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Molecules 2011, 16(12), 10695-10708; doi:10.3390/molecules161210695

Cleavage of Oligonucleotides Containing a P3’→N5’ Phosphoramidate Linkage Mediated by Single-Stranded Oligonucleotide Templates

1
Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
2
BNA Inc., 7-7-20 Saito-asagi, Ibaraki, Osaka 567-0085, Japan
*
Author to whom correspondence should be addressed.
Received: 1 November 2011 / Revised: 9 December 2011 / Accepted: 13 December 2011 / Published: 20 December 2011
(This article belongs to the Special Issue DNA-Templated Synthesis)
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Abstract

Double-stranded DNA (dsDNA) templates can hybridize to and accelerate cleavage of oligonucleotides containing a P3’→N5’ phosphoramidate (P-N) linkage. This dsDNA-templated cleavage of P-N linkages could be due to conformational strain placed on the linkage upon triplex formation. To determine whether duplex formation also induced conformational strain, we examined the reactivity of the oligonucleotides with a P-N linkage in the presence of single-stranded templates, and compared these reactions to those with dsDNA templates. P-N oligonucleotides that are cleaved upon duplex formation could be used as probes to detect single-stranded nucleic acids.
Keywords: bridged nucleic acids; DNA sensing; P3’→N5’ phosphoramidate bridged nucleic acids; DNA sensing; P3’→N5’ phosphoramidate
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Ito, K.R.; Kodama, T.; Makimura, F.; Hosoki, N.; Osaki, T.; Orita, A.; Imanishi, T.; Obika, S. Cleavage of Oligonucleotides Containing a P3’→N5’ Phosphoramidate Linkage Mediated by Single-Stranded Oligonucleotide Templates. Molecules 2011, 16, 10695-10708.

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