Spatial confinement induces hairpins in nicked circular DNA

Area of Science:

• Molecular Biology
• Biophysics
• Structural Biology

Background:

• DNA in living cells is densely packed via condensing agents, proteins, and supercoiling.
• The effects of spatial confinement on DNA's local structure are poorly understood due to experimental challenges.

Purpose of the Study:

• To investigate the impact of spatial confinement on the global and local conformational properties of DNA.
• To assess how confinement influences DNA structure using atomic force microscopy and numerical simulations.

Main Methods:

• High-resolution atomic force microscopy (AFM) imaging of circular DNA within well-characterized slits of varying sizes.
• Numerical simulations to support experimental findings and analyze DNA mechanical stress.

Main Results:

• Confinement induces significant mechanical stress on DNA, leading to pronounced anisotropy and altered tangent-tangent correlation functions compared to unconfined DNA.
• Strongest confinement conditions revealed nanometer-sized hairpins and interwound structures, particularly at nicked sites within the DNA sequence.

Conclusions:

• Spatial confinement of DNA imposes mechanical stress, affecting its global and local conformations.
• Confinement may promote the formation of localized DNA defects (e.g., hairpins) at mechanically vulnerable sites.
• These confinement-induced defects could play a role in in vivo biological regulatory functions.