375,247 results match your criteria dna binding


Wnt antagonists suppress herpes simplex virus type 1 productive infection.

Antiviral Res 2021 May 4:105082. Epub 2021 May 4.

Oklahoma State University, College of Veterinary Medicine, Department of Veterinary Pathobiology, Stillwater, OK 74078. Electronic address:

Following acute infection of mucosal surfaces, herpes simplex virus 1 (HSV-1) establishes life-long latent infections within neurons, including sensory neurons in trigeminal ganglia (TG). Periodically, reactivation from latency occurs resulting in virus transmission and recurrent disease. In the absence of lytic cycle viral transcriptional proteins, host factors are predicted to mediate early stages of reactivation from latency. Read More

View Article and Full-Text PDF

AHNAK controls 53BP1-mediated p53 response by restraining 53BP1 oligomerization and phase separation.

Mol Cell 2021 Apr 29. Epub 2021 Apr 29.

Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, 67404 Illkirch, France; Centre National de Recherche Scientifique, UMR7104, 67404 Illkirch, France; Université de Strasbourg, 67081 Strasbourg, France. Electronic address:

p53-binding protein 1 (53BP1) regulates both the DNA damage response and p53 signaling. Although 53BP1's function is well established in DNA double-strand break repair, how its role in p53 signaling is modulated remains poorly understood. Here, we identify the scaffolding protein AHNAK as a G1 phase-enriched interactor of 53BP1. Read More

View Article and Full-Text PDF

Protein-DNA/RNA Interactions: An Overview of Investigation Methods in the -Omics Era.

J Proteome Res 2021 May 7. Epub 2021 May 7.

Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy.

The fields of application of functional proteomics are not limited to the study of protein-protein interactions; they also extend to those involving protein complexes that bind DNA or RNA. These interactions affect fundamental processes such as replication, transcription, and repair in the case of DNA, as well as transport, translation, splicing, and silencing in the case of RNA. Analytical or preparative experimental approaches, both and , have been developed to isolate and identify DNA/RNA binding proteins by exploiting the advantage of the affinity shown by these proteins toward a specific oligonucleotide sequence. Read More

View Article and Full-Text PDF

The role of profilin-1 in cardiovascular diseases.

J Cell Sci 2021 May 7;134(9). Epub 2021 May 7.

Bioengineering, University of Pittsburgh.

Dynamic remodeling of the actin cytoskeleton is an essential feature for virtually all actin-dependent cellular processes, including cell migration, cell cycle progression, chromatin remodeling and gene expression, and even the DNA damage response. An altered actin cytoskeleton is a structural hallmark associated with numerous pathologies ranging from cardiovascular diseases to immune disorders, neurological diseases and cancer. The actin cytoskeleton in cells is regulated through the orchestrated actions of a myriad of actin-binding proteins. Read More

View Article and Full-Text PDF

The RNA Structurome in the Asexual Blood Stages of Malaria Pathogen .

RNA Biol 2021 May 7. Epub 2021 May 7.

Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223.

is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and noncoding transcripts from the asexual developmental cycle in in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite's asexual RBC cycle. Read More

View Article and Full-Text PDF

Identification of a New DNA Aptamer by Tissue-SELEX for Cancer Recognition and Imaging.

Anal Chem 2021 May 7. Epub 2021 May 7.

State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecule Engineering of Hunan Province, Hunan University, Changsha 410082, China.

Cancer has become one of the most common diseases with high mortality in humans. Early and accurate diagnosis of cancer is of great significance to enhance the survival rate of patients. Therefore, effective molecular ligands capable of selectively recognizing cancer are urgently needed. Read More

View Article and Full-Text PDF

Harmine targets inhibitor of DNA binding-2 and activator protein-1 to promote preosteoclast PDGF-BB production.

J Cell Mol Med 2021 May 7. Epub 2021 May 7.

Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.

