Topoisomerases may unknot by recognizing specific DNA juxtapositions. The physical basis of this hypothesis is investigated by considering single-loop conformations in a coarse-grained polymer model. We determine the statistical relationship between the local geometry of a juxtaposition of two chain segments and whether the loop is knotted globally, and ascertain how the knot/unknot topology is altered by a topoisomerase-like segment passage at the juxtaposition. Segment passages at a "free" juxtaposition tend to increase knot probability. In contrast, segment passages at a "hooked" juxtaposition cause more transitions from knot to unknot than vice versa, resulting in a steady-state knot probability far lower than that at topological equilibrium. The reduction in knot population by passing chain segments through a hooked juxtaposition is more prominent for loops of smaller sizes, n, but remains significant even for larger loops: steady-state knot probability is only approximately 2%, and approximately 5% of equilibrium, respectively, for n=100 and 500 in the model. An exhaustive analysis of approximately 6000 different juxtaposition geometries indicates that the ability of a segment passage to unknot correlates strongly with the juxtaposition's "hookedness". Remarkably, and consistent with experiments on type-2 topoisomerases from different organisms, the unknotting potential of a juxtaposition geometry in our polymer model correlates almost perfectly with its corresponding decatenation potential. These quantitative findings suggest that it is possible for topoisomerases to disentangle by acting selectively on juxtapositions with "hooked" geometries.
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http://dx.doi.org/10.1016/j.jmb.2006.06.005 | DOI Listing |
Taiwan J Obstet Gynecol
January 2025
Department of Obstetrics, Fujian Maternity and Child Health Hospital, Fuzhou 350000, Fujian, China. Electronic address:
Objective: To investigate the pregnancy outcomes and independent risk factors associated with true knots of the umbilical cord (TKUC).
Materials And Methods: This retrospective study included 8140 deliveries at Fujian Maternal and Child Health Hospital from 2017 to 2021. Mothers and newborns diagnosed with TKUC were included in the TKUC group, while the others were included in the control group.
Pediatr Allergy Immunol
January 2025
EPIUnit-Institute of Public Health, University of Porto, Porto, Portugal.
Background: We aimed to investigate the association between maternal caffeine intake during pregnancy and asthma in children by 10 years of age.
Methods: We considered 5585 mother-child pairs enrolled in a population-based birth cohort. Consumption of regular and decaffeinated coffee, black and green tea, and cola beverages before and during pregnancy was obtained through face-to-face interviews within 72 h after giving birth, and total caffeine intake (mg/day) was estimated.
J Cardiovasc Surg (Torino)
December 2024
Department of Cardiovascular and Thoracic Surgery, Dijon University Hospital, Dijon, France.
Background: In the last years, the Cor-Knot device has been increasingly used in heart valve surgery. Our aim was to investigate the incidence of valvular complications in patients who underwent valvular surgery using the Cor-Knot device in multicentric cohorts at one-year follow-up.
Methods: Three hundred and sixty-eight patient underwent heart valve repair or replacement surgery using automated titanium suture fasteners in four cardiothoracic surgery departments between September 2018 and January 2020.
Biometrics
October 2024
Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada.
Precision medicine is transforming healthcare by offering tailored treatments that enhance patient outcomes and reduce costs. As our understanding of complex diseases improves, clinical trials increasingly aim to detect subgroups of patients with enhanced treatment effects. Biomarker-driven adaptive enrichment designs, which initially enroll a broad population and later restrict to treatment-sensitive patients, are gaining popularity.
View Article and Find Full Text PDFPlant Environ Interact
December 2024
Plant Agriculture, Ontario Agricultural College University of Guelph Guelph Ontario Canada.
Little is known regarding the genes, compounds and physiological alternations that take place upon infection of black knot disease. This research aimed to unravel the genetic mechanism responsible for the resistance of Japanese plum ( L.) trees against black knot ( Schwein.
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