Programmable DNA Folding Modulates Phase Behavior and Dynamics of DNA/Peptide Condensates

Area of Science:

• Biophysics
• Molecular Biology
• Virology

Background:

• Membraneless compartments formed by liquid-liquid phase separation (LLPS) are crucial for biological processes, including viral replication.
• Nucleocapsid (NC) protein in retroviruses guides RNA folding and assembly for efficient viral particle packaging.

Purpose of the Study:

• To investigate how nucleic acid folding and structure affect LLPS.
• To determine if an HIV NC-derived peptide (HNP) can modulate LLPS through chaperone activity.

Main Methods:

• Designed a programmable single-stranded DNA (ssDNA) library with varying folding and palindromic architectures.
• Employed circular dichroism, FRET, SAXS, and coarse-grained simulations to analyze DNA conformations and phase behavior.
• Correlated DNA structural order and dimerization with condensate properties like viscosity.

Main Results:

• HNP interactions promote DNA folding.
• Increased DNA order suppresses LLPS, while structural disorder enhances it.
• Palindromic linkers inducing DNA dimerization increase phase separation and condensate viscosity.

Conclusions:

• Identified local structural order and palindromic dimerization as key programmable determinants of DNA/peptide condensate behavior.
• Provided mechanistic insights into viral genome organization.
• Offered principles for tuning the properties of synthetic condensates.