[Complementary addressed alkylation of Escherichia coli 16S rRNA with 2',3'-O-[4-2-chloroethyl)-N-methylamino]benzylidene derivatives of deoxyribooligonucleotides. II. The nature of rapid interaction at 0 degrees C].

Fast non-covalent interactions of 16S rRNA Escherichia coli with 14C labeled 2',3'-O-[4-N-(2-chloroethyl)-N-methylamino]benzylidene derivatives of deoxyribooligonucleotides d(pACCTTGTT)rA, d[pTTACGATC)rU, d(pTTTGCTCCCC)rA (less than[14C]CHRCl-reagents) observed at 0 degrees C were investigated. It was shown, that 16S rRNA and [14C]CHRCl-reagents at 0 degrees C form stable complexes which can not be disrupted under mild acidic conditions (pH 4, 40 degrees C) and under denaturing conditions (7 M urea, 50 degrees C), but are completely disrupted in the course of centrifugation in sucrose density gradient in the presence of SDS. Formation of such complexes of 16S rRNA with greater than[14C]CHRCl-reagents at 0 degrees C was observed due to the presence in the reagent preparation of a number of unidentified products, formed in the course of the synthesis of benzylidene derivatives, and having a hydrophobicity larger, than those for greater than CHRCl-derivatives of deoxyribooligonucleotide. Preparation of [14C]CHRCl-reagents, subjected for purification by reverse-phase chromatography, were unable to form such a complex with 16S rRNA at 0 degrees C. Studies on the complementary addressed modification at 0 degrees C (or incubation at 0 degrees C) with the use of the oligonucleotide benzylidene derivatives not purified from hydrophobic contaminations may lead to alkylation within these complexes during subsequent treatments and in such a way give incorrect information about the level of alkylation within the complex under investigation.