Shim Ji Wook, Tan Qiulin, Gu Li-Qun
Department of Biological Engineering, Dalton Cardiovascular Research Center, University of Missouri, Columbia, MO, USA.
Nucleic Acids Res. 2009 Feb;37(3):972-82. doi: 10.1093/nar/gkn968. Epub 2008 Dec 26.
Guanine-rich nucleic acids can form G-quadruplexes that are important in gene regulation, biosensor design and nano-structure construction. In this article, we report on the development of a nanopore encapsulating single-molecule method for exploring how cations regulate the folding and unfolding of the G-quadruplex formed by the thrombin-binding aptamer (TBA, GGTTGGTGTGGTTGG). The signature blocks in the nanopore revealed that the G-quadruplex formation is cation-selective. The selectivity sequence is K(+) > NH(4)(+) approximately Ba(2+) > Cs(+) approximately Na(+) > Li(+), and G-quadruplex was not detected in Mg(2+) and Ca(2+). Ba(2+) can form a long-lived G-quadruplex with TBA. However, the capability is affected by the cation-DNA interaction. The cation-selective formation of the G-quadruplex is correlated with the G-quadruplex volume, which varies with cation species. The high formation capability of the K(+)-induced G-quadruplex is contributed largely by the slow unfolding reaction. Although the Na(+)- and Li(+)-quadruplexes feature similar equilibrium properties, they undergo radically different pathways. The Na(+)-quadruplex folds and unfolds most rapidly, while the Li(+)-quadruplex performs both reactions at the slowest rates. Understanding these ion-regulated properties of oligonucleotides is beneficial for constructing fine-tuned biosensors and nano-structures. The methodology in this work can be used for studying other quadruplexes and protein-aptamer interactions.
富含鸟嘌呤的核酸可形成G-四链体，这在基因调控、生物传感器设计和纳米结构构建中具有重要意义。在本文中，我们报道了一种纳米孔包裹单分子方法的进展，用于探究阳离子如何调节由凝血酶结合适体（TBA，GGTTGGTGTGGTTGG）形成的G-四链体的折叠与解折叠。纳米孔中的特征性阻断表明G-四链体的形成具有阳离子选择性。选择性顺序为K(+) > NH(4)(+) ≈ Ba(2+) > Cs(+) ≈ Na(+) > Li(+)，在Mg(2+)和Ca(2+)中未检测到G-四链体。Ba(2+)可与TBA形成寿命较长的G-四链体。然而，这种能力受阳离子与DNA相互作用的影响。G-四链体的阳离子选择性形成与G-四链体体积相关，而G-四链体体积随阳离子种类而变化。K(+)诱导的G-四链体的高形成能力在很大程度上归因于缓慢的解折叠反应。尽管Na(+)和Li(+)的四链体具有相似的平衡性质，但它们经历的途径截然不同。Na(+)的四链体折叠和解折叠最快，而Li(+)的四链体进行这两种反应的速率最慢。了解寡核苷酸的这些离子调节特性有助于构建微调的生物传感器和纳米结构。这项工作中的方法可用于研究其他四链体以及蛋白质与适体的相互作用。
