Department of Chemistry and Biochemistry, Nanoscale & Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701, United States.
J Phys Chem B. 2023 Mar 23;127(11):2450-2456. doi: 10.1021/acs.jpcb.3c00777. Epub 2023 Mar 14.
Single-molecule DNA studies have improved our understanding of the DNAs' structure and their interactions with other molecules. A variety of DNA labeling dyes are available for single-molecule studies, among which the bis-intercalating dye YOYO-1 and mono-intercalating dye YO-PRO-1 are widely used. They have an extraordinarily strong affinity toward DNA and are bright with a high quantum yield (>0.5) when bound to DNAs. However, it is still not clear how these dyes behave in DNA molecules under higher ionic strength and strong buffer flow. Here, we have studied the effect of ionic strength and flow rate of buffer on their binding in single DNA molecules. The larger the flow rate and the higher the ionic strength, the faster the intercalated dyes are washed away from the DNAs. In the buffer with 1 M ionic strength, YOYO-1 and YO-PRO-1 are mostly washed away from DNA within 2 min of moderate buffer flow.
单分子 DNA 研究提高了我们对 DNA 结构及其与其他分子相互作用的理解。有多种 DNA 标记染料可用于单分子研究，其中双嵌入染料 YOYO-1 和单嵌入染料 YO-PRO-1 被广泛使用。它们与 DNA 具有极强的亲和力，与 DNA 结合时非常亮，量子产率>0.5。然而，目前尚不清楚在较高离子强度和强缓冲液流动条件下，这些染料在 DNA 分子中的行为如何。在这里，我们研究了离子强度和缓冲液流速对它们在单链 DNA 分子中结合的影响。流速越大，缓冲液离子强度越高，嵌入染料从 DNA 上被洗脱的速度就越快。在离子强度为 1 M 的缓冲液中，YOYO-1 和 YO-PRO-1 在中等缓冲液流速下，2 分钟内大部分从 DNA 上被洗脱。
