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

Area of Science:

• Biophysics
• Molecular Biology
• Genetics

Background:

• G-rich DNA sequences are known to form G-quadruplex structures in the presence of cations.
• The conformational changes of DNA can influence its physical properties and interactions with dyes.

Purpose of the Study:

• To investigate the effect of potassium ion (K+) concentration on the structural and fluorescent properties of short G-rich DNA.
• To analyze the diffusion coefficient and fluorescence intensity of TAMRA-labeled G-rich DNA using fluorescence correlation spectroscopy.

Main Methods:

• Utilized fluorescence correlation spectroscopy (FCS) to study short G-rich DNA (G3T1)4 labeled with TAMRA.
• Varied the K+ ion concentration to observe conformational changes and their impact on DNA diffusion and fluorescence.

Main Results:

• G-rich DNA transitioned from single-strand to G-quadruplex structure at K+ concentrations > 200 mM.
• G-quadruplex formation resulted in an 86% size reduction compared to single-strand DNA at 0 M K+.
• DNA size and TAMRA fluorescence intensity remained constant between 200-800 mM K+, indicating stability of the G-quadruplex-dye complex.

Conclusions:

• The G-quadruplex structure and TAMRA fluorescence are stable in K+ concentrations ranging from 200 to 800 mM.
• The binding of TAMRA to DNA is stable at K+ concentrations below 100 mM, contributing to consistent fluorescence.
• Findings provide a basis for analyzing longer G-rich DNA structures and dye variations.