Minor-groove binding hairpin polyamides (PAs) bind specific DNA sequences. Synthetic modifications can improve PA–DNA binding affinity and include flexible modules, such as β-alanine (β) motifs to replace pyrroles (Py), and increasing compound charge using N-terminal cationic substituents. To better understand the variations in kinetics and affinities caused by these modifications on PA–DNA interactions, a comprehensive set of PAs with different numbers and positions of β and different types of N-cationic groups was systematically designed and synthesized to bind their cognate sequence, the λB motif. The λB motif is also a strong binding promoter site of the major groove targeting transcription factor PU.1. The PA binding affinities and kinetics were evaluated using a spectrum of powerful biophysical methods: thermal melting, biosensor surface plasmon resonance and circular dichroism. The results show that β inserts affect PA–DNA interactions in a number and position dependent manner. Specifically, a β replacement between two imidazole heterocycles (ImβIm) generally strengthens binding. In addition, N-terminal cationic groups can accelerate the association between PA and DNA, but the bulky size of TMG can cause steric hindrance and unfavourable repulsive electrostatic interactions in some PAs. The future design of stronger binding PA requires careful combination of βs and cationic substituents.

中文翻译：

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β-丙氨酸和N端阳离子取代基会影响聚酰胺与DNA的结合

小沟结合发夹聚酰胺（PAs）结合特定的DNA序列。合成修饰可以提高PA-DNA的结合亲和力，并包括灵活的模块，例如β-丙氨酸（β）图案来取代吡咯（Py），并使用N端阳离子取代基增加化合物电荷。为了更好地理解由于这些修饰对PA-DNA相互作用而引起的动力学和亲和力变化，我们提供了一整套具有不同数量和位置的β和不同类型N的PA对阳离子基团进行了系统地设计和合成，以结合其同源序列λB基序。λB基序也是主要凹槽靶向转录因子PU.1的强结合启动子位点。使用一系列强大的生物物理方法（热熔，生物传感器表面等离振子共振和圆二色性）评估了PA的结合亲和力和动力学。结果表明，β插入片段以数量和位置相关的方式影响PA-DNA的相互作用。具体而言，两个咪唑杂环（ImβIm）之间的β取代通常会增强结合。此外，N端阳离子基团可以促进PA和DNA之间的缔合，但是TMG的庞大尺寸会在某些PA中引起位阻和不利的排斥静电相互作用。