Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Life Sciences, Linyi University, Linyi 276005, P. R. China.
Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China.
ACS Sens. 2021 Jul 23;6(7):2691-2699. doi: 10.1021/acssensors.1c00712. Epub 2021 Jul 8.
i-Motifs are DNA secondary structures present in cytosine-rich sequences. These structures are formed in regulatory regions of the human genome and play key regulatory roles. The investigation of sequences capable of forming i-motif structures at the single-molecule level is highly important. In this study, we used α-hemolysin nanopores to systematically study a series of DNA sequences at the nanometer scale by providing structure-dependent signature current signals to gain in-sights into the i-motif DNA sequence and structural stability. Increasing the length of the cytosine tract in a range of 3-10 nucleobases resulted in a longer translocation time through the pore, indicating improved stability. Changing the loop sequence and length in the sequences did not affect the formation of the i-motif structure but changed its stability. Importantly, the application of all-atom molecular dynamics simulations revealed the structural morphology of all sequences. Based on these results, we postulated a folding rule for i-motif formation, suggesting that thousands of cytosine-rich sequences in the human genome might fold into i-motif structures. Many of these were found in locations where structure formation is likely to play regulatory roles. These findings provide insights into the application of nanopores as a powerful tool for discovering potential i-motif-forming sequences and lay a foundation for future studies exploring the biological roles of i-motifs.
i- 基序是存在于富含胞嘧啶序列中的 DNA 二级结构。这些结构形成于人类基因组的调控区域，发挥着关键的调控作用。在单细胞水平上对能够形成 i- 基序结构的序列进行研究具有重要意义。在这项研究中，我们使用 α- 溶血素纳米孔，通过提供结构依赖性的特征电流信号，在纳米尺度上系统地研究了一系列 DNA 序列，从而深入了解 i- 基序 DNA 序列和结构稳定性。在 3-10 个核碱基范围内增加胞嘧啶链的长度，会导致通过孔的迁移时间延长，表明稳定性提高。改变序列中的环序列和长度不会影响 i- 基序结构的形成，但会改变其稳定性。重要的是，全原子分子动力学模拟的应用揭示了所有序列的结构形态。基于这些结果，我们提出了 i- 基序形成的折叠规则，表明人类基因组中数千个富含胞嘧啶的序列可能折叠成 i- 基序结构。其中许多序列位于结构形成可能发挥调控作用的位置。这些发现为纳米孔作为发现潜在 i- 基序形成序列的有力工具提供了新的见解，并为未来探索 i- 基序的生物学作用的研究奠定了基础。
