- 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 : 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 : Hörberg, Johanna; Reymer, Anna (2019) - Torsional stress on DNA, introduced by molecular motors, constitutes an important regulatory mechanism of transcriptional control. Torsional stress can modulate specific binding of transcription factors to DNA and introduce local conformational changes that facilitate the opening of promoters and nucleosome remodeling. Using all-atom microsecond scale molecular dynamics simulations together with a torsional restraint that controls the total helical twist of a DNA fragment, ...
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- Journal article
Authors : Bernacchia, Lorenzo (2023) - Cancer chemotherapeutics kill rapidly dividing cells, which includes cells of the immune system. The 12 resulting neutropenia predisposes patients to infection, which delays treatment and is a major cause 13 of morbidity and mortality. Here we have exploited the cytotoxicity of the anti-cancer compound 14 cisplatin to screen for FDA-approved drugs that impair bacterial nucleotide excision DNA repair (NER), 15 the primary mechanism bacteria use to repair ...
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- Journal Article
Authors : Gaydar, Vera (2023) - -
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- 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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- Journal article
Authors : Alghoul, Emile (2023) - SLX4, disabled in Fanconi anemia group P, is a scaffolding protein that coordinates the action of
structure-specific endonucleases and other proteins involved in replication-coupled repair of DNA
interstrand crosslinks (ICLs). Here we show that SLX4 dimerization and SUMO-SIM interactions drive
the assembly of SLX4 membraneless compartments in the nucleus called condensates. Superresolution
microscopy reveals that SLX4 forms chromatin-bound clusters of nanocondensat...
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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 : Rzechorzek, Neil J; Hardwick, Steven W; Jatikusumo, Vincentius A (2020) - DNA unwinding in eukaryotic replication is performed by the Cdc45-MCM-GINS (CMG) helicase. Although the CMG architecture has been elucidated, its mechanism of DNA unwinding and replisome interactions remain poorly understood. Here we report the cryoEM structure at 3.3 Å of human CMG bound to fork DNA and the ATP-analogue ATPγS. Eleven nucleotides of single-stranded (ss) DNA are bound within the C-tier of MCM2-7 AAA+ ATPase domains. All MCM subunits&...
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- Journal article
Authors : Johanna, Hörberg (2023) - Transcription factors (TFs) regulate eukaryotic transcription through selecting DNA-binding,
can also specifically interact with RNA, which may present another layer of transcriptional
control. The mechanisms of the TFs-DNA recognition are often well-characterised, while the
details of TFs-RNA complexation are less understood. Here we investigate the dual
recognition mechanism of the glucocorticoid receptor (GR), which interacts with similar
affinities with consen...
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- Journal article
Authors : Tuan, Pham Minh (2023) - In bacterial cells, DNA damage tolerance is manifested by the action of translesion DNA
polymerases that can synthesize DNA across template lesions that typically block the replicative
DNA polymerase III. It has been suggested that one of these TLS DNA polymerases, DNA
polymerase IV, can either act in concert with the replisome, switching places on the b sliding
clamp with DNA polymerase III to bypass the template damage, or&...
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- Thesis
Authors : Phuong Trung Dung; Advisor : Phuong Dinh Tam; Mai Anh Tuan (2012) - -
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- Journal article
Authors : Das, Ritam (2021) - Mycobacteriophages are viruses of Mycobacterium spp. with promising diagnostic and therapeutic potential. Phage genome exploration and characterization of their proteomes are essential to gain a better understanding of their role in phage biology. So far, about 2014 mycobacteriophages have been genomically defined and 1563 phage protein families (phamilies) are identified. However, the function of only a fraction (about 15%) is known and a majority of ORFs in...
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- Journal article
Authors : Dannenberg, Rachel L. (2023) - During DNA replication, DNA lesions present in lagging strand templates are initially encountered by DNA polymerase (pol ). The historical view for what transpires from these encounters is that replication of the afflicted lagging strand template abruptly stops, activating DNA damage tolerance (DDT) pathways that replicate the offending lesion and adjacent DNA sequence, allowing pol to resume downstream. However, qualitative studies observed that human p...
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- Journal article
Authors : Dauzier, N. Lobato- (2023) - Complex organisms perceive their surroundings with sensory neurons which encode physical
stimuli into spikes of electrical activities. The past decade has seen reports of DNA-based
chemical neurons that mimic artificial neural networks with chemical reactions. Yet, they lack
the physical sensing and temporal coding of sensory biological neurons. Here we report a
thermosensory chemical neuron based on DNA and enzymes that spikes with chemical act...
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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 : 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 : Thrall, Elizabeth S. (2023) - Translesion synthesis (TLS) polymerases bypass DNA lesions that block replicative polymerases, allowing cells to tolerate DNA damage encountered during replication. It is well known that most bacterial TLS polymerases must interact with the sliding clamp processivity factor to carry out TLS, but recent work in Escherichia coli has revealed that single-stranded DNA-binding protein (SSB) plays a key role in enriching the TLS polymerase Pol IV at stalled re...
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- Journal Article
Authors : Islam, Azharul (2023) - Mammalian polynucleotide kinase 3’-phosphatase (PNKP) is a dual-function DNA endprocessing
enzyme with 3’-phosphatase and 5’-kinase activities, which generate 3’-OH and 5’-
phosphate termini respectively, as substrates for DNA polymerase and DNA ligase to complete
DNA repair. PNKP is thus involved in multiple DNA repair pathways, including base excision
(BER), single-strand break (SSBR), and double-strand break repair (DSBR). However, little is
known as&...
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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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