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Related Concept Videos

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Single-Strand DNA Binding Proteins

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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In structural engineering, the stability of columns under compressive axial loads is a critical consideration, described as buckling. A typical example involves a column PQ, which is pin-connected at both ends and subjected to a centric axial load F applied at one end, with a reaction force of F' = -F at the other end. Here, it is crucial to understand that when an applied load exceeds the critical load, buckling occurs as the system becomes unstable.
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Studying DNA Looping by Single-Molecule FRET
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Euler buckling and nonlinear kinking of double-stranded DNA.

Alexander P Fields1, Elisabeth A Meyer, Adam E Cohen

  • 1Biophysics Program, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA and Department of Physics, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.

Nucleic Acids Research
|August 20, 2013
PubMed
Summary

Researchers developed a molecular vise to study DNA bending stiffness. They observed Euler buckling in DNA segments, finding that salt concentration and mismatches influence DNA

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Area of Science:

  • Molecular Biology
  • Biophysics
  • Materials Science

Background:

  • The bending stiffness of double-stranded DNA (dsDNA) is crucial for its biological functions.
  • Experimental investigation of dsDNA at high curvatures has been challenging, leading to inconsistent literature findings.
  • Understanding DNA elasticity under compressive forces is essential for molecular biology and nanotechnology.

Purpose of the Study:

  • To experimentally probe the bending stiffness of dsDNA at high curvatures using a novel 'molecular vise'.
  • To investigate the phenomenon of Euler buckling in short dsDNA segments.
  • To analyze the influence of salt concentration, divalent cations, and single-nucleotide mismatches on DNA elasticity.

Main Methods:

  • Development of a 'molecular vise' utilizing base-pairing interactions to apply compressive force on dsDNA segments.
  • Monitoring Euler buckling transitions using Förster Resonance Energy Transfer (FRET) between appended fluorophores.
  • Systematic variation of monovalent salt concentrations, inclusion of Mg(2+), and introduction of single-nucleotide mismatches.

Main Results:

  • Short dsDNA segments (<41 base pairs) resisted compression, while longer segments exhibited Euler buckling.
  • Results aligned with the worm-like chain (WLC) model at low-to-moderate salt concentrations.
  • Increased salt concentrations or Mg(2+) induced an apparent softening, attributed to a kinked state, potentially locally melted, correlating with thermodynamic destabilization caused by mismatches.

Conclusions:

  • The molecular vise effectively measures sequence-dependent linear and nonlinear elastic properties of dsDNA.
  • DNA bending stiffness is modulated by ionic conditions and sequence integrity.
  • The study provides new insights into DNA mechanics at high curvature, relevant to DNA packaging and protein-DNA interactions.