Probing the stabilizing effects of modified nucleotides in the bacterial decoding region of 16S ribosomal RNA.

Bioorg Med Chem 2013 May 21;21(10):2720-6. Epub 2013 Mar 21.

Department of Chemistry, Wayne State University, Detroit, MI 48202, USA.

The bacterial decoding region of 16S ribosomal RNA has multiple modified nucleotides. In order to study the role of N(4),2'-O-dimethylcytidine (m(4)Cm), the corresponding phosphoramidite was synthesized utilizing 5'-silyl-2'-ACE chemistry. Using solid-phase synthesis, m(4)Cm, 5-methylcytidine (m(5)C), 3-methyluridine (m(3)U), and 2'-O-methylcytidine (Cm) were site-specifically incorporated into small RNAs representing the decoding regions of different bacterial species. Biophysical studies were then used to provide insight into the stabilizing roles of the modified nucleotides. These studies reveal that methylation of cytidine and uridine has different effects. The same modifications at different positions or sequence contexts within similar RNA constructs also have contrasting roles, such as stabilizing or destabilizing the RNA helix.

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.bmc.2013.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3683315PMC
May 2013
4 Reads

Publication Analysis

Top Keywords

modified nucleotides
12
decoding region
8
region 16s
8
16s ribosomal
8
ribosomal rna
8
bacterial decoding
8
effects modifications
4
chemistry solid-phase
4
m3u 2'-o-methylcytidine
4
contexts rna
4
2'-o-methylcytidine site-specifically
4
incorporated small
4
uridine effects
4
site-specifically incorporated
4
sequence contexts
4
3-methyluridine m3u
4
5-methylcytidine m5c
4
positions sequence
4
synthesis m4cm
4
m5c 3-methyluridine
4

Similar Publications