Osteoporosis is one of the most common metabolic bone diseases affecting millions of people. We previously found that harmine prevents bone loss in ovariectomized mice via increasing preosteoclast platelet-derived growth factor-BB (PDGF-BB) production and type H vessel formation. However, the molecular mechanisms by which harmine promotes preosteoclast PDGF-BB generation are still unclear. Read More

View Article and Full-Text PDF

Insights into the substrate discrimination mechanisms of methyl-CpG-binding domain 4.

Biochem J 2021 May 7. Epub 2021 May 7.

The University of Texas at Austin, Austin, Texas, United States.

G:T mismatches, the major mispairs generated during DNA metabolism, are repaired in part by mismatch-specific DNA glycosylases such as methyl-CpG-binding domain 4 (MBD4) and thymine DNA glycosylase (TDG). Mismatch-specific DNA glycosylases must discriminate the mismatches against million-fold excess correct base pairs. MBD4 efficiently removes thymine opposite guanine but not opposite adenine. Read More

View Article and Full-Text PDF

M1 Macrophages Are More Susceptible to Necroptosis.

J Cell Immunol 2021 ;3(2):97-102

Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, Texas, USA.

Macrophages play a crucial role in host innate immune defense against infection and tissue injury. Although macrophage activation and polarization has been well studied, we know less regarding the role of macrophage activation/polarization in inflammation-associated necrotic cell death. By using bone marrow-derived macrophages, we have recently demonstrated that M1 macrophages are much more susceptible than M0 and M2 subtypes of macrophages to necrotic cell death. Read More

View Article and Full-Text PDF
January 2021

PprA Protein Inhibits DNA Strand Exchange and ATP Hydrolysis of RecA and Regulates the Recombination in Gamma-Irradiated Cells.

Front Cell Dev Biol 2021 20;9:636178. Epub 2021 Apr 20.

Molecular Biology Division, Bhabha Atomic Research Centre, Mumbai, India.

DrRecA and PprA proteins function are crucial for the extraordinary resistance to γ-radiation and DNA strand break repair in . DrRecA mediated homologous recombination help in DNA strand break repair and cell survival, while the PprA protein confers radio-resistance its roles in DNA repair, genome maintenance, and cell division. Genetically and genes interact and constitute an epistatic group however, the mechanism underlying their functional interaction is not clear. Read More

View Article and Full-Text PDF

c-Rel Is the Pivotal NF-κB Subunit in Germinal Center Diffuse Large B-Cell Lymphoma: A LYSA Study.

Front Oncol 2021 20;11:638897. Epub 2021 Apr 20.

CNRS UMR-7276, INSERM U1262, CRIBL, University of Limoges, and Hematology Laboratory of Dupuytren Hospital University Center (CHU) of Limoges, Limoges, France.

Relationships between c-Rel and GCB-DLBCLs remain unclear. We found that strong c-Rel DNA-binding activity was mostly found in GCBs on two independent series of 48 DLBCLs and 66 DLBCLs, the latter issued from the GHEDI series. c-Rel DNA-binding activity was associated with increased mRNA expression. Read More

View Article and Full-Text PDF

CTCF As an Example of DNA-Binding Transcription Factors Containing Clusters of C2H2-Type Zinc Fingers.

Acta Naturae 2021 Jan-Mar;13(1):31-46

Institute of Gene Biology RAS, Moscow, 119334 Russia.

In mammals, most of the boundaries of topologically associating domains and all well-studied insulators are rich in binding sites for the CTCF protein. According to existing experimental data, CTCF is a key factor in the organization of the architecture of mammalian chromosomes. A characteristic feature of the CTCF is that the central part of the protein contains a cluster consisting of eleven domains of C2H2-type zinc fingers, five of which specifically bind to a long DNA sequence conserved in most animals. Read More

View Article and Full-Text PDF

Genetically encoded multivalent liquid glycan array displayed on M13 bacteriophage.

Nat Chem Biol 2021 May 6. Epub 2021 May 6.

Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.

The central dogma of biology does not allow for the study of glycans using DNA sequencing. We report a liquid glycan array (LiGA) platform comprising a library of DNA 'barcoded' M13 virions that display 30-1,500 copies of glycans per phage. A LiGA is synthesized by acylation of the phage pVIII protein with a dibenzocyclooctyne, followed by ligation of azido-modified glycans. Read More

View Article and Full-Text PDF

Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells.

