Correlation of local effects of DNA sequence and position of β-alanine inserts with polyamide-DNA complex binding affinities and kinetics.

In order to better understand the effects of β-alanine (β) substitution and the number of heterocycles on DNA binding affinity and selectivity, the interactions of an eight-ring hairpin polyamide (PA) and two β derivatives as well as a six-heterocycle analog have been investigated with their cognate DNA sequence, 5′-TGGCTT-3′. Binding selectivity and the effects of β have been investigated with the cognate and five mutant DNAs. A set of powerful and complementary methods have been employed for both energetic and structural evaluations: UV-melting, biosensor-surface plasmon resonance, isothermal titration calorimetry, circular dichroism and a DNA ligation ladder global structure assay. The reduced number of heterocycles in the six-ring PA weakens the binding affinity; however, the smaller PA aggregates significantly less than the larger PAs, and allows us to obtain the binding thermodynamics. The PA-DNA binding enthalpy is large and negative with a large negative ΔCp, and is the primary driving component of the Gibbs free energy. The complete SPR binding results clearly show that β substitutions can substantially weaken the binding affinity of hairpin PAs in a position-dependent manner. More importantly, the changes in PA binding to the mutant DNAs further confirm the position-dependent effects on PA-DNA interaction affinity. Comparison of mutant DNA sequences also shows a different effect in recognition of T•A versus A•T base pairs. The effects of DNA mutations on binding of a single PA as well as the effects of the position of β substitution on binding tell a clear and very important story about sequence dependent binding of PAs to DNA.

为了更好地理解β - 丙氨酸（β）取代以及杂环数量对DNA结合亲和力和选择性的影响，我们研究了一种八环发夹聚酰胺（PA）、两种β衍生物以及一种六杂环类似物与它们的同源DNA序列5′ - TGGCTT - 3′之间的相互作用。通过同源DNA和五种突变DNA研究了结合选择性以及β的影响。我们采用了一系列强大且互补的方法进行能量和结构评估：紫外熔解、生物传感器 - 表面等离子体共振、等温滴定量热法、圆二色性以及DNA连接梯状全局结构测定。六环PA中杂环数量的减少削弱了结合亲和力；然而，较小的PA聚集程度明显低于较大的PA，这使我们能够获得结合热力学数据。PA - DNA结合焓很大且为负值，同时具有较大的负ΔCp，是吉布斯自由能的主要驱动成分。完整的表面等离子体共振结合结果清楚地表明，β取代能够以位置依赖的方式大幅削弱发夹PA的结合亲和力。更重要的是，PA与突变DNA结合的变化进一步证实了对PA - DNA相互作用亲和力的位置依赖效应。突变DNA序列的比较还显示了在识别T•A与A•T碱基对方面的不同影响。DNA突变对单个PA结合的影响以及β取代位置对结合的影响，清晰且非常重要地揭示了PA与DNA的序列依赖结合情况。