Site-specific fluorescent labeling of large RNAs with pyrene.

Mary K. Smalley, Scott K. Silverman

Research output: Contribution to journalArticlepeer-review


Pyrene is a useful chromophore for monitoring the tertiary structure and folding of large RNAs. This unit describes the general preparation of a large RNA (>80 nucleotides in length) that has been site-specifically modified with pyrene at the 2'-position of an individual internal nucleotide. A protocol is provided for derivatizing a 2'-amino-RNA oligonucleotide with a suitably activated pyrene reagent. This pyrene-labeled oligonucleotide is then assembled with other RNA(s) either by covalent ligation or by noncovalent hybridization to form a full-length structured RNA, which may then be studied by equilibrium and stopped-flow fluorescence spectroscopy.

Original languageEnglish (US)
Pages (from-to)Unit 11.11
JournalCurrent protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.]
VolumeChapter 11
StatePublished - Dec 2004

ASJC Scopus subject areas

  • Biochemistry
  • Organic Chemistry


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