Nucleic Acids Research, 1981, Vol. 9, No. 2 267-275
© 1981
MOLECULAR BIOLOGY |
Adenosine dimethylation of 16S ribosomal RNA: effect of the methylgroups on local conformational stability as deduced from electrophoretic mobility of RNA fragments in denaturing polyacrylamide gels
Department of Biochemistry, State University of Leiden P.O. Box 9505, 2300 RA Leiden, The Netherlands
Received November 10, 1980. The electrophoretic mobility of RNA fragments derived from the 3'-end of 16s rRNA on slabs of polyacrylamide gel in the presence of urea is strongly influenced by dimethylation of the N6-aminogroup of two adjacent adenosines. This is not due to the presence of the methylgroups per se, but must be ascribed to an effect of methylation on long range intramolecular interactions at these denaturing conditions. When it is assumed that the electro-phoretic mobilities of the RNA fragments in the polyacrylamide matrix are determined by the conformational state(s) of the fragments, dimethylation ofthe adenosines leads in the smaller fragments to a less compact average conformation and in the larger fragments to a more compact average conformation. An effort is made to comprehend the effects of adenosine dimethylation interms of secondary structure based on nucleotide sequence.