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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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The DNA Replication Fork01:02

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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...
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DNA Replication02:40

DNA Replication

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DNA replication involves the separation of the two strands of the double helix, with each strand serving as a template from which the new complementary strand is copied.  After replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. This is known as semiconservative replication. The resulting DNA molecules have the same sequence and are divided equally into the two daughter cells.
Replication in Prokaryotes
DNA replication...
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Lagging Strand Synthesis01:59

Lagging Strand Synthesis

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During replication, the complementary strands in double-stranded DNA are synthesized at different rates. Replication first begins on the leading strand. Replication starts later, occurs more slowly, and proceeds discontinuously on the lagging strand.
There are several major differences between synthesis of the leading strand and synthesis of the lagging strand. 1) Leading strand synthesis happens in the direction of replication fork opening, whereas lagging strand synthesis happens in the...
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Chromosome Replication02:31

Chromosome Replication

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Before a cell can divide, it must accurately replicate all of its chromosomes, including the DNA and its associated histone and non-histone proteins.  This process begins at numerous origins of replication during the S phase of the cell cycle in each of a cell’s chromosomes simultaneously. Certain nucleotides can act as origins of replication, but these sequences are not well defined - especially in complex, multi-cellular, eukaryotic species. The length of DNA that spans an origin...
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Replication in Eukaryotes02:31

Replication in Eukaryotes

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Visualizing Single-molecule DNA Replication with Fluorescence Microscopy
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DNA replication: In vitro single-molecule manipulation data analysis and models.

Javier Jarillo1, Borja Ibarra2, Francisco Javier Cao-García2,3

  • 1University of Namur, Institute of Life-Earth-Environment, Namur Center for Complex Systems, Rue de Bruxelles 61, 5000 Namur, Belgium.

Computational and Structural Biotechnology Journal
|July 21, 2021
PubMed
Summary

Single-molecule techniques offer new insights into DNA replication, a vital cell cycle process. This review details methods for analyzing DNA polymerase and helicase kinetics, enhancing our understanding of DNA replication mechanisms.

Keywords:
DNA polymeraseDNA replicationDNA unwindingHelicaseReal-time kineticsSingle-molecule

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Biophysics

Background:

  • DNA replication is a fundamental cellular process essential for cell division and genetic stability.
  • Ensemble studies have limitations in capturing the dynamic and heterogeneous nature of DNA replication.
  • Single-molecule techniques provide unprecedented resolution for studying molecular mechanisms.

Purpose of the Study:

  • To introduce and review essential techniques for analyzing and modeling in vitro single-molecule DNA replication data.
  • To facilitate the understanding and application of these methods for studying DNA replication.
  • To promote the use of single-molecule approaches in nucleic acid metabolism research.

Main Methods:

  • Review of established and adaptable techniques for single-molecule manipulation and data analysis.
  • Focus on methods for real-time kinetic analysis of DNA polymerase and DNA helicase.
  • Discussion of modeling approaches for interpreting single-molecule data.

Main Results:

  • Single-molecule analysis provides detailed insights into kinetics rates, equilibrium constants, and conformational changes.
  • The reviewed techniques enable a deeper understanding of replisome motor function.
  • These methods are applicable to studying other nucleic acid-processing proteins.

Conclusions:

  • Proper analysis of single-molecule data is critical for a comprehensive understanding of DNA replication.
  • The presented techniques are valuable tools for advancing the study of DNA replication and related processes.
  • This work aims to broaden the accessibility and application of single-molecule biophysics in molecular biology.