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Related Concept Videos

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.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...

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Related Experiment Video

Updated: Jun 27, 2026

Studying DNA Looping by Single-Molecule FRET
11:27

Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

DNA Cut-Ligation Cyclization Surpasses Jacobson-Stockmayer J-Factor Expectations by over Threefold.

Roman Teo Oliynyk1,2, George M Church1,3

  • 1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

Biomolecules
|June 26, 2026
PubMed
Summary
This summary is machine-generated.

Researchers exceeded the long-standing physical limit on DNA cyclization efficiency using simultaneous restriction cutting and ligation. This breakthrough in molecular biology offers new enzyme systems for DNA circularization.

Keywords:
BsaIJ-factorJacobson–StockmayerT4 DNA ligaseT5 exonucleasecircularizationcyclizationefficiencytype IIs restriction enzyme

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Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
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Last Updated: Jun 27, 2026

Studying DNA Looping by Single-Molecule FRET
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Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae
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Detection of Homologous Recombination Intermediates via Proximity Ligation and Quantitative PCR in Saccharomyces cerevisiae

Published on: September 11, 2022

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • The Jacobson-Stockmayer J-factor has historically defined the physical limit for DNA cyclization efficiency.
  • Exceeding this limit is crucial for advancements in synthetic biology and genetic engineering.

Purpose of the Study:

  • To investigate methods for surpassing the established J-factor limit in DNA cyclization.
  • To identify and characterize enzyme systems capable of high-efficiency DNA circularization.

Main Methods:

  • Utilized simultaneous restriction cutting and ligation with Type IIS enzyme BsaI-HFv2 and T4 DNA ligase.
  • Experimentally determined circularization efficiency at a concentration of 120 ng/μL for 452 bp minicircles.
  • Calibrated the J-factor using DNA with pre-cut and purified overhangs to compare experimental results with theoretical predictions.

Main Results:

  • Achieved 75% circularization efficiency, significantly exceeding classical theoretical expectations.
  • Demonstrated that cut-ligation with BsaI-HFv2 enhances efficiency by 3.4-fold compared to theoretical J-factor values.
  • Identified potential mechanisms for enhanced performance with additional enzymes like Esp3I and BbsI.

Conclusions:

  • The study demonstrates biological mechanisms that can dramatically increase effective local DNA concentration, surpassing free-diffusion expectations.
  • Established a novel method that exceeds the long-standing theoretical limitations on DNA cyclization by over threefold.
  • Paves the way for discovering new enzyme systems that significantly improve DNA circularization efficiency.