Nucleosome selection of minor groove binding drug sites in DNA

Abstract

Minor Groove Binding Drugs (MGBDs) have been shown to have an effect on cancerous tumors, but not enough is known about their interaction and sequence specificity within the minor groove of DNA. We have used an in vitro approach to transition to a better understanding of the in vivo behavior of MGBDs. We constructed a 146 bp library of synthetic DNA containing 12 blocks of 5 random bases and selected for the ability of sequences to bind the MGBD Hoechst 33258 during a nucleosome exchange reaction. After each generation was completed, the ability of the population to bind Hoechst was tested using fluorescence enhancement. We also conducted DNA sequencing to monitor changes in sequence composition. After seven generations, fluorescence enhancement was increased and A/T rich sequences were more prevalent in the 12 random blocks of DNA. The data support the use of the nucleosome selection protocol to discover DNA sequences that can be bound by MGBDs in the context of chromatin. This research was supported through funding from NIH Grant 1R15CA096723-01.