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Issue 5, 2012
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DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes

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Abstract

We have previously reported DNA triplexes containing the unnatural base triad G-PPI·C3, in which PPI is an indole-fused cytosine derivative incorporated into DNA duplexes and C3 is an abasic site in triplex-forming oligonucleotides (TFOs) introduced by a propylene linker. In this study, we developed a new unnatural base triad A-ψ·CR1 where ψ and CR1 are base moieties 2′-deoxypseudouridine and 5-substituted deoxycytidine, respectively. We examined several electron-withdrawing substituents for R1 and found that 5-bromocytosine (CBr) could selectively recognize ψ. In addition, we developed a new PPI derivative, PPIMe, having a methyl group on the indole ring in order to achieve selective triplex formation between DNA duplexes incorporating various Watson–Crick base pairs, such as T-A, C-G, A-ψ, and G-PPIMe, and TFOs containing T, C, CBr, and C3. We studied the selective triplex formation between these duplexes and TFOs using UV-melting and gel mobility shift assays.

Graphical abstract: DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes

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Publication details

The article was received on 18 Aug 2011, accepted on 19 Oct 2011 and first published on 20 Oct 2011


Article type: Paper
DOI: 10.1039/C1OB06411H
Citation: Org. Biomol. Chem., 2012,10, 1007-1013
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    DNA duplexes and triplex-forming oligodeoxynucleotides incorporating modified nucleosides forming stable and selective triplexes

    T. Kanamori, Y. Masaki, M. Mizuta, H. Tsunoda, A. Ohkubo, M. Sekine and K. Seio, Org. Biomol. Chem., 2012, 10, 1007
    DOI: 10.1039/C1OB06411H

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