STUDY OF THE SECONDARY STRUCTURE OF A SIN GLE-STRANDED-DNA FRAGMENT BY THE USE OF A SELFMODIFICATION REACTION

Electrophoretic analysis of the products of chemical destruction at mo dified base residues was used to determine the site-directedness of se lfalkylation of the 26-mer DNA fragment pTTGCCTTGAATGGGAAGAGGGTCATT (T 26). This fragment possesses a 4-[N-methyl-N-(2-chloroethyl)amino]benz ylamido group (ClR-), covalently attached to the S-terminal phosphate group both in the presence and in the absence of the oligonucleotide e ffector (Phn-L)pTGACCCTCp(L-Phn), where Phn is an N-(2-hydroxyethyl)ph enazinium residue and L is an ethylenediamine linker. Molecular modeli ng with the method of molecular mechanics/dynamics (MM/D) was used to investigate the secondary structure of the ClR-T26 conjugate and to in terpret the change of the alkylation site upon treatment with ClR-T26 in the presence of an effector.