Selective Recognition and Ultra-Sensitive Detection of i-Motif DNA Using a Novel Fluorescent Probe with PCA-Enhanced...

Area of Science:

• Molecular Biology
• Biochemistry
• Chemical Biology

Background:

• Noncanonical nucleic acid structures like i-motifs (iM) play roles in gene regulation and disease.
• Limited availability of selective ligands and fluorescent probes hinders iM structure studies.
• Understanding iM dynamics is crucial for their potential biomedical applications.

Purpose of the Study:

• To introduce BT-Cy-1, a novel fluorescent probe for selective i-motif recognition.
• To enable ultrasensitive detection and quantification of i-motif DNA structures in vitro.
• To establish a platform for studying noncanonical DNA structures and their relevance.

Main Methods:

• Development of a novel fluorescent probe, BT-Cy-1.
• Utilized multichannel fluorescence response and principal component analysis for DNA structure discrimination.
• Assessed probe performance in diluted fetal bovine serum for biological relevance.

Main Results:

• BT-Cy-1 selectively recognizes and detects i-motif structures with high sensitivity (detection limit of 3.77 nM).
• Principal component analysis of fluorescence data enables reliable discrimination between i-motifs and other DNA structures (G-quadruplexes, dsDNA, ssDNA).
• The probe maintains structural discrimination and detection sensitivity in a biological matrix (fetal bovine serum).

Conclusions:

• BT-Cy-1 is a robust tool for the selective and ultrasensitive detection of i-motif DNA structures.
• The probe facilitates accurate in vitro quantification of i-motif DNA.
• This work provides a foundation for developing nucleic acid-based diagnostics and molecular recognition technologies.