Duplex DNA Is Weakened in Nanoconfinement.

Area of Science:

• Biophysics
• Nanotechnology
• Molecular Biology

Background:

• Nanoconfinement is known to stabilize protein and DNA secondary structures like G-quadruplexes and i-motifs.
• The behavior of the common B-DNA duplex under nanoconfinement remains largely unexplored.

Purpose of the Study:

• To investigate the folding and unfolding transitions of a B-DNA duplex hairpin within a DNA origami nanocavity.
• To compare the mechanical and thermodynamic stabilities of DNA hairpins in free solution versus nanoconfined environments.

Main Methods:

• Utilized a 17-bp DNA duplex in a hairpin stem configuration.
• Employed a DNA origami nanocavity with a 15 × 15 nm cross section for confinement.
• Analyzed folding/unfolding transitions and free energy profiles.

Main Results:

• DNA hairpin stability significantly decreased inside the nanocavity (mechanical: 20 → 9 pN; thermodynamic: 25 → 6 kcal/mol).
• Activation energy for unzipping reduced dramatically (28 → 8 kcal/mol), with the transition state shifting closer to the unfolded state.
• In DNA hairpins with sequences favoring G-quadruplex (GQ) or i-motif (iM) formation, Hoogsteen base pairing was preferred over Watson-Crick base pairing.

Conclusions:

• Nanoconfinement unexpectedly weakens the stability of B-DNA duplex hairpins.
• The findings illuminate DNA behavior in nanochannels and nanopores, relevant to biological and synthetic systems.
• Suggests nanoconfinement can promote noncanonical DNA structures over B-DNA in cellular environments abundant with nanocavities.