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Related Concept Videos

The Replisome03:01

The Replisome

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DNA replication is carried out by a large complex of proteins that act in a coordinated matter to achieve high-fidelity DNA replication. Together this complex is known as the DNA replication machinery or the replisome.
The synthesis of the leading and lagging strands is a highly coordinated process. To explain this, the “Trombone model” was proposed by Bruce Alberts in 1980. The DNA loop formation starts when a primer is synthesized on the parent lagging strand. The loop grows with...
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Single-Strand DNA Binding Proteins01:03

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Nucleosome Remodeling02:54

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Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
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Translesion DNA Polymerases02:10

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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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DNA as a Genetic Template02:05

DNA as a Genetic Template

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Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
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DNA Topoisomerases02:02

DNA Topoisomerases

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Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
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Related Experiment Video

Updated: Jul 15, 2025

Studying DNA Looping by Single-Molecule FRET
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Studying DNA Looping by Single-Molecule FRET

Published on: June 28, 2014

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Current working models of SMC-driven DNA-loop extrusion.

Kyoung-Wook Moon1, Je-Kyung Ryu1

  • 1Department of Physics and Astronomy, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, South Korea.

Biochemical Society Transactions
|September 28, 2023
PubMed
Summary
This summary is machine-generated.

Structural maintenance of chromosome (SMC) proteins extrude DNA loops, but the exact mechanism remains unclear. This review examines single-molecule assays and structural studies to compare models of SMC-mediated DNA-loop extrusion.

Keywords:
Brownian-ratchet modelDNA loop extrusionDNA-segment capture/DNA pumping modelSMChold-and-feed modelscrunching model

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Author Spotlight: Investigating the Motion Dynamics of the Eukaryotic Replisome Components at the Single-Molecule Level
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Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Structural Maintenance of Chromosome (SMC) proteins are essential for organizing the genome.
  • SMC proteins are hypothesized to extrude DNA loops, a process crucial for chromosome condensation.
  • The precise molecular mechanism of SMC-mediated DNA-loop extrusion is currently debated.

Approach:

  • Review of single-molecule assays providing direct evidence for DNA-loop extrusion.
  • Analysis of recent cryo-electron microscopy (Cryo-EM) structures of SMC complexes.
  • Comparison of conserved DNA-binding sites across different SMC complexes.

Key Points:

  • ATP hydrolysis drives conformational changes in SMCs, enabling DNA-loop extrusion.
  • Cryo-EM structures reveal conserved DNA-binding interfaces critical for dynamic extrusion.
  • Four distinct working models for SMC-mediated DNA-loop extrusion are presented and discussed.

Conclusions:

  • Understanding SMC protein function is key to deciphering chromosome organization.
  • Integrating structural and single-molecule data provides insights into the ATP-dependent extrusion mechanism.
  • This review synthesizes current knowledge and highlights areas for future research into DNA-loop extrusion.