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Int. J. Mol. Sci. 2015, 16(6), 13259-13286; doi:10.3390/ijms160613259

Small RNA Detection by in Situ Hybridization Methods

Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 Str., 61-704 Poznan, Poland
These authors contributed equally to this work.
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Author to whom correspondence should be addressed.
Academic Editor: Michael Ladomery
Received: 29 April 2015 / Accepted: 3 June 2015 / Published: 10 June 2015
(This article belongs to the Special Issue RNA Interference)
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Abstract

Small noncoding RNAs perform multiple regulatory functions in cells, and their exogenous mimics are widely used in research and experimental therapies to interfere with target gene expression. MicroRNAs (miRNAs) are the most thoroughly investigated representatives of the small RNA family, which includes short interfering RNAs (siRNAs), PIWI-associated RNA (piRNAs), and others. Numerous methods have been adopted for the detection and characterization of small RNAs, which is challenging due to their short length and low level of expression. These include molecular biology methods such as real-time RT-PCR, northern blotting, hybridization to microarrays, cloning and sequencing, as well as single cell miRNA detection by microscopy with in situ hybridization (ISH). In this review, we focus on the ISH method, including its fluorescent version (FISH), and we present recent methodological advances that facilitated its successful adaptation for small RNA detection. We discuss relevant technical aspects as well as the advantages and limitations of ISH. We also refer to numerous applications of small RNA ISH in basic research and molecular diagnostics. View Full-Text
Keywords: short interfering RNA; Piwi-interacting RNA; LNA probe; rolling circle amplification; padlock probes; enzyme-labeled fluorescence signal amplification; TIRCA; PLA; tyramide signal amplification short interfering RNA; Piwi-interacting RNA; LNA probe; rolling circle amplification; padlock probes; enzyme-labeled fluorescence signal amplification; TIRCA; PLA; tyramide signal amplification
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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

Urbanek, M.O.; Nawrocka, A.U.; Krzyzosiak, W.J. Small RNA Detection by in Situ Hybridization Methods. Int. J. Mol. Sci. 2015, 16, 13259-13286.

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