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Nucleic Acids Research Advance Access originally published online on January 30, 2007
Nucleic Acids Research 2007 35(4):1169-1177; doi:10.1093/nar/gkm012
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Nucleic Acids Research, 2007, Vol. 35, No. 4 1169-1177
© 2007 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

Raman and Raman optical activity (ROA) analysis of RNA structural motifs in Domain I of the EMCV IRES

Alison J. Hobro, Mansour Rouhi, Ewan W. Blanch* and Graeme L. Conn

Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK

*To whom correspondence should be addressed. Tel: +44 (0)161 3065819; Fax: 0161 3065201; E-mail: E.Blanch{at}manchester.ac.uk. Correspondence may also be addressed to Graeme. L. Conn. Tel: +44 (0)161 3064218; Fax: 0161 3065201; E-mail: graeme.l.conn{at}manchester.ac.uk

Received October 18, 2006. Revised December 20, 2006. Accepted December 27, 2006.

Raman and Raman optical activity (ROA) spectra were collected for four RNA oligonucleotides based on the EMCV IRES Domain I to assess the contributions of helix, GNRA tetraloop, U·C mismatch base pair and pyrimidine-rich bulge structures to each. Both Raman and ROA spectra show overall similarities for all oligonucleotides, reflecting the presence of the same base paired helical regions and GNRA tetraloop in each. Specific bands are sensitive to the effect of the mismatch and asymmetric bulge on the structure of the RNA. Raman band changes are observed that reflect the structural contexts of adenine residues, disruption of A-form helical structure, and incorporation of pyrimidine bases in non-helical regions. The ROA spectra are also sensitive to conformational mobility of ribose sugars, and verify a decrease in A-type helix content upon introduction of the pyrimidine-rich bulge. Several Raman and ROA bands also clearly show cooperative effects between the mismatch and pyrimidine-rich bulge motifs on the structure of the RNA. The complementary nature of Raman and ROA spectra provides detailed and highly sensitive information about the local environments of bases, and secondary and tertiary structures, and has the potential to yield spectral signatures for a wide range of RNA structural motifs.


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