3,942 results match your criteria probes dna-binding


Simple and versatile imaging of genomic loci in live mammalian cells and early pre-implantation embryos using CAS-LiveFISH.

Sci Rep 2021 Jun 9;11(1):12220. Epub 2021 Jun 9.

Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.

Visualizing the 4D genome in live cells is essential for understanding its regulation. Programmable DNA-binding probes, such as fluorescent clustered regularly interspaced short palindromic repeats (CRISPR) and transcription activator-like effector (TALE) proteins have recently emerged as powerful tools for imaging specific genomic loci in live cells. However, many such systems rely on genetically-encoded components, often requiring multiple constructs that each must be separately optimized, thus limiting their use. Read More

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Generation of Fluorescent Versions of Saccharomyces cerevisiae RPA to Study the Conformational Dynamics of Its ssDNA-Binding Domains.

Methods Mol Biol 2021 ;2281:151-168

Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, USA.

Replication protein A (RPA) is an essential single-stranded DNA (ssDNA)-binding protein that sequesters ssDNA and protects it from nucleolytic degradation. The RPA-ssDNA nucleoprotein acts as a hub to recruit over two dozen DNA metabolic enzymes onto ssDNA to coordinate DNA replication, repair, and recombination. RPA functions as a heterotrimer composed of RPA70, RPA32, and RPA14 subunits and has multiple DNA-binding and protein-interaction domains. Read More

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Tryptophan Probes of TDP-43 C-Terminal Domain Amyloid Formation.

J Phys Chem B 2021 04 9;125(15):3781-3789. Epub 2021 Apr 9.

Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States.

Aggregated TAR DNA-binding protein 43 (TDP-43) forms the cytoplasmic hallmarks associated with patients suffering from amyotrophic lateral sclerosis and frontotemporal lobar degeneration with ubiquitin. Under normal conditions, TDP-43 is a 414-amino acid protein; however, aggregates are enriched with N-terminal truncations which contain residues 267-414, known as the C-terminal domain of TDP-43 (TDP-43). To gain residue-specific information on the aggregation process of TDP-43, we created three single-Trp containing mutants (W385F/W412F, W334F/W412F, and W334F/W385F) by substituting two of the three native Trp residues with Phe, yielding fluorescent probes at W334, W385, and W412, respectively. Read More

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The Interaction Efficiency of XPD-p44 With Bulky DNA Damages Depends on the Structure of the Damage.

Front Cell Dev Biol 2021 11;9:617160. Epub 2021 Mar 11.

Laboratory of Bioorganic Chemistry of Enzymes, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia.

The successful elimination of bulky DNA damages via the nucleotide excision repair (NER) system is largely determined by the damage recognition step. This step consists of primary recognition and verification of the damage. The TFIIH helicase XPD plays a key role in the verification step during NER. Read More

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Cellular senescence in hepatocellular carcinoma induced by a long non-coding RNA-encoded peptide PINT87aa by blocking FOXM1-mediated .

Theranostics 2021 4;11(10):4929-4944. Epub 2021 Mar 4.

Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, PR China.

Recently, long non-coding RNAs (lncRNAs), known to be involved in human cancer progression, have been shown to encode peptides with biological functions, but the role of lncRNA-encoded peptides in cellular senescence is largely unexplored. We previously reported the tumor-suppressive role of PINT87aa, a peptide encoded by the long intergenic non-protein coding RNA, p53 induced transcript ( Here, we investigated PINT87aa's role in hepatocellular carcinoma (HCC) cellular senescence. We examined PINT87aa and truncated PINT87aa functions by monitoring cell proliferation and performed flow cytometry, senescence-associated β-galactosidase staining, JC-1 staining indicative of mitochondrial membrane potential, the ratio of the overlapping area of light chain 3 beta (LC3B) and mitochondrial probes and the ratio of lysosomal associated membrane protein 1 (LAMP1) overlapping with cytochrome c oxidase subunit 4I1 (COXIV) denoting mitophagy. Read More

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Association of expression of epigenetic molecular factors with DNA methylation and sensitivity to chemotherapeutic agents in cancer cell lines.

Clin Epigenetics 2021 Mar 6;13(1):49. Epub 2021 Mar 6.

Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA.

Background: Altered DNA methylation patterns play important roles in cancer development and progression. We examined whether expression levels of genes directly or indirectly involved in DNA methylation and demethylation may be associated with response of cancer cell lines to chemotherapy treatment with a variety of antitumor agents.

Results: We analyzed 72 genes encoding epigenetic factors directly or indirectly involved in DNA methylation and demethylation processes. Read More

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Effects of oxidative stress-induced increases in Zn concentrations in human gingival epithelial cells.

J Periodontal Res 2021 Jun 28;56(3):512-522. Epub 2021 Feb 28.

Department of Periodontology, Osaka University Graduate School of Dentistry, Osaka, Japan.

Background And Objective: Previous studies have reported that oxidative stress increases intracellular Zn concentrations and induces cytotoxicity. However, no studies have investigated whether oxidative stress induces such changes in periodontal tissue cells. In the present study, we investigated the effect of oxidative stress on intracellular Zn concentration in periodontium constituent cells and its potential relationship with periodontal disease. Read More

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Probing E. coli SSB protein-DNA topology by reversing DNA backbone polarity.

Biophys J 2021 04 23;120(8):1522-1533. Epub 2021 Feb 23.

Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, Missouri. Electronic address:

Escherichia coli single-strand (ss) DNA binding protein (SSB) is an essential protein that binds ssDNA intermediates formed during genome maintenance. SSB homotetramers bind ssDNA in two major modes, differing in occluded site size and cooperativity. The (SSB) mode in which ssDNA wraps, on average, around two subunits is favored at low [NaCl] and high SSB/DNA ratios and displays high unlimited, nearest-neighbor cooperativity forming long protein clusters. Read More

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Programmable tools for targeted analysis of epigenetic DNA modifications.

Curr Opin Chem Biol 2021 Feb 12;63:1-10. Epub 2021 Feb 12.

Faculty of Chemistry and Chemical Biology, TU Dortmund University Otto-Hahn-Str. 4a, 44227 Dortmund, Germany. Electronic address:

Modifications of the cytosine 5-position are dynamic epigenetic marks of mammalian DNA with important regulatory roles in development and disease. Unraveling biological functions of such modified nucleobases is tightly connected with the potential of available methods for their analysis. Whereas genome-wide nucleobase quantification and mapping are first-line analyses, targeted analyses move into focus the more genomic sites with high biological significance are identified. Read More

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February 2021

DNA-Targeted Metallodrugs: An Untapped Source of Artificial Gene Editing Technology.

Chembiochem 2021 Feb 11. Epub 2021 Feb 11.

School of Chemical Sciences and National Institute for Cellular Biotechnology and Nano Research Facility, Dublin City University Glasnevin, Dublin, 9, Ireland.

DNA binding metal complexes are synonymous with anticancer drug discovery. Given the array of structural and chemical reactivity properties available through careful design, metal complexes have been directed to bind nucleic acid structures through covalent or noncovalent binding modes. Several recognition modes - including crosslinking, intercalation, and oxidation - are central to the clinical success of broad-spectrum anticancer metallodrugs. Read More

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February 2021

Cafeteria diet induces global and -specific hypomethylation in male Wistar rats.

Adipocyte 2021 12;10(1):108-118

Biomedical Research and Innovation Platform, South African Medical Research Council , Tygerberg, South Africa.

Increased visceral adipose tissue (VAT) is associated with metabolic dysfunction, while subcutaneous adipose tissue (SAT) is considered protective. The mechanisms underlying these differences are not fully elucidated. This study aimed to investigate molecular differences in VAT and SAT of male Wistar rats fed a cafeteria diet (CD) or a standard rodent diet (STD) for three months. Read More

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December 2021

Fluorescent thermal shift-based method for detection of NF-κB binding to double-stranded DNA.

Sci Rep 2021 Jan 27;11(1):2331. Epub 2021 Jan 27.

Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020, Innsbruck, Austria.

