Enhanced Recognition of a Herbal Compound Epiberberine by a DNA Quadruplex-Duplex Structure

作者：Xuan Zhan, L. Deng, Yun Lian, Zhiyu Shu, Yunong Xu, Xinyi Mai, Manchugondanahalli S. Krishna, Rongguang Lu, Anni Wang, Shiyao Bai, Fangyu Zhou, Chi Xiong, Yingyi Xu, Jie Ni, J. Jeya Vandana, Zi Wang, Yuqing Li, Dongmei Sun, Shaohui Huang, Jingyan Liu, Gui‐Juan Cheng, Song Wu, Ying‐Chih Chiang, Goran Stjepanović, Cheng Jiang, Yong Shao, Gang Chen · 发表于：Analytical Chemistry · 年份：2024 · DOI：10.1021/acs.analchem.4c02054 · 被引用次数：9 · 研究领域：DNA and Nucleic Acid Chemistry、RNA and protein synthesis mechanisms、Advanced biosensing and bioanalysis techniques

The small molecule epiberberine (EPI) is a natural alkaloid with versatile bioactivities against several diseases including cancer and bacterial infection. EPI can induce the formation of a unique binding pocket at the 5′ side of a human telomeric G-quadruplex (HTG) sequence with four telomeric repeats (Q4), resulting in a nanomolar binding affinity ( K D approximately 26 nM) with significant fluorescence enhancement upon binding. It is important to understand (1) how EPI binding affects HTG structural stability and (2) how enhanced EPI binding may be achieved through the engineering of the DNA binding pocket. In this work, the EPI-binding-induced HTG structure stabilization effect was probed by a peptide nucleic acid (PNA) invasion assay in combination with a series of biophysical techniques. We show that the PNA invasion-based method may be useful for the characterization of compounds binding to DNA (and RNA) structures under physiological conditions without the need to vary the solution temperature or buffer components, which are typically needed for structural stability characterization. Importantly, the combination of theoretical modeling and experimental quantification allows us to successfully engineer Q4 derivative Q4-ds-A by a simple extension of a duplex structure to Q4 at the 5′ end. Q4-ds-A is an excellent EPI binder with a K D of 8 nM, with the binding enhancement achieved through the preformation of a binding pocket and a reduced dissociation rate. The tight bin...