Molecular Crowding Suppresses Mechanical Stress-Driven DNA Strand Separation

Area of Science:

• Biophysics
• Molecular Biology
• Genetics

Background:

• Molecular crowding is prevalent in cells and influences DNA mechanics.
• Understanding DNA supercoiling under crowding conditions is key to bridging in vitro and in vivo findings.

Purpose of the Study:

• To quantify the effects of molecular crowding on DNA supercoiling using single-molecule techniques.
• To investigate how different co-solutes alter DNA supercoiling behavior.

Main Methods:

• Utilized single-molecule magnetic tweezers to apply stretching force and induce DNA supercoiling.
• Studied DNA supercoiling in buffers with and without crowding co-solutes like glycerol and polyethylene glycol (PEG).

Main Results:

• In standard buffer, negatively supercoiled DNA forms locally melted regions.
• Glycerol destabilizes base pairs in negatively supercoiled DNA.
• Polyethylene glycol suppresses local strand separation, leading to plectoneme formation even under negative supercoiling.

Conclusions:

• Crowding agents significantly alter DNA supercoiling mechanisms.
• Polyethylene glycol's effect on DNA supercoiling is distinct from dehydrating agents like glycerol.
• Findings provide insights into DNA behavior in conditions mimicking the cellular environment.