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Issue 31, 2013
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Deconstructing RNA: optical measurement of composition and structure

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Abstract

RNA molecules are involved in many pathways within the cell and their sequence composition, structure, conformational transitions and interactions with other molecules are all important factors in determining RNA function. Here we present a method for systematically and quantitatively determining characteristics of RNA using Raman spectroscopy. This method can be used to assess the composition and structure of a given RNA molecule, including ribose-phosphate sugar-pucker conformation, face-to-face base stacking and hydrogen bonding interactions. Three RNA molecules with different sequence and structural features (the exon splicing silencer 3 from HIV-1, an RNA aptamer against Runt-related transcription factor, and the SARS coronaviral stem loop 2) are presented as examples where the structure is crucial to the function of the RNA. We carry out piecewise analysis of the RNA spectra and show that using a nucleotide spectra library helps to unlock the entire ensemble of vibrational information. This analysis demonstrates the extent to which RNA characteristics can be elucidated, using purely optical methods.

Graphical abstract: Deconstructing RNA: optical measurement of composition and structure

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Publication details

The article was received on 10 Jun 2013, accepted on 26 Jun 2013 and first published on 27 Jun 2013


Article type: Paper
DOI: 10.1039/C3CP52406J
Phys. Chem. Chem. Phys., 2013,15, 13199-13208

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    Deconstructing RNA: optical measurement of composition and structure

    A. J. Hobro, D. M. Standley, S. Ahmad and N. I. Smith, Phys. Chem. Chem. Phys., 2013, 15, 13199
    DOI: 10.1039/C3CP52406J

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