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Translesion DNA Polymerases02:10

Translesion DNA Polymerases

Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
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An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication forks, one in...
The DNA Replication Fork01:02

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Related Experiment Video

Updated: Jun 8, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

Protein-mediated DNA loop formation and breakdown in a fluctuating environment.

Yih-Fan Chen1, J N Milstein, Jens-Christian Meiners

  • 1Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA.

Physical Review Letters
|September 28, 2010
PubMed
Summary

Cellular environments fluctuate, impacting gene regulation. DNA loop formation, crucial for transcription, is enhanced by noise, yet mechanical tension-based gene switches show surprising robustness against these fluctuations.

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Last Updated: Jun 8, 2026

Studying DNA Looping by Single-Molecule FRET
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Published on: October 13, 2011

Area of Science:

  • Biophysics
  • Molecular Biology
  • Systems Biology

Background:

  • Living cells create dynamic, non-equilibrium environments essential for coordinating gene expression.
  • DNA looping is a key mechanism for gene regulation, inherently stochastic due to thermal motion and cellular fluctuations.

Purpose of the Study:

  • To investigate the impact of fluctuating forces, mimicking cellular environments, on DNA loop formation and breakdown.
  • To assess the robustness of DNA mechanical tension as a regulatory switch in noisy cellular conditions.

Main Methods:

  • Single-molecule measurements of DNA loop dynamics.
  • Application of artificial fluctuating forces to DNA to simulate cellular noise.

Main Results:

  • DNA loop formation is significantly enhanced by the presence of low-level noise (a fraction of k_{B}T).
  • Despite noise, regulatory mechanisms utilizing DNA mechanical tension demonstrate unexpected resilience.

Conclusions:

  • Cellular noise can amplify DNA looping, a fundamental process in gene regulation.
  • Mechanical tension-based gene regulation may possess inherent robustness against environmental fluctuations, offering a stable control mechanism.