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DNA Topoisomerases02:02

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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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During mitosis, chromosome movements occur through the interplay of multiple piconewton level forces. In prometaphase, these forces help in chromosome assembly or congression at the equatorial plane, eventually leading to their alignment at the metaphase plate. The forces acting on the chromosomes are space and time-dependent; therefore, they vary with the position of the chromosomes as the cell progresses through mitosis. 
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DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
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Mapping deformation dynamics to composition of topologically-active DNA blends.

Karthik R Peddireddy1, Ryan McGorty1, Rae M Robertson-Anderson1

  • 1Department of Physics and Biophysics, University of San Diego, 5998 Alcala Park, San Diego, CA 92110, USA. randerson@sandiego.edu.

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Polymer topology significantly impacts blend dynamics. Researchers found that blends with balanced circular and linear DNA, free of supercoiling, exhibit maximum strain-coupling, revealing key insights into polymer entanglement and rheology.

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Area of Science:

  • Polymer physics
  • Rheology
  • Biophysics

Background:

  • The influence of polymer topology (circular vs. linear) on blend rheology and dynamics is a long-standing research question.
  • Linear polymers typically exhibit larger coils and more entanglements than circular polymers.
  • Threading of circular polymers by linear chains can introduce constraints, altering blend mobility and rheological properties.

Purpose of the Study:

  • To experimentally map the stress response and deformation dynamics of DNA blends across a wide range of topological compositions.
  • To investigate the role of supercoiling in the behavior of circular-linear polymer blends.
  • To understand the interplay between polymer topology, entanglement, and threading propensity.

Main Methods:

  • Utilized in situ enzymatic topological conversion to create DNA blends with over 70 fractions of linear, ring, and supercoiled molecules.
  • Employed optical tweezers integrating differential dynamic microscopy (OpTiDDM) to precisely measure strain-induced deformation dynamics.
  • Quantified strain-coupling through superdiffusive dynamics aligned with applied strain.

Main Results:

  • Strain-coupling is maximized in blends with comparable fractions of ring and linear polymers, specifically when supercoiling is absent.
  • Increasing the fraction of supercoiled molecules significantly reduces strain-coupling.
  • Converting ring polymers to linear chains results in a more moderate reduction in strain-coupling compared to supercoiling.

Conclusions:

  • The observed strain-coupling is a direct result of the balance between polymer overlap and threading probability, which is influenced by topological composition.
  • Optimal strain-coupling occurs in blends with a high proportion of circular polymers and a low proportion of supercoiled molecules.
  • Enzymatic topological conversion and advanced microscopy techniques enable high-resolution mapping of polymer blend dynamics.