Effects of Mg²⁺ and ATP on YOYO-1 labeling of genomic DNA in single molecule experiments.

ABSTRACT: Nanofluidic channels have emerged as a suitable tool to study DNA-protein interactions. Many DNA-interacting proteins require ATP to fully function and use Mg²⁺ as a cofactor. Mg²⁺ and ATP are however also known to influence the binding of dyes, such as the commonly used YOYO-1, to DNA. This study investigates the effects of Mg²⁺ ions and ATP on YOYO-1 labeled genomic DNA and shows, via single molecule experiments in nanochannels, that Mg²⁺ reduces the fluorescence intensity of YOYO-1 labeled DNA, as well as the extension of the DNA, at both low and high dye loadings. When combined, ATP counteracts the loss of fluorescence caused by Mg²⁺, but only at comparable concentrations. Additionally, while increasing the photobleaching rate, Mg<

SUBMITTER: Moller C 

PROVIDER: S-EPMC12455114 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature