Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA.
Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
Nucleic Acids Res. 2019 Apr 23;47(7):3295-3305. doi: 10.1093/nar/gkz135.
To modulate biological functions, G-quadruplexes in genome are often non-specifically targeted by small molecules. Here, specificity is increased by targeting both G-quadruplex and its flanking duplex DNA in a naturally occurring dsDNA-ssDNA telomere interface using polyamide (PA) and pyridostatin (PDS) conjugates (PA-PDS). We innovated a single-molecule assay in which dissociation constant (Kd) of the conjugate can be separately evaluated from the binding of either PA or PDS. We found Kd of 0.8 nM for PA-PDS, which is much lower than PDS (Kd ∼ 450 nM) or PA (Kd ∼ 35 nM). Functional assays further indicated that the PA-PDS conjugate stopped the replication of a DNA polymerase more efficiently than PA or PDS. Our results not only established a new method to dissect multivalent binding into actions of individual monovalent components, they also demonstrated a strong and specific G-quadruplex targeting strategy by conjugating highly specific duplex-binding molecules with potent quadruplex ligands.
为了调节生物功能，基因组中的 G-四链体经常被小分子非特异性靶向。在这里，通过使用聚酰胺（PA）和吡啶硫酮（PDS）缀合物（PA-PDS）在天然存在的双链 DNA-单链 DNA 端粒界面上靶向 G-四链体及其侧翼双链 DNA，提高了特异性。我们创新了一种单分子测定法，其中可以分别从 PA 或 PDS 的结合中评估缀合物的离解常数（Kd）。我们发现 PA-PDS 的 Kd 为 0.8 nM，远低于 PDS（Kd ∼ 450 nM）或 PA（Kd ∼ 35 nM）。功能测定进一步表明，PA-PDS 缀合物比 PA 或 PDS 更有效地阻止 DNA 聚合酶的复制。我们的结果不仅建立了一种将多价结合分解为单价成分作用的新方法，还通过将高度特异性的双链结合分子与有效的四链配体缀合，展示了一种强特异性 G-四链体靶向策略。
