- Journal article
Authors : Chang, Seungwoo; Thrall, Elizabeth S; Laureti, Luisa (2020) - DNA replication is mediated by the coordinated actions of multiple enzymes within replisomes. Processivity clamps tether many of these enzymes to DNA, allowing access to the primer/template junction. Many clamp-interacting proteins (CLIPs) are involved in genome maintenance pathways including translesion synthesis (TLS). Despite their abundance, DNA replication in bacteria is not perturbed by these CLIPs. Here we show that while the TLS polymerase Pol IV is&#...
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- Periodicals (Báo – Tạp chí)
Authors : Luteran, E. M; Kahn, J. D (2020) - This article addresses the stability of the d(CGA) triplet motif and variants in solution. Our study reveals changes in thermodynamic stability and nuclease resistance in response to pH. The identity of the 5′-nucleobase within each triplet and the position and frequency of different triplets within stretches of d(CGA) triplets can tune parallel-stranded duplex stability. This tunability can be used for nanotechnological applications where the specificity of ...
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- Periodicals (Báo – Tạp chí)
Authors : Mäkinen, Janne J; Shin, Yeonoh (2020) - RNA polymerases (RNAPs) synthesize RNA from NTPs, whereas DNA polymerases synthesize DNA from 2’dNTPs. DNA polymerases select against NTPs by using steric gates to exclude the 2’ OH, but RNAPs have to employ alternative selection strategies. In single-subunit RNAPs, a conserved Tyr residue discriminates against 2’dNTPs, whereas selectivity mechanisms of multi-subunit RNAPs remain hitherto unknown. Here we show that a conserved Arg residue uses a two-pronged s...
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- Journal article
Authors : Shah, Shanaya Shital; Hartono, Stella; Chédin, Frédéric (2020) - Displacement loops (D-loops) are signature intermediates formed during homologous recombination. Numerous factors regulate D-loop formation and disruption, thereby influencing crucial aspects of DNA repair, including donor choice and the possibility of a crossover outcome. While D-loop detection methods exist, it is currently unfeasible to assess the relationship between D-loop editors and D-loop characteristics such as length and position. Here, we developed a novel in...
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- Journal article
Authors : Kash, Kazutoshi; Stojkovič, Gorazd; Ruiz, Cristina Velázquez (2020) - Replication forks often stall at damaged DNA. Resumption of DNA synthesis can occur by replacement of the replicative DNA polymerase with specialized, error-prone translesion DNA polymerases (TLS), that have higher tolerance for damaged substrates. Several of these polymerases (Polλ, Polη and PrimPol) are stimulated in DNA synthesis through interaction with PolDIP2, however the mechanism of this PolDIP2-dependent stimulation is still unclear. Here we show that Pri...
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- Journal article
Authors : Paudel, Bishnu P; Moye, Aaron Lavel; Assi, Hala Abou (2020) - Telomeric G-quadruplexes (G4) were long believed to form a protective structure at telomeres, preventing their extension by the ribonucleoprotein telomerase. Contrary to this belief, we have previously demonstrated that parallel-stranded conformations of telomeric G4 can be extended by human and ciliate telomerase. However, a mechanistic understanding of the interaction of telomerase with structured DNA remained elusive. Here, we use single-molecule fluorescence resonance energy...
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- Journal article
Authors : Bignon, Emmanuelle; Claerbout, Victor; Jiang, Tao (2020) - Apurinic/apyrimidinic (AP) sites are the most common DNA lesions, which benefit from a most efficient repair by the base excision pathway. The impact of losing a nucleobase on the conformation and dynamics of B-DNA is well characterized. Yet AP sites seem to present an entirely different chemistry in nucleosomal DNA, with lifetimes reduced up to 100-fold, and the much increased formation of covalent DNA-protein cross-links, refractory to repair....
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- Journal article
Authors : Strickfaden, Hilmar; Tolsma, Thomas; Sharma, Ajit (2020) - The association of nuclear DNA with histones to form chromatin is essential to the temporal and spatial control of eukaryotic genomes. In this study, we examined the physical state of chromatin in vitro and in vivo. Our in vitro studies demonstrate that MgCl2-dependent self-association of native chromatin fragments or reconstituted nucleosomal arrays produced supramolecular condensates whose constituents are physically constrained and solid-like. Liquid chromatin conde...
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- Journal article
Authors : Rao, Maya V; Grasty, Kimberly C; Mehetre, Prajakta D (2020) - Ubiquitin signaling networks modulate almost all aspects of eukaryotic biology, and their outputs reflect the dynamic balance between ubiquitin attachment and removal. The latter process is catalyzed by deubiquitinating enzymes (DUBs), which must be carefully regulated to ensure that their activities are applied appropriately. Ataxin3 is a DUB that participates in quality-control pathways that support cellular health; however, the regulation of its activity has remaine...
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- Journal article
Authors : Capdevila, Daiana A; Walsh, Brenna J. C; Zhang, Yifan (2020) - Cysteine thiol-based transcriptional regulators orchestrate coordinated regulation of redox homeostasis and other cellular processes by “sensing” or detecting a specific redox-active molecule, which in turn activates the transcription of a specific detoxification pathway. The extent to which these sensors are truly specific in cells for a singular class of reactive small molecule stressors, e.g., reactive oxygen or sulfur species, is largely unknown. Here we report...
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