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Methods Mol Biol. 2016;1402:135-145. doi: 10.1007/978-1-4939-3378-5_11.

Simultaneous RNA-DNA FISH.

Author information

1
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
2
Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore.
3
Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371, Singapore. fwshao@ntu.edu.sg.
4
School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore. zhanglf@ntu.edu.sg.

Abstract

A highly useful tool for studying lncRNAs is simultaneous RNA-DNA FISH, which reveals the localization and quantitative information of RNA and DNA in cellular contexts. However, a simple combination of RNA FISH and DNA FISH often generates disappointing results because the fragile RNA signals are often damaged by the harsh conditions used in DNA FISH for denaturing the DNA. Here, we describe a robust and simple RNA-DNA FISH protocol, in which amino-labeled nucleic acid probes are used for RNA FISH. The method is suitable to detect single-RNA molecules simultaneously with DNA.

KEYWORDS:

Amino-labeled probes; Fluorescence in situ hybridization (FISH); Simultaneous RNA–DNA FISH; Single-molecule RNA FISH; lncRNA

PMID:
26721488
DOI:
10.1007/978-1-4939-3378-5_11
[Indexed for MEDLINE]

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