Nat Biotechnol 2021 May 6. Epub 2021 May 6.

Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.

The biological roles of DNA methylation have been elucidated by profiling methods based on whole-genome or reduced-representation bisulfite sequencing, but these approaches do not efficiently survey the vast numbers of non-coding regulatory elements in mammalian genomes. Here we present an extended-representation bisulfite sequencing (XRBS) method for targeted profiling of DNA methylation. Our design strikes a balance between expanding coverage of regulatory elements and reproducibly enriching informative CpG dinucleotides in promoters, enhancers and CTCF binding sites. Read More

View Article and Full-Text PDF

YTHDF2 is a potential target of AML1/ETO-HIF1α loop-mediated cell proliferation in t(8;21) AML.

Oncogene 2021 May 6. Epub 2021 May 6.

Department of Hematology, Chinese PLA General Hospital, Beijing, China.

The t(8;21) fusion product, AML1/ETO, and hypoxia-inducible factor 1α (HIF1α) form a feed-forward transcription loop that cooperatively transactivates the DNA methyltransferase 3a gene promoter that leads to DNA hypermethylation and drives leukemia cell growth. Suppression of the RNA N-methyladenosine (mA)-reader enzyme YTH N-methyladenosine RNA binding protein 2 (YTHDF2) specifically compromises cancer stem cells in acute myeloid leukemia (AML) but promotes hematopoietic stem cell expansion without derailing normal hematopoiesis. However, the relevance of expression between AML1/ETO-HIF1α loop and YTHDF2, and its functional relationship with t(8;21) AML have not been documented. Read More

View Article and Full-Text PDF

Unraveling the binding characteristics of small ligands to telomeric DNA by pressure modulation.

Sci Rep 2021 May 6;11(1):9714. Epub 2021 May 6.

Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany.

Recently, non-canonical DNA structures, such as G-quadruplexes (GQs), were found to be highly pressure sensitive, suggesting that pressure modulation studies can provide additional mechanistic details of such biomolecular systems. Using FRET and CD spectroscopy as well as binding equilibrium measurements, we investigated the effect of pressure on the binding reaction of the ligand ThT to the quadruplex 22AG in solutions containing different ionic species and a crowding agent mimicking the intracellular milieu. Pressure modulation helped us to identify the different conformational substates adopted by the quadruplex at the different solution conditions and to determine the volumetric changes during complex formation and the conformational transitions involved. Read More

View Article and Full-Text PDF

Comprehensive molecular dissection of TIFY Transcription factors reveal their dynamic responses to biotic and abiotic stress in wheat (Triticum aestivum L.).

Sci Rep 2021 May 6;11(1):9739. Epub 2021 May 6.

Department of Bio-Engineering, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India.

The plant specific TIFY (previously known as ZIM) transcription factor (TF) family plays crucial roles in cross talk between Jasmonic Acid and other phytohormones like gibberellins, salicylic acid, abscisic acid, auxin, and ethylene signaling pathways. Wheat yield is severely affected by rust diseases and many abiotic stresses, where different phytohormone signaling pathways are involved. TIFYs have been studied in many plants yet reports describing their molecular structure and function in wheat are lacking. Read More

View Article and Full-Text PDF

Antibacterial and antioxidant activities of extracts and isolated compounds from the roots extract of Cucumis prophetarum and in silico study on DNA gyrase and human peroxiredoxin 5.

BMC Chem 2021 May 6;15(1):32. Epub 2021 May 6.

Department of Applied Chemistry, School of Applied Natural Science, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia.

Background: Cucumis prophetarum is traditionally used to treat liver and lung disorders, heart failure, diarrhea, gonorrhea, skin infections, intestinal problems and cancer. In the present work, the isolation of two novel compounds along with their antibacterial and antioxidant activities is reported for the first time.

