SITE-SPECIFIC MODIFICATION OF 4.5S RNA APICAL DOMAIN BY COMPLEMENTARYOLIGODEOXYNUCLEOTIDES CARRYING AN ALKYLATING GROUP

Site-specific alkylation of RNA by reactive oligodeoxynucleotides prov ides structural information and represents the first step towards the design of RNA derivatives to be used for functional studies. Specific alkylation of 4.5S RNA at G53, the first base of the apical tetraloop, was achieved by incubation with oligodeoxynucleotide ON2, complementa ry to nucleotides 38-53, which carries a p-(N-2-chloroethyl-N-methylam ino) benzylamidophosphate group at the 5' end. Alkylation efficiency w as increased by a factor of 6, without alteration of specificity, in t he presence of a helper oligodeoxynucleotide, ON1, complementary to nu cleotides 58-71 of the opposite strand of the RNA helix. A second reac tive oligodeoxynucleotide, ON1-3'-R, was obtained by attaching the alk ylating group to the 3' end of ON1. ON1-3'-R was able to modify G58. I n the presence of ON2 as a helper oligodeoxynucleotide, the specificit y of ON1-3'-R changes and efficient alkylation of nucleotides G54, A56 and G57 of the apical region of 4.5S RNA was observed.