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DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
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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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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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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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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.
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Structural basis for DNA strand separation by a hexameric replicative helicase.

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Hexameric helicases like papillomavirus E1 unwind DNA using a novel mechanism. DNA enters a side tunnel, and strand separation occurs internally, challenging existing models of DNA unwinding.

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • Biochemistry

Background:

  • Hexameric helicases are crucial for DNA replication and unwinding.
  • The precise mechanism by which these enzymes engage with replication forks remains unclear.
  • Existing models, such as 'steric exclusion,' propose external strand separation.

Purpose of the Study:

  • To elucidate the structural mechanism of hexameric helicase E1 engaging with a DNA replication fork.
  • To investigate the DNA entry and strand separation process during unwinding.
  • To challenge and refine current models of DNA unwinding by hexameric helicases.

Main Methods:

  • Electron microscopy and single particle analysis to determine structures of E1-DNA complexes.
  • Site-specific labeling of DNA replication fork with streptavidin and Fab fragments.
  • Nuclease footprinting assays to map DNA-protein interactions.

Main Results:

  • Structures revealed papillomavirus E1 helicase bound to a DNA replication fork.
  • At least 10 bp of double-stranded DNA (dsDNA) enter E1 via a side tunnel.
  • Strand separation occurs within a chamber inside the helicase, with the 5' ssDNA exiting through a separate tunnel.

Conclusions:

  • The findings propose a new model for DNA unwinding by hexameric helicases.
  • Strand separation occurs internally within the E1 helicase, contradicting the 'steric exclusion' model.
  • This study provides critical structural insights into the mechanism of DNA replication fork processing.