Negative DNA supercoiling makes protein-mediated looping deterministic and ergodic within the bacterial doubling time

Area of Science:

• Molecular Biology
• Genetics
• Biophysics

Background:

• Protein-mediated DNA looping is crucial for gene regulation.
• In purified systems, DNA looping occurs stochastically with broad probability distributions.
• Existing proteins can increase looping probability but do not narrow the distribution.

Purpose of the Study:

• To investigate the role of DNA supercoiling in modulating stochastic DNA looping.
• To determine if DNA supercoiling can impose emergent, time-constrained behavior on molecular looping.
• To understand how DNA supercoiling impacts the distribution of looping probabilities.

Main Methods:

• Studied lac repressor-mediated DNA looping in individual molecules.
• Utilized HU protein to compact DNA and analyzed looping probability distributions.
• Applied increased negative supercoiling to DNA molecules.
• Observed molecular behavior over time to assess emergent properties.

Main Results:

• Individual DNA looping probabilities ranged from 0-100% in purified systems.
• HU protein compacted DNA but did not narrow the looping probability distribution.
• Increased negative supercoiling led to individual molecules resembling the ensemble average.
• Within 12 minutes, most molecules exhibited ensemble looping probability under supercoiling.

Conclusions:

• DNA supercoiling, a genomic feature, imposes time-constrained, emergent behavior on random DNA looping.
• Supercoiling ensures that molecular activity aligns with ensemble behavior within biologically relevant timescales.
• This finding has implications for understanding gene regulation dynamics in vivo.