Among the number of complementary complexes of 23S RNA with alkylating derivatives of complementary oligonucleotides ((Ap)3-5 ARCl, (Cp)5CRCl and (Np)5NRCl) some complexes of peculiar conformation are observed. The rate constant of alkylaation within the peculiar complexes is four fold greater than that within the rest complexes. The latter are alkylated via an active intermediate that is formed in the first rate determining step by two step alkylation. Both individual 23S RNAs and one in the rRNA mixture are alkylated in the peculiar complexes. But 16S RNA is alkylated only by the two step alkylation. There is a single binding site in the rRNA that is alkylated with the alkylating derivatives of the definite nucleotide sequence at the definite base. The reagments with different sequences can alkylate different bases. The alkylating derivatives of hexa-nucleotide isoplits that are complementary to rRNA alkylate up to 45 +/- 10 complexes simultaneously. The conformation of these complexes enables alkylation with the higher rate constant mentioned above.