Hydrogen Exchange Study of DNA Duplexes Containing the Consensus Binding Site for Arabidopsis thaliana SPL14 Transcription Factor

Abstract

To understand the DNA binding mechanism ofAtSPL14 protein, the imino proton exchange rates weremeasured for the DNA duplex containing the consensusDNA-binding site for the AtSPL14 transcription factor(referred to as wt-SPL14 duplex, Fig. 1). To further under-stand the correlation between the base pair stability/dynamicsand DNA binding affinity of the AtSPL14, the exchange rateconstants of the imino protons for the wt-SPL14 duplexwere compared with those of the mutant SPL14 duplexes(see Fig. 1), which display different binding affinities forAtSPL14 protein. Experimental SectionAll DNA oligonucleotides were purchased from M-bio-tech Co. (Seoul, Korea). The oligonucleotides were purifiedby reverse-phase HPLC and desalted by Sephadex G-25 column.DNA duplexes were prepared by dissolving two strands at a1:1 stoichiometric ratio in an NMR buffer (90% H