Comparative evaluation and design of a G-triplex/thioflavin T-based molecular beacon

Area of Science:

• Biochemistry
• Molecular Biology
• Analytical Chemistry

Background:

• G-quadruplex (G4) and G-triplex (G3) DNA structures exhibit unique binding affinities.
• Thioflavin T (ThT) is a fluorescent dye that can interact with G4 and G3 structures.
• Label-free molecular beacons (MBs) can be constructed using G4/ThT or G3/ThT interactions.

Purpose of the Study:

• To comparatively evaluate G3/ThT-based MBs and G4/ThT-based MBs.
• To investigate the structural parameters influencing G3/ThT-based MB performance.
• To propose an optimized design for G3/ThT-based MBs.

Main Methods:

• Construction and characterization of G3/ThT and G4/ThT molecular beacons.
• Comparative analysis of sensitivity and response kinetics.
• Systematic study of stem length and base pairing variations in G3/ThT MBs.

Main Results:

• G3/ThT-based MBs demonstrated superior sensitivity and faster response times compared to G4/ThT-based MBs.
• The study identified optimal stem lengths and base pairing configurations for G3/ThT MBs.
• Shorter G3 structures were found to be more suitable for MB stem construction.

Conclusions:

• G3/ThT-based molecular beacons represent a promising platform for sensitive and rapid biosensing.
• Rational design principles for G3/ThT MBs have been established.
• This work facilitates the development of simple, homogeneous biosensing methods.