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

• Type of Material: Article
• Authors: Alison J. Hobro, University of Manchester; Mansour Rouhi, University of Manchester; Ewan W. Blanch, University of Manchester; Graeme Conn, Emory University
• Language: English
• Date: 2007-02-01
• Publisher: Oxford University Press (OUP): Policy C - Option B
• Publication Version: Final Published Version
• Copyright Statement: © 2007 Oxford University Press. 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.
• Final Published Version (URL): http://dx.doi.org/10.1093/nar/gkm012
• Title of Journal or Parent Work: Nucleic Acids Research
• ISSN: 0305-1048
• Volume: 35
• Issue: 4
• Start Page: 1169
• End Page: 1177
• Grant/Funding Information: This work was funded by The Wellcome Trust (grant ref. 076060). Funding to pay the Open Access publication charge was provided by The Wellcome Trust.
• Keywords: VIRUS; Biochemistry & Molecular Biology; Life Sciences & Biomedicine; UV ABSORPTION; HAIRPINS; Science & Technology; INITIATION; BIOCHEMISTRY & MOLECULAR BIOLOGY; NUCLEIC-ACIDS; SCATTERING INTENSITIES; CONFORMATIONAL DEPENDENCE; TRANSLATION; RIBOSOME ENTRY SITE; SPECTROSCOPY

Abstract

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.