The nuclear factor kappa B (NF-κB) family of dimeric transcription factors regulates a wide range of genes by binding to their specific DNA regulatory sequences. NF-κB is an important therapeutic target linked to a number of cancers as well as autoimmune and inflammatory diseases. Therefore, effective high-throughput methods for the detection of NF-κB DNA binding are essential for studying its transcriptional activity and for inhibitory drug screening. Read More

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January 2021

Experimental and theoretical studies of Palladium-hydrazide complexes' interaction with DNA and BSA, in vitro cytotoxicity activity and plasmid cleavage ability.

Comput Biol Chem 2021 Apr 15;91:107435. Epub 2021 Jan 15.

Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan 84156-83111, Iran.

New palladium complexes with general formula trans-[Pd(L)(OAc)] (1,2), (L = Benzhydrazide and 2-Furoic hydrazide) have been synthesized and characterized with various methods including elemental analysis, FT-IR, HNMR and mass spectroscopy. Afterward their interactions with bovine serum albumin and calf thymus deoxyribonucleic acid have been investigated by UV-vis absorption, fluorescence emission and circular dichroism spectroscopy. Also, site-selective replacement experiments with site probes have been carried out. Read More

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Rice protein-binding microarrays: a tool to detect cis-acting elements near promoter regions in rice.

Planta 2021 Jan 21;253(2):40. Epub 2021 Jan 21.

Department of Biosciences and Bioinformatics, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin, Gyeonggi-do, 17060, Republic of Korea.

Main Conclusion: The present study showed that a rice (Oryza sativa)-specific protein-binding microarray (RPBM) can be applied to analyze DNA-binding motifs with a TF where binding is evaluated in extended natural promoter regions. The analysis may facilitate identifying TFs and their downstream genes and constructing gene networks through cis-elements. Transcription factors (TFs) regulate gene expression at the transcriptional level by binding a specific DNA sequence. Read More

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January 2021

Multispectroscopic and molecular docking studies on DNA binding of guaifenesin drug.

Nucleosides Nucleotides Nucleic Acids 2021 19;40(3):317-335. Epub 2021 Jan 19.

Faculty of Chemistry, Department of Inorganic Chemistry, Razi University, Kermanshah, Iran.

The interaction mechanism of guaifenesin drug; ()-3-(2-methoxyphenoxy)propane-1,2-diol; and calf thymus DNA was characterized by multiple spectroscopic and molecular docking approaches. The changes in drug electronic absorption with increasing DNA concentration and also the observed significant quenching of guaifenesin emission in the presence of DNA proved the complex formation between guaifenesin and DNA during the interactions. Both the binding constant and thermodynamic parameters for the interaction have been calculated in 283, 298, and 310 K at pH 7. Read More

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Controlled Fluorescence Enhancement of DNA-Binding Dye Through Chain Length Match between Oligoguanine and TOTO.

J Phys Chem B 2021 01 10;125(2):518-527. Epub 2021 Jan 10.

School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China.

Fluorescent DNA-binding dyes are extensively employed as probe and biosensing in biological detection and imaging. Experiments and theoretical calculations of thiazole orange homodimeric (TOTO) dye binding to a single-strand DNA (ssDNA), poly(dG) ( = 2, 4, 6, 8), reveal that the = 6 complex shows about 300-fold stronger fluorescence than = 2, 4 and a slightly stronger one than = 8 complexes, which is benefited from the length match between TOTO and poly(dG). The machine learning, based on molecular dynamics trajectories, indicates that TOTO is featured by the dihedral angle along its backbone and its end-to-end distance, in which the latter one defines the stretch and hairpin structures of TOTO, respectively. Read More

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January 2021

Spectroscopic Studies on the Interaction of Naphthyridines with DNA and Fluorescent Detection of DNA in Agarose Gel.

J Fluoresc 2021 Mar 3;31(2):327-338. Epub 2021 Jan 3.

Department of Chemistry, Gandhigram Rural Institute, Deemed to be University, Gandhigram, 624 302, India.

Four new naphthyridine derivatives (R1-R4) possessing amino acid or boronic acid moieties have been synthesized and characterized using H and C NMR, FT-IR, and mass spectral techniques. The mechanism of binding of these probes with calf thymus DNA (CT-DNA) has been delineated through UV-Vis, fluorescence, and circular dichroism (CD) spectral techniques along with thermodynamic and molecular docking studies. Small hypochromicity in absorption maximum of the probes without any shift in wavelength of absorption suggests groove binding mode of interaction of these probes with CT-DNA, confirmed by CD and 1H NMR spectral data competitive binding assay with ethidium bromide (EB). Read More

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Mapping DNA conformations and interactions within the binding cleft of bacteriophage T4 single-stranded DNA binding protein (gp32) at single nucleotide resolution.

Nucleic Acids Res 2021 01;49(2):916-927

Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403, USA.

In this study, we use single-stranded DNA (oligo-dT) lattices that have been position-specifically labeled with monomer or dimer 2-aminopurine (2-AP) probes to map the local interactions of the DNA bases with the nucleic acid binding cleft of gp32, the single-stranded binding (ssb) protein of bacteriophage T4. Three complementary spectroscopic approaches are used to characterize these local interactions of the probes with nearby nucleotide bases and amino acid residues at varying levels of effective protein binding cooperativity, as manipulated by changing lattice length. These include: (i) examining local quenching and enhancing effects on the fluorescence spectra of monomer 2-AP probes at each position within the cleft; (ii) using acrylamide as a dynamic-quenching additive to measure solvent access to monomer 2-AP probes at each ssDNA position; and (iii) employing circular dichroism spectra to characterize changes in exciton coupling within 2-AP dimer probes at specific ssDNA positions within the protein cleft. Read More

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January 2021

Reverse Chromatin Immunoprecipitation (R-ChIP) enables investigation of the upstream regulators of plant genes.

Commun Biol 2020 12 14;3(1):770. Epub 2020 Dec 14.

State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, 830011, China.

DNA binding proteins carry out important and diverse functions in the cell, including gene regulation, but identifying these proteins is technically challenging. In the present study, we developed a technique to capture DNA-associated proteins called reverse chromatin immunoprecipitation (R-ChIP). This technology uses a set of specific DNA probes labeled with biotin to isolate chromatin, and the DNA-associated proteins are then identified using mass spectrometry. Read More

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December 2020

Mitochondrial Transcription Factor A Binds to and Promotes Mutagenic Transcriptional Bypass of -Alkylthymidine Lesions.

Anal Chem 2021 01 8;93(2):1161-1169. Epub 2020 Dec 8.

Department of Chemistry, University of California, Riverside, California 92521-0403, United States.

- and -alkylated thymidine lesions are known to be poorly repaired and persist in mammalian tissues. To understand how mammalian cells sense the presence and regulate the repair of these lesions, we employed a quantitative proteomic method to discover regioisomeric - and -butylthymidine (- and -BudT)-binding proteins. We were able to identify 21 and 74 candidate DNA damage recognition proteins for -BudT- and -BudT-bearing DNA probes, respectively. Read More

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January 2021

Antimicrobial, cytotoxicity, molecular modeling and DNA cleavage/binding studies of zinc-naproxen complex: switching DNA binding mode of naproxen by coordination to zinc ion.

J Biomol Struct Dyn 2020 Dec 4:1-13. Epub 2020 Dec 4.

Phamaceutical Analysis Research Center and Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.

The intercalation DNA binding mode of the naproxen, a non-steroidal anti-inflammatory drug, has been reported previously. In this study, calf thymus deoxyribonucleic acid (CT-DNA) binding of zinc-naproxen complex, [Zn(naproxen)(MeOH)], at physiological pH has been investigated by multi-spectroscopic techniques and molecular docking. Zinc-naproxen complex displays significant binding property to the CT-DNA ( = 0. Read More

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December 2020

Far-red switching DNA probes for live cell nanoscopy.

Chem Commun (Camb) 2020 Nov;56(94):14797-14800

Chromatin Labeling and Imaging Group, Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

Herein we present DNA probes composed of Hoechst 33258 and spontaneously blinking far-red hydroxymethyl silicon-rhodamine (HMSiR). The best performing probe, 5-HMSiR-Hoechst, contains the 5'-regioisomer, shows ∼400-fold fluorescence increase upon DNA binding and is compatible with wash-free single molecule localization and 3D stimulated emission depletion microscopy of chromatin nanostructures in living cells. Read More

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November 2020

In Vitro Production of Perdeuterated Proteins in HO for Biomolecular NMR Studies.

