Raman and Raman optical activity (ROA) analysis of RNA structural motifs

Abstract

Raman and Raman optical activity (ROA) spectroscopies are well suited to the study of ribonucleic acids (RNA) as they are both sensitive to a large amount of structural information and applicable to most RNAs and experimental conditions. As such, they can fill the current gap between high- and low-resolution techniques currently used by RNA biologists. In this study we illustrate the complementarity of Raman and ROA spectroscopies by their application to two functional RNAs, a 37 nucleotide RNA fragment from Domain I of the encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES) RNA and the L11 binding domain ribosomal RNA (LBD rRNA). Fingerprint spectra unique to the structure of each RNA are presented. We then discuss the Raman and ROA spectra of several oligonucleotides containing three common secondary structural motifs all found within the EMCV RNA; the GNRA tetraloop, pyrimidine-rich asymmetric bulge and a base mismatch. We show that highly detailed structural information can be obtained from these spectra.