Poster abstracts

Poster number 42 submitted by Santosh Mahto

A study of the roles of modified nucleosides in the E. coli 16S ribosomal RNA decoding region

Santosh K. Mahto (Chemistry Department, Wayne State University, Detroit, MI 48202), Christine S. Chow (Chemistry Department, Wayne State University, Detroit, MI 48202)

Abstract:
Protein synthesis by the ribosome is an essential process in all cells. The decoding region (helix 44) of 16S ribosomal RNA (rRNA) of the small subunit is a very important functional region; it is involved in binding to mRNA, tRNAs, and the large subunit rRNA. This decoding region is involved in translational accuracy, so that proteins are synthesized essentially without errors. This region is also responsible for translocation. In addition, some of the known antibiotics bind to the decoding region. There are three modified nucleosides in decoding site of E. coli 16S rRNA, namely 5-methylcytidine (m5C), 3-methyluridine (m3U), and N4, 2'-O-dimethylcytidine (m4Cm). The functional significance of those modified nucleosides is not completely understood. Out of the three modified nucleosides, m3U and m5C are commercially available. In contrast, m4Cm, one of the modified nucleosides in which both the base and sugar are methylated, must be prepared in laboratory. In order to carry out detailed studies on the roles of m4Cm and additional analogues, m4C and Cm, they were first chemically synthesized by a new method. Circular dichroism and 1D NOE NMR spectra for these nucleosides were compared with cytidine. Phosphoramidites of these nucleosides were prepared to construct a series of A-site/P-site (decoding region) RNA models. Biophysical studies were then carried out to determine the significance of the modified nucleosides within the context of the decoding region of 16S rRNA.

Keywords: modified nucleosides, decoding region, N4, 2-O-dimethylcytidine (m4Cm)