Department of Biology, Institute of Resources and Environment, Henan Polytechnic University , Jiaozuo, 454000, People's Republic of China.
Beijing National Laboratory for Molecular Sciences, Key Laboratory of Analytical Chemistry for Living Biosystems, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences , Beijing, 100190, People's Republic of China.
Anal Chem. 2017 Aug 1;89(15):8162-8169. doi: 10.1021/acs.analchem.7b01992. Epub 2017 Jul 20.
Putative G-quadruplex (G4) forming sequences (PQS) are highly prevalent in the genome and transcriptome of various organisms and are considered as potential regulation elements in many biological processes by forming G4 structures. The formation of G4 structures highly depends on the sequences and the environment. In most cases, it is difficult to predict G4 formation by PQS, especially PQS containing G2 tracts. Therefore, the experimental identification of G4 formation is essential in the study of G4-related biological functions. Herein, we report a rapid and simple method for the detection of G4 structures by using a pair of complementary reporters, hemin and BMSP. This method was applied to detect G4 structures formed by PQS (DNA and RNA) searched in the genome and transcriptome of Oryza sativa. Unlike most of the reported G4 probes that only recognize part of G4 structures, the proposed method based on combined probes positively responded to almost all G4 conformations, including parallel, antiparallel, and mixed/hybrid G4, but did not respond to non-G4 sequences. This method shows potential for high-throughput identification of G4 structures in genome and transcriptome. Furthermore, BMSP was observed to drive some PQS to form more stable G4 structures or induce the G4 formation of some PQS that cannot form G4 in normal physiological conditions, which may provide a powerful molecular tool for gene regulation.
假定的 G-四链体 (G4) 形成序列 (PQS) 在各种生物体的基因组和转录组中高度普遍存在，并且被认为是通过形成 G4 结构在许多生物过程中作为潜在的调节元件。G4 结构的形成高度依赖于序列和环境。在大多数情况下，很难通过 PQS 预测 G4 的形成，尤其是含有 G2 片段的 PQS。因此，实验鉴定 G4 的形成对于研究 G4 相关的生物学功能至关重要。在此，我们报告了一种通过使用一对互补报告分子血红素和 BMSP 快速简便地检测 G4 结构的方法。该方法应用于检测在水稻基因组和转录组中搜索到的 PQS（DNA 和 RNA）形成的 G4 结构。与大多数仅识别部分 G4 结构的报道的 G4 探针不同，该基于组合探针的方法积极响应几乎所有 G4 构象，包括平行、反平行和混合/杂交 G4，但不响应非 G4 序列。该方法显示出在基因组和转录组中高通量鉴定 G4 结构的潜力。此外，观察到 BMSP 促使一些 PQS 形成更稳定的 G4 结构，或诱导在正常生理条件下不能形成 G4 的一些 PQS 形成 G4，这可能为基因调控提供了一种强大的分子工具。
