Sequence Specificity Of Reaction Research Articles

Locating cobalt-binding sites on dna using restriction endonucleases

The interactions of simple metal complexes with DNA have been widely studied. The interaction specificities of these molecules range from simple outside binding, such as observed with [Co(NH 3 ) 6 ] 3+ , to covalent binding as observed with Pt(NH 3 ) 2 Cl 2 , to reactions involving DNA oxidative cleavage through Fenton or related chemistries. One important feature of such interactions, especially those leading to covalent binding, is the sequence specificity of the reaction. This chapter presents a facile and fast method that can be employed to assess the sequence specificity of a ligand's reaction with DNA. Although the reagent used here covalently binds to DNA, this method should also work for reversible interactions as well, as long as the ligand has a high affinity for the DNA. To assess the sequence specificity, if any, of the reaction of [Co(NH 3 ) 5 (OH 2 )] 3+ with DNA, a series of four different model DNA oligomers was synthesized and treated with the cobalt complex according to established protocols. Each oligomer is self-complementary and possesses a unique restriction endonuclease site containing one or two G bases. A thermodynamic approach was used to assess the sequence specificity of the interaction. To summarize the results of these studies, each oligomer was incubated with [Co(NH 3 ) 5 (OH 2 )] 3+ and then exhaustively dialyzed to remove nonspecifically bound cobalt complex.

Hybrid molecules containing propargylic sulfones and DNA minor groove-binding lexitropsins: synthesis, sequence specificity of reaction with DNA and biological evaluation.

A series of hybrids, 4-13, incorporating propargylic sulfones and minor groove-binding oligopeptide carriers, was synthesized. The anticipated preferential binding at adenine sites within the minor groove was confirmed by sequencing determination of these agents on high-resolution gels, indicating preferential alkylation at guanine, and significantly, high selectivity for 5'-GACG and 5'-GGTG. The ability of these hybrids to cleave DNA, as determined by agarose-gel assay, is consistent with the ethidium bromide fluorescence assay. The cytotoxicities of these compounds were also determined against human KB cells in vitro. Higher cytotoxic activities were observed for the compounds containing fewer N-methylpyrrole units, an imidazole group and a 2,3-disubstituted naphthyl moiety.