Effective and selective modification of a single-stranded DNA fragment with alkylating oligonucleotide derivatives in the presence of N-(2-hydroxyethyl)phenazinium oligonucleotide derivatives as effectors

V. F. Zarytova, I. V. Kutyavin, S. V. Mamaev, M. A. Podyminogin

Institute of Bioorganic Chemistry, Siberian Division, Academy of Sciences of the USSR, Novosibirsk

Abstract: Tri-, tetra-, ponta- and hexanucleotides bearing a reactive 4-(N-methylamino-N-2-chloroethyl)benzylamide group can effectively and selectively modify a single-stranded DNA fragment (302 nucleotides) in the presence of effectors, N-(2-hydroxyethyl)phenazi-nium derivatives of oligonucleotides complementary to DNA sequences adjacent to the binding site of the reagent. The reagents investigated modify not only single-stranded but also secondary-structured DNA regions. The modification extent depends on the length of oligonucleotide parts of the reagent and effector. A gap between the two stretches associated with the target DNA prevents the effector from functioning. The substitution of an octanuclootide effector by two tetranucleotide ones only slightly reduces the modification extent with a hexanucleotide reagent. A very efficient and specific modification Can be achieved by using two effectors flanking the reactive oligonucleotide derivative. The approach leads to the modification extent of up to 89% with a hexanucleotide reagent.

Russian Journal of Bioorganic Chemistry 1990, 16 (12):1653-1660

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