Methods: Silica gel column chromatography was applied to separate constituents of the roots of C. Read More

View Article and Full-Text PDF

Acidic pH-responsive changes of DNA structure and surface dynamics as probed with ultrasensitive Raman spectroscopy.

Spectrochim Acta A Mol Biomol Spectrosc 2021 Apr 21;258:119866. Epub 2021 Apr 21.

Institute of Biological Research, Branch of National Institute of Research and Development for Biological Sciences, Republicii 48, 400015 Cluj-Napoca, Romania.

In this work structural and (sub)picosecond surface dynamical changes of genomic DNA isolated from different medicinal plants (Hyssopus officinalis, Majorana hortensis, Melissa officinalis, Mentha piperita, Mentha piperita cv "Cristal", Monarda didyma and Matricaria chamomilla), as probed with surface-enhanced Raman spectroscopy (SERS), are discussed upon modifying the acidic pH of mixtures consisting of silver colloidal suspension and DNA samples, respectively. Binding affinity changes of DNA with silver NPs and nucleic acids protonation are supposed to take place upon lowering the pH. A small percentage of Hoogsteen GC basepairs was found in Mentha piperita cv "Cristal" DNA, at low acidic pH. Read More

View Article and Full-Text PDF

Mechanisms of DNA-protein cross-link formation and repair.

Biochim Biophys Acta Proteins Proteom 2021 May 3:140669. Epub 2021 May 3.

Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, United States. Electronic address:

Covalent binding of DNA to proteins produces DNA-protein cross-links (DPCs). DPCs are formed as intermediates of enzymatic processes, generated from the reactions of protein nucleophiles with DNA electrophiles, and produced by endogenous and exogenous cross-linking agents. DPCs are heterogeneous due to the variations of DNA conjugation sites, flanking DNA structures, protein sizes, and cross-link bonds. Read More

View Article and Full-Text PDF

How structural biology transformed studies of transcription regulation.

J Biol Chem 2021 May 3:100741. Epub 2021 May 3.

Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205. Electronic address:

The past four decades have seen remarkable advances in our understanding of the structural basis of gene regulation. Technological advances in protein expression, nucleic acid synthesis and structural biology made it possible to study the proteins that regulate transcription in the context of ever larger complexes containing proteins bound to DNA. This review, written on the occasion of the 50 anniversary of the founding of the Protein Data Bank (PDB) focuses on the insights gained from structural studies of protein-DNA complexes, and the role the PDB has played in driving this research. Read More

View Article and Full-Text PDF

Structures and Functions of Chromatin Fibers.

Annu Rev Biophys 2021 May;50:95-116

National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; email:

In eukaryotes, genomic DNA is packaged into chromatin in the nucleus. The accessibility of DNA is dependent on the chromatin structure and dynamics, which essentially control DNA-related processes, including transcription, DNA replication, and repair. All of the factors that affect the structure and dynamics of nucleosomes, the nucleosome-nucleosome interaction interfaces, and the binding of linker histones or other chromatin-binding proteins need to be considered to understand the organization and function of chromatin fibers. Read More

View Article and Full-Text PDF

DNA polymerase gamma mutations that impair holoenzyme stability cause catalytic subunit depletion.

Nucleic Acids Res 2021 May 6. Epub 2021 May 6.

Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/B-35131 Padova, Italy.

Mutations in POLG, encoding POLγA, the catalytic subunit of the mitochondrial DNA polymerase, cause a spectrum of disorders characterized by mtDNA instability. However, the molecular pathogenesis of POLG-related diseases is poorly understood and efficient treatments are missing. Here, we generate the PolgA449T/A449T mouse model, which reproduces the A467T change, the most common human recessive mutation of POLG. Read More

View Article and Full-Text PDF

Direct and Efficient Conjugation of Quantum Dots to DNA Nanostructures with Peptide-PNA.

ACS Nano 2021 May 6. Epub 2021 May 6.

Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory Code 6900, Washington, DC 20375, United States.

