Size matters: DNA binding site kinetics as a function of polyamide size

Hairpin polyamides (PAs) are remarkable minor groove-binding DNA ligands that demonstrate high affinity and sequence selectivity. Following extensive studies of 6-8 ring hairpin PAs have been more recent descriptions of larger PAs (14 rings or more) and their distinguishing properties and biological activities. However, there are no comparative kinetic studies of PA DNA binding behaviors over a range of PA sizes, making it difficult to understand important structure-activity relationships related to PA size. Described herein is the first comparative kinetic study as a function of hairpin PA size that examines the complexities of PA-DNA binding behaviors with unprecedented detail. DNA binding kinetics of PAs with 6 (PA6) and 20 (PA20) rings are extensively characterized by fluorescence spectroscopy, and the properties compared with those of 8 and 14 ring hairpin PAs. PA6 has a 1:1 binding site stoichiometry but exhibits biphasic association kinetics, consistent with populating more than one binding mode. One decay constant is at the diffusion controlled limit, and the other is 400-fold slower. In contrast, PA20 has high binding site stoichiometry (2.5:1) but displays a much simpler association kinetic trace with a decay constant of 1e6 M^-1s^-1. Due to the variability and complexity of association kinetics, it is difficult to identify trends in this behavior as a function of PA size. However, even though hairpin PAs of 8 or more rings bind DNA with similar affinities, residence times increase as PA size increases, ranging from 20 s to over 2500 s. Particularly compelling is that the antiviral PA20 shows little to no dissociation from DNA when challenged with competitor DNA, suggesting that high residence times are important for this biological activity.