DNA binding site kinetics of a large antiviral polyamide

Polyamides (PAs) are powerful DNA ligands that can bind the minor groove of DNA with high affinity and specificity. While the characterization of PA-DNA behavior has focused principally on hairpin PAs 6-8 rings in size, there is increasing evidence that their behavior does not necessarily reflect the complexities that are emerging from studies of larger hairpin PAs, particularly concerning sequence mismatch tolerance and observed but unaddressed high PA-target site binding stoichiometries. To explore these complexities in more detail, kinetics studies of binding a large anti-HPV hairpin polyamide to an isolated DNA recognition site are described. Using a fluorescence assay, two distinct binding phases are observed for the first time in hairpin PA literature. PA14 concentration dependence analysis indicates that the faster binding event is diffusion-controlled; the apparent, second event is significantly slower (350-1500 fold). Both association phases are sampled in 1:1 complexes, consistent with cooperative binding of two PA molecules even under this condition. Fitting of the slow phase to a biexponential model yields two lambda(on,app) that differ by 4-5-fold, which is consistent with the high mismatch tolerance and binding site stoichiometry previously observed. A/T patterns in the recognition sequence do not affect these decay constants significantly. Dissociation decay constants are among the slowest reported for hairpin PAs (10(-3) s(-1)), independent of A/T pattern, and may point to the efficacy of PA14 as an antiviral. (C) 2021 Elsevier B.V. and Societe Francaise de Biochimie et Biologie Moleculaire (SFBBM). All rights reserved.

Automated summary

Polyamides are powerful DNA ligands that can bind DNA with high affinity and specificity. Studies on the binding kinetics of a large anti-HPV hairpin polyamide to DNA revealed two distinct binding phases, indicating high mismatch tolerance and binding site stoichiometry. This suggests the potential efficacy of polyamide as an antiviral agent.