26 papers · ranked by Valyu relevance
Adam R. Leman, Eishi Noguchi
Eukaryotic cells must accurately and efficiently duplicate their genomes during each round of the cell cycle. Multiple linear chromosomes, an abundance of regulatory elements, and chromosome packaging are all challenges that the eukaryotic DNA replication machinery must successfully overcome. The replication machinery…
Scott Berger, Gheorghe Chistol
During cell division, the genome of each eukaryotic cell is copied by thousands of replisomes – large protein complexes consisting of several dozen proteins. Recent studies suggest that the eukaryotic replisome is much more dynamic than previously thought. To directly visualize replisome dynamics in a physiological…
Maria Anna Rapsomaniki, Stella Maxouri, Manuel Ramirez Garrastacho, Patroula Nathanailidou + 4 more
DNA replication is a complex and remarkably robust process: despite its inherent uncertainty, manifested through stochastic replication timing at a single-cell level, multiple control mechanisms ensure its accurate and timely completion across a population. Disruptions in these mechanisms lead to DNA re-replication…
Omer Markovitch, Juntian Wu, Otto Sijbren
Copying information is vital for life's propagation. Current life forms maintain a low error rate in replication using complex machinery to prevent and correct errors. However, primitive life had to deal with higher error rates, limiting its ability to evolve. Discovering mechanisms to reduce errors would alleviate…
Sylwia Barańska, Monika Glinkowska, Anna Herman-Antosiewicz, Monika Maciąg-Dorszyńska + 4 more
'Monika Maciąg-Dorszyńska' 'Dariusz Nowicki' 'Agnieszka Szalewska-Pałasz' 'Alicja Węgrzyn' 'Grzegorz Węgrzyn'] Precise regulation of DNA replication is necessary to ensure the inheritance of genetic features by daughter cells after each cell division. Therefore, determining how the regulatory processes operate to…
Monika Maciąg-Dorszyńska, Joanna Morcinek-Orłowska, Sylwia Barańska, Tae-Hong Kang
'Tae-Hong Kang'] DNA replication is a fundamental process in the cell on which the functioning of the entire cell as well as the maintenance of the entire species depends. This process is synchronized with all other processes within the cell as well as with external, environmental factors. This complex network of…
Diletta Ciardo, Olivier Haccard, Francesco de Carli, Olivier Hyrien + 2 more
Large vertebrate genomes duplicate by activating tens of thousands of DNA replication origins, irregularly spaced along the genome. The spatial and temporal regulation of the replication process is not yet fully understood. To investigate the DNA replication dynamics, we developed a methodology called RepliCorr, which…
Thomas LaBar, Arend Hintze, Christoph Adami
The role of historical contingency in the origin of life is one of the great unknowns in modern science. Only one example of life exists– one that proceeded from a single self-replicating organism (or a set of replicating hyper-cycles) to the vast complexity we see today in Earth's biosphere. We know that emergent life…
Stuart A. Sevier
Central to the function of cellular life is the reading, storage and replication of DNA. Due to the helical structure of DNA, a complicated topological braiding of new strands follows the duplication of the old strands. Even though this was discovered over 60 years ago, the mathematical and physical questions this…
Deepak Bhat, Samuel Hauf, Charles Plessy, Yohei Yokobayashi + 1 more
Replisomes are multi-protein complexes that replicate genomes with remarkable speed and accuracy. Despite their importance, their dynamics is poorly characterized, especially in vivo. In this paper, we present an approach to infer the replisome dynamics from the DNA abundance distribution measured in a growing…
Razie Yousefi, Maga Rowicka, Dominik Wodarz
Eukaryotic DNA replication is elaborately orchestrated to duplicate the genome timely and faithfully. Replication initiates at multiple origins from which replication forks emanate and travel bi-directionally. The complex spatio-temporal regulation of DNA replication remains incompletely understood. To study it…
Arach Goldar, Hélène Labit, Kathrin Marheineke, Olivier Hyrien + 1 more
'Nick Rhind'] Background Eukaryotic cells seem unable to monitor replication completion during normal S phase, yet must ensure a reliable replication completion time. This is an acute problem in early Xenopus embryos since DNA replication origins are located and activated stochastically, leading to the random…
Erik Johansson, John F.X Diffley
Single-stranded DNA breaks, including simple nicks, are amongst the most common forms of DNA damage in cells. They can be readily repaired by ligation; however, if a nick occurs just ahead of an approaching replisome, the outcome is a ‘collapsed’ replication fork in which the nick is converted into a single-ended…
