Molecules 2013, 18(12), 15357-15397; doi:10.3390/molecules181215357
Review

Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells

1 Muséum National d'Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France 2 Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia 3 Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
* Author to whom correspondence should be addressed.
Received: 23 September 2013; in revised form: 20 November 2013 / Accepted: 5 December 2013 / Published: 11 December 2013
(This article belongs to the Special Issue Synthesis of Nucleosides, Nucleotides and Their Derivatives)
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Abstract: This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
Keywords: fluorescent probes; living cells; RNA; DNA; imaging; triplex-forming oligonucleotides; minor groove binders; fluorophores; molecular beacons; binary probes

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MDPI and ACS Style

Boutorine, A.S.; Novopashina, D.S.; Krasheninina, O.A.; Nozeret, K.; Venyaminova, A.G. Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells. Molecules 2013, 18, 15357-15397.

AMA Style

Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells. Molecules. 2013; 18(12):15357-15397.

Chicago/Turabian Style

Boutorine, Alexandre S.; Novopashina, Darya S.; Krasheninina, Olga A.; Nozeret, Karine; Venyaminova, Alya G. 2013. "Fluorescent Probes for Nucleic Acid Visualization in Fixed and Live Cells." Molecules 18, no. 12: 15357-15397.

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