Rupture force between the third strand and the double strand within a triplex DNA

Area of Science:

• Molecular Biology
• Biophysics
• Nanotechnology

Background:

• DNA can form complex structures beyond the canonical double helix.
• Triplex DNA, involving three strands, presents unique structural and functional properties.
• Understanding the mechanical stability of DNA structures is crucial for molecular engineering and biological insights.

Purpose of the Study:

• To quantify the rupture force required to separate the third strand from duplex DNA in a triplex structure.
• To investigate the mechanical properties and stability of DNA triplexes using atomic force spectroscopy.
• To explore the thermal dissociation process of DNA triplexes.

Main Methods:

• Functionalization of atomic force microscopy (AFM) tip and sample surfaces with specific oligodeoxyribonucleotides.
• Formation of DNA duplexes on the sample surface followed by triplex formation under specific pH and ionic conditions.
• Measurement of rupture forces using AFM force-distance curves and analysis of rupture force histograms.

Main Results:

• Observed distinct signals for single and multiple triplex DNA rupture events.
• Determined a rupture force of 42.6 ± 1.9 pN for separating the third strand from duplex DNA at a tip velocity of 400 nm/s.
• Demonstrated that the rupture force exhibits velocity dependence, characteristic of a thermal dissociation process.

Conclusions:

• The mechanical stability of DNA triplexes can be accurately measured using AFM.
• The rupture force of triplex DNA is comparable to that of double-stranded DNA, suggesting similar dissociation mechanisms.
• The formation and rupture of triplex DNA can be controlled by adjusting oligonucleotide concentrations, offering potential for molecular manipulation.