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Molecules 2017, 22(11), 1856; doi:10.3390/molecules22111856

Zinc Ion-Dependent Peptide Nucleic Acid-Based Artificial Enzyme that Cleaves RNA—Bulge Size and Sequence Dependence

1
Department of Chemistry, University of Turku, 20014 Turku, Finland
2
Department of Biosciences and Nutrition, Karolinska Institutet, Novum, 141 83 Huddinge, Stockholm, Sweden
*
Authors to whom correspondence should be addressed.
Received: 5 October 2017 / Revised: 25 October 2017 / Accepted: 27 October 2017 / Published: 29 October 2017
(This article belongs to the Special Issue Molecular Properties and the Applications of Peptide Nucleic Acids)
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Abstract

In this report, we investigate the efficiency and selectivity of a Zn2+-dependent peptide nucleic acid-based artificial ribonuclease (PNAzyme) that cleaves RNA target sequences. The target RNAs are varied to form different sizes (3 and 4 nucleotides, nt) and sequences in the bulge formed upon binding to the PNAzyme. PNAzyme-promoted cleavage of the target RNAs was observed and variation of the substrate showed a clear dependence on the sequence and size of the bulge. For targets that form 4-nt bulges, we identified systems with an improved efficacy (an estimated half-life of ca 7–8 h as compared to 11–12 h for sequences studied earlier) as well as systems with an improved site selectivity (up to over 70% cleavage at a single site as compared to 50–60% with previous targets sequences). For targets forming 3-nt bulges, the enhancement compared to previous systems was even more pronounced. Compared to a starting point of targets forming 3-nt AAA bulges (half-lives of ca 21–24 h), we could identify target sequences that were cleaved with half-lives three times lower (ca 7–8 h), i.e., at rates similar to those found for the fastest 4-nt bulge system. In addition, with the 3-nt bulge RNA target site selectivity was improved even further to reach well over 80% cleavage at a specific site. View Full-Text
Keywords: artificial ribonuclease; oligonucleotide; PNA; PNAzyme; phosphodiester cleavage; sequence selectivity; RNA bulge artificial ribonuclease; oligonucleotide; PNA; PNAzyme; phosphodiester cleavage; sequence selectivity; RNA bulge
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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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Murtola, M.; Ghidini, A.; Virta, P.; Strömberg, R. Zinc Ion-Dependent Peptide Nucleic Acid-Based Artificial Enzyme that Cleaves RNA—Bulge Size and Sequence Dependence. Molecules 2017, 22, 1856.

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