DNA nanotechnology has proven to be a powerful strategy for the bottom-up preparation of colloidal nanoparticle (NP) superstructures, enabling the coordination of multiple NPs with orientation and separation approaching nanometer precision. To do this, NPs are often conjugated with chemically modified, single-stranded (ss) DNA that can recognize complementary ssDNA on the DNA nanostructure. The limitation is that many NPs cannot be easily conjugated with ssDNA, and other conjugation strategies are expensive, inefficient, or reduce the specificity and/or precision with which NPs can be placed. Read More

View Article and Full-Text PDF

Photoperiod-responsive changes in chromatin accessibility in phloem companion and epidermis cells of Arabidopsis leaves.

Plant Cell 2021 May;33(3):475-491

Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, and College of Life Sciences, Capital Normal University, Beijing 100048, China.

Photoperiod plays a key role in controlling the phase transition from vegetative to reproductive growth in flowering plants. Leaves are the major organs perceiving day-length signals, but how specific leaf cell types respond to photoperiod remains unknown. We integrated photoperiod-responsive chromatin accessibility and transcriptome data in leaf epidermis and vascular companion cells of Arabidopsis thaliana by combining isolation of nuclei tagged in specific cell/tissue types with assay for transposase-accessible chromatin using sequencing and RNA-sequencing. Read More

View Article and Full-Text PDF

Zinc finger proteins in the host-virus interplay: multifaceted functions based on their nucleic acid-binding property.

FEMS Microbiol Rev 2021 May;45(3)

Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China.

Zinc finger proteins (ZFPs) are a huge family comprised of massive, structurally diverse proteins characterized by zinc ion coordinating. They engage in the host-virus interplay in-depth and occupy a significant portion of the host antiviral arsenal. Nucleic acid-binding is the basic property of certain ZFPs, which draws increasing attention due to their immense influence on viral infections. Read More

View Article and Full-Text PDF

Yeast Nucleolin Nsr1 Impedes Replication and Elevates Genome Instability at an Actively Transcribed Guanine-Rich G4 DNA-Forming Sequence.

Genetics 2020 Dec;216(4):1023-1037

Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, Texas 77030.

A significant increase in genome instability is associated with the conformational shift of a guanine-run-containing DNA strand into the four-stranded G-quadruplex (G4) DNA. The mechanism underlying the recombination and genome rearrangements following the formation of G4 DNA in vivo has been difficult to elucidate but has become better clarified by the identification and functional characterization of several key G4 DNA-binding proteins. Mammalian nucleolin (NCL) is a highly specific G4 DNA-binding protein with a well-defined role in the transcriptional regulation of genes with associated G4 DNA-forming sequence motifs at their promoters. Read More

View Article and Full-Text PDF
December 2020

Hmx3a Has Essential Functions in Zebrafish Spinal Cord, Ear and Lateral Line Development.

Genetics 2020 Dec;216(4):1153-1185

Department of Biology, Syracuse University, New York 13244.

Transcription factors that contain a homeodomain DNA-binding domain have crucial functions in most aspects of cellular function and embryonic development in both animals and plants. Hmx proteins are a subfamily of NK homeodomain-containing proteins that have fundamental roles in development of sensory structures such as the eye and the ear. However, Hmx functions in spinal cord development have not been analyzed. Read More

View Article and Full-Text PDF
December 2020

Diverse DNA Sequence Motifs Activate Meiotic Recombination Hotspots Through a Common Chromatin Remodeling Pathway.

Genetics 2019 Nov;213(3):789-803

Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199.

Homologous recombination is induced to high levels in meiosis and is clustered at hotspots that regulate its frequency and distribution in the genome. By studying five different classes of DNA sequence-dependent recombination hotspots in the fission yeast.. Read More

View Article and Full-Text PDF
November 2019

Diverse DNA Sequence Motifs Activate Meiotic Recombination Hotspots Through a Common Chromatin Remodeling Pathway.

Genetics 2019 Nov;213(3):789-803

Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205-7199.

Homologous recombination is induced to high levels in meiosis and is clustered at hotspots that regulate its frequency and distribution in the genome. By studying five different classes of DNA sequence-dependent recombination hotspots in the fission yeast.. Read More

View Article and Full-Text PDF
November 2019