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Molecules 2015, 20(8), 13780-13793; doi:10.3390/molecules200813780

Mixed-Sequence Recognition of Double-Stranded DNA Using Enzymatically Stable Phosphorothioate Invader Probes

Department of Chemistry, University of Idaho, Moscow, ID 83844-2343, USA
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Author to whom correspondence should be addressed.
Academic Editor: Ramon Eritja
Received: 1 July 2015 / Revised: 23 July 2015 / Accepted: 24 July 2015 / Published: 29 July 2015
(This article belongs to the Special Issue Frontiers in Nucleic Acid Chemistry)
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Abstract

Development of probes that allow for sequence-unrestricted recognition of double-stranded DNA (dsDNA) continues to attract much attention due to the prospect for molecular tools that enable detection, regulation, and manipulation of genes. We have recently introduced so-called Invader probes as alternatives to more established approaches such as triplex-forming oligonucleotides, peptide nucleic acids and polyamides. These short DNA duplexes are activated for dsDNA recognition by installment of +1 interstrand zippers of intercalator-functionalized nucleotides such as 2′-N-(pyren-1-yl)methyl-2′-N-methyl-2′-aminouridine and 2′-O-(pyren-1-yl)methyluridine, which results in violation of the nearest neighbor exclusion principle and duplex destabilization. The individual probes strands have high affinity toward complementary DNA strands, which generates the driving force for recognition of mixed-sequence dsDNA regions. In the present article, we characterize Invader probes that are based on phosphorothioate backbones (PS-DNA Invaders). The change from the regular phosphodiester backbone furnishes Invader probes that are much more stable to nucleolytic degradation, while displaying acceptable dsDNA-recognition efficiency. PS-DNA Invader probes therefore present themselves as interesting probes for dsDNA-targeting applications in cellular environments and living organisms. View Full-Text
Keywords: DNA recognition; oligonucleotides; pyrene DNA recognition; oligonucleotides; pyrene
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Anderson, B.A.; Karmakar, S.; Hrdlicka, P.J. Mixed-Sequence Recognition of Double-Stranded DNA Using Enzymatically Stable Phosphorothioate Invader Probes. Molecules 2015, 20, 13780-13793.

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