Analysis of Cation-Dependent DNA (G3T1)4 Shape Change Using Fluorescence Correlation Spectroscopy.

Abstract

In G-rich DNA, it is well known that the form changes from single-strand DNA to G-quadruplex due to cations. In this study, we analyze the diffusion coefficient and fluorescence intensity obtained by fluorescence correlation spectroscopy for short G-rich DNA of the (G3T1)4 sequence labeled as 5-Carboxytetramethylrhodamine (TAMRA) with variation of the K+ ion concentration. At a K+ ion concentration of more than 200mM, the single-strand DNA was changed to the G-quadruplex. The size of the G-quadruplex decreased to 86% than the size of the single strand DNA at K+ ion concentration of 0M. The size of the G-quadruplex and the fluorescence intensity of TAMRA attached to the DNA were constant with an increase in the K+ ion concentration between 200 and 800mM. This means that the size of the DNA and the fluorescence intensity of the TAMRA are not affected by the K+ ion concentration at the G-quadruplex structure because the binding structure of DNA and TAMRA dye leads to stability at a concentration of less than 100mM K+. Based on our short G-rich DNA results, longer G-rich DNA is analyzed for the diffusion coefficient of the DNA and the fluorescence intensity variation of fluorescence dye attached to the DNA.