Nucleotide sequence-dependent opening of double-stranded DNA at an electrically charged surface

Area of Science:

• Electrochemistry
• Biophysics
• Molecular Biology

Background:

• DNA double helix stability is crucial for biological processes.
• Electrode surfaces can influence DNA structure.
• Previous studies indicated DNA unwinding at mercury electrodes.

Purpose of the Study:

• To investigate the interaction of synthetic DNA with mercury electrodes.
• To compare DNA double helix opening in alternating sequences versus homopolymer pairs.
• To understand the role of nucleotide sequence in DNA unwinding at charged surfaces.

Main Methods:

• Electrochemical analysis of synthetic polynucleotides (poly(dA-dT).poly(dA-dT), poly(dA-dU).poly(dA-dU), poly(dG-dC).poly(dG-dC), poly(dA).poly(dT), poly(rA).poly(rU), poly(dG).poly(dC)) at a hanging mercury drop electrode.
• Monitoring changes in polynucleotide reducibility to detect double helix opening.
• Analyzing the potential range and rate of DNA unwinding.

Main Results:

• Polynucleotides with alternating sequences showed a narrow potential range (region U) for double helix opening, unlike natural DNA.
• Homopolymer pairs exhibited a broader region U, comparable to natural DNA, but with two distinct phases.
• Poly(dG).poly(dC) did not show a region U.
• The rate of DNA unwinding was highly potential-dependent for alternating sequences but less so for homopolymer pairs.
• Differences in base pair adsorption were proposed as the cause for varied unwinding behaviors.

Conclusions:

• The nucleotide sequence significantly influences DNA double helix opening at charged surfaces.
• Mercury electrodes serve as effective models for biological surfaces like membranes.
• Electrically charged surfaces may play a role in biological processes through sequence-dependent DNA unwinding.