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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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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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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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Probing helical transitions in a DNA duplex.

Debayan Chakraborty1, David J Wales1

  • 1Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, UK. dc550@cam.ac.uk dw34@cam.ac.uk.

Physical Chemistry Chemical Physics : PCCP
|December 13, 2016
PubMed
Summary

The B-DNA to Z-DNA transition involves helix-handedness inversion. This study maps the energy landscape to reveal two pathways for this complex DNA conformational change.

Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Chemistry

Background:

  • The transition between B-DNA and Z-DNA forms is a complex conformational change involving helix-handedness inversion.
  • Understanding this transition is crucial for comprehending DNA dynamics and function.
  • Previous studies faced challenges in defining reaction coordinates for this multi-degree-of-freedom process.

Purpose of the Study:

  • To investigate the B-DNA to Z-DNA transition using a potential energy landscape approach.
  • To construct a kinetic transition network for the B-DNA to Z-DNA conformational change.
  • To provide microscopic insights into the mechanisms and kinetics of the B-DNA to Z-DNA transition.

Main Methods:

  • Utilized a potential energy landscape perspective to map the conformational space.

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  • Constructed a kinetic transition network based on local minima and transition states.
  • Analyzed geometrically defined discrete paths connecting different DNA conformations.

    • Main Results:

    • Identified two competing mechanisms for helix-handedness inversion: one involving stretched intermediates and another involving a B-Z junction.
    • The free energy landscape suggests the B-DNA to Z-DNA transition is slow under physiological conditions.
    • Provided detailed microscopic insights into the B-DNA to Z-DNA transition pathways.

    Conclusions:

    • The B-DNA to Z-DNA transition can proceed through distinct mechanistic pathways.
    • The kinetics of the B-DNA to Z-DNA transition are likely slow in cellular environments.
    • This work provides a foundation for further studies on factors influencing the B-DNA to Z-DNA landscape, such as ionic strength and supercoiling.