA-recognition efficiency of these so-called Invader probes can be improved by using larger intercalators than pyrene. Oligodeoxyribonucleotides modified with 2′-O-(triphenylen-2-yl)methyl-uridine monomer X and 2′-O-(coronen-1-yl)methyl-uridine monomer Z form extraordinarily stabilized duplexes with complementary DNA (ΔTm's per modification of up to 13 °C and 20 °C, respectively). Invader probes based on X- and Z-monomers are shown to recognize model dsDNA targets with exceptional binding specificity, but are less efficient than reference probes modified with 2′-O-(pyren-1-yl)methyl-uridine monomer Y. The insight from this study will inform further optimization of Invader probes.

Graphical abstract: Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers

Back to tab navigation

Supplementary files

Publication details

The article was received on 01 Aug 2017, accepted on 14 Oct 2017 and first published on 14 Oct 2017


Article type: Paper
DOI: 10.1039/C7OB01920C
Citation: Org. Biomol. Chem., 2017,15, 9362-9371
  •   Request permissions

    Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2′-triphenylene- and coronene-functionalized RNA monomers

    S. Karmakar, D. C. Guenther, B. C. Gibbons and P. J. Hrdlicka, Org. Biomol. Chem., 2017, 15, 9362
    DOI: 10.1039/C7OB01920C

Search articles by author

Spotlight

Advertisements