Johannes Menzel, Philip Tatman, Joshua C Black
Changes in gene copy number contribute to genomic instability, the onset and progression of cancer, developmental abnormalities and adaptive potential. The origins of gene amplifications have remained elusive; however, DNA rereplication has been implicated as a source of gene amplifications. The inability to determine…
Shreerang Pande, Debarshi Mitra, A. C. Chatterji
The mechanism underlying the spatio-temporal chromosome organization in Escherichia coli cells remains an open question, though experiments have been able to visually see the evolving chromosome organization in fast and slow growing cells. We had proposed [D. Mitra et al., Soft Matter, 18, 5615-5631(2022)] that The DNA…
Katie H. Jameson, Christian J. Rudolph, Michelle Hawkins
The complete and accurate duplication of genomic information is vital to maintain genome stability in all domains of life. In Escherichia coli, replication termination, the final stage of the duplication process, is confined to the ‘replication fork trap’ region by multiple unidirectional fork barriers formed by the…
Anca Rǎdulescu, Abraham Longbotham
We introduce mutations in replication systems, in which the intact copying mechanism is performed by discrete iterations of a complex quadratic map in the family fc(z) = z 2 +c. More specifically, we consider a "correct" function fc1 acting on the complex plane (representing the space of genes to be copied). A…
Mats Walldén, David Fange, Özden Baltekin, Johan Elf
Isogenic Escherichia coli growing exponentially in a constant environment display large variation in growth-rates, division-sizes and generation-times. It is unclear how these seemingly random cell cycles can be reconciled with the precise regulation required under conditions where the generation time is shorter than…
Mareike Berger, Pieter Rein ten Wolde
The bacterium Escherichia coli initiates replication once per cell cycle at a precise volume per origin and adds an on average constant volume between successive initiation events, independent of the initiation size. Yet, a molecular model that can explain these observations has been lacking. Experiments indicate that…
Po-Yi Ho, Ariel Amir
Bacteria are able to maintain a narrow distribution of cell sizes by regulating the timing of cell divisions. In rich nutrient conditions, cells divide much faster than their chromosomes replicate. This implies that cells maintain multiple rounds of chromosome replication per cell division by regulating the timing of…
Davide Michieletto, Davide Marenduzzo, Susanne Matthew
We study theoretically the replication of Kinetoplast DNA consisting of several thousands separate mini-circles found in organisms of the class Kinetoplastida. When the cell is not actively dividing these are topologically connected in a marginally linked network of rings with only one connected component. During cell…
Louie Slocombe, Jim Al-Khalili, Marco Sacchi
The misincorporation of a non-complimentary DNA base in the polymerase active site is a critical source of replication errors that can lead to genetic mutations. In this work, we model the mechanism of wobble mispairing and the subsequent rate of misincorporation errors by coupling first-principles quantum chemistry…
Authors not listed
Nonenzymatic self-replication is considered as one of the most primordial functions of RNA, which likely preceded the emergence of more complex ribozymes. Among different possible scenarios, nucleotide activation with imidazole derivatives attracted substantial attention over the last years. However, despite the…
Authors not listed
DNA polymerases are essential enzymes responsible for accurate genome replication and repair, with divalent metal cofactors playing a crucial role in their catalytic function. Polymerase gamma (Pol γ) is the primary DNA polymerase in mitochondria, ensuring the faithful replication of mitochondrial DNA. The choice of…
Authors not listed
Detailed structural investigation of DNA self-replication on RNA template. The results show a clear dependence of the helix type and efficiency of the nonenzymatic primer extension as the RNA template introduces A-type helicity on the hybrid helix.
Benjamin King, Max Winokan, Paul Stevenson, Jim Al-Khalili + 2 more
The adenine-thymine tautomer (A-T) has previously been discounted as a spontaneous mutagenesis mechanism due to the energetic instability of the tautomeric configuration. We study the stability of A-T while the nucleobases undergo DNA strand separation. Our calculations indicate an increase in the stability of A-T as…