Arabidopsis C-terminal domain phosphatase-like 1 functions in miRNA accumulation and DNA methylation. [PDF]
PLoS ONE, 2013 Arabidopsis CTD-PHOSPHATASE-LIKE 1 (CPL1) is a protein phosphatase that can dephosphorylate RNA polymerase II C-terminal domain (CTD). Unlike typical CTD-phosphatases, CPL1 contains a double-stranded (ds) RNA-binding motif (dsRBM) and has been implicated
In Sil Jeong +7 more
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Morphological and Molecular Characterization of Pseudocercospora chionanthi-retusi Causing Leaf Spot on Chionanthus retusus in Korea [PDF]
Research in Plant Disease, 2022 Leaves of Chionanthus retusus were found to be damaged by leaf spot disease associated with a fungus in Iksan, Korea. Leaf spots were angular to irregular, vein-limited, scattered, 1–8 mm diameter, brownish-gray to dark brown when dry, with heavy ...
In-Young Choi +3 more
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Heterochromatic siRNAs and DDM1 independently silence aberrant 5S rDNA transcripts in Arabidopsis. [PDF]
PLoS ONE, 2009 5S ribosomal RNA gene repeats are arranged in heterochromatic arrays (5S rDNA) situated near the centromeres of Arabidopsis chromosomes. The chromatin remodeling factor DDM1 is known to maintain 5S rDNA methylation patterns while silencing transcription ...
Todd Blevins +3 more
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Density- and elongation speed-dependent error correction in RNA polymerization [PDF]
, 2021 Backtracking of RNA polymerase (RNAP) is an important pausing mechanism during DNA transcription that is part of the error correction process that enhances transcription fidelity. We model the backtracking mechanism of RNA polymerase, which usually happens when the polymerase tries to incorporate a mismatched nucleotide triphosphate.
arxiv +1 more source
Scientific Reports, 2022 In biological systems, the synthesis of nucleic acids, such as DNA and RNA, is catalyzed by enzymes in various aqueous solutions. However, substrate specificity is derived from the chemical properties of the residues, which implies that perturbations of ...
Shuntaro Takahashi +5 more
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Accuracy and speed of elongation in a minimal model of DNA replication [PDF]
, 2021 Being a dual purpose enzyme, the DNA polymerase is responsible for elongation of the newly formed DNA strand as well as cleaving the erroneous growth in case of a misincorporation. The efficiency of replication depends on the coordination of the polymerization and exonuclease activity of DNA polymerase.
arxiv +1 more source
Pol IV-Dependent siRNA Production is Reduced in Brassica rapa
Biology, 2013 Plants produce a diverse array of small RNA molecules capable of gene regulation, including Pol IV-dependent short interfering (p4-si)RNAs that trigger transcriptional gene silencing.
Rebecca A. Mosher +2 more
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Kinetics and thermodynamics of exonuclease-deficient DNA polymerases [PDF]
Phys. Rev. E 93, 042419 (2016), 2016 A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of Markovian DNA sequences from a Bernoullian template. The dependences on nucleotide concentrations and template sequence
arxiv +1 more source
Inhibitors of HIV-1 Reverse Transcriptase—Associated Ribonuclease H Activity
Biology, 2012 HIV-1 enzyme reverse transcriptase (RT) is a major target for antiviral drug development, with over half of current FDA-approved therapeutics against HIV infection targeting the DNA polymerase activity of this enzyme. HIV-1 RT is a multifunctional enzyme
Michael A. Parniak +4 more
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Computational Investigations on Polymerase Actions in Gene Transcription and Replication Combining Physical Modeling and Atomistic Simulations [PDF]
Chin. Phys. B Vol. 25, No. 1 (2016) 018706, 2015 Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles.
arxiv +1 more source