Methods Mol Biol 2021 ;2199:127-149

CNRS, CEA, Institut de Biologie Structurale (IBS), University of Grenoble Alpes, Grenoble, France.

The cell-free synthesis is an efficient strategy to produce in large scale protein samples for structural investigations. In vitro synthesis allows for significant reduction of production time, simplification of purification steps and enables production of both soluble and membrane proteins. The cell-free reaction is an open system and can be performed in presence of many additives such as cofactors, inhibitors, redox systems, chaperones, detergents, lipids, nanodisks, and surfactants to allow for the expression of toxic membrane proteins or intrinsically disordered proteins. Read More

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LINC00355 promoted the progression of lung squamous cell carcinoma through regulating the miR-466/LYAR axis.

Braz J Med Biol Res 2020 21;53(12):e9317. Epub 2020 Oct 21.

Department of Thoracic Surgery, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China.

LINC00355 has been reported aberrantly over-expressed and associated with poor prognosis in various types of cancer. However, reports regarding the effect of LINC00355 on lung squamous cell carcinoma (SCC) are rare. This study aimed to explore the function of LINC00355 in the development and progression of lung SCC and reveal the underlying mechanism. Read More

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January 2021

Assessing The Key Photophysical Properties of Triangulenium Dyes for DNA Binding by Alteration of the Fluorescent Core.

Chemistry 2021 Feb 23;27(7):2523-2536. Epub 2020 Dec 23.

Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, London, W12 0BZ, UK.

Four-stranded G-quadruplex (G4) DNA is a non-canonical DNA topology that has been proposed to form in cells and play key roles in how the genome is read and used by the cellular machinery. Previously, a fluorescent triangulenium probe (DAOTA-M2) was used to visualise G4s in cellulo, thanks to its distinct fluorescence lifetimes when bound to different DNA topologies. Herein, the library of available triangulenium probes is expanded to explore how modifications to the fluorescent core of the molecule affect its photophysical characteristics, interaction with DNA and cellular localisation. Read More

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February 2021

Two classes of active transcription sites and their roles in developmental regulation.

Proc Natl Acad Sci U S A 2020 10 8;117(43):26812-26821. Epub 2020 Oct 8.

Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706

The expression of genes encoding powerful developmental regulators is exquisitely controlled, often at multiple levels. Here, we investigate developmental expression of three conserved genes, , , and which encode homologs of ERK/MAPK and core components of the Notch-dependent transcription complex, respectively. We use single-molecule FISH (smFISH) and MATLAB to visualize and quantify nuclear nascent transcripts and cytoplasmic mRNAs as a function of position along the germline developmental axis. Read More

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October 2020

Stimuli-Responsive DNA Binding by Synthetic Systems.

Acc Chem Res 2020 10 30;53(10):2286-2298. Epub 2020 Sep 30.

Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS) and Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.

DNA is the molecule responsible for the storage and transmission of the genetic information in living organisms. The expression of this information is highly regulated. In eukaryotes, it is achieved mainly at the transcription level thanks to specialized proteins called (TFs) that recognize specific DNA sequences, thereby promoting or inhibiting the transcription of particular genes. Read More

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October 2020

Engineered TALE Repeats for Enhanced Imaging-Based Analysis of Cellular 5-Methylcytosine.

Chembiochem 2021 Feb 6;22(4):645-651. Epub 2020 Nov 6.

Faculty of Chemistry and Chemical Biology, Dortmund University, Otto-Hahn Strasse 6, 44227, Dortmund, Germany.

Transcription-activator-like effectors (TALEs) are repeat-based, programmable DNA-binding proteins that can be engineered to recognize sequences of canonical and epigenetically modified nucleobases. Fluorescent TALEs can be used for the imaging-based analysis of cellular 5-methylcytosine (5 mC) in repetitive DNA sequences. This is based on recording fluorescence ratios from cell co-stains with two TALEs: an analytical TALE targeting the cytosine (C) position of interest through a C-selective repeat that is blocked by 5 mC, and a control TALE targeting the position with a universal repeat that binds both C and 5 mC. Read More

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February 2021

Common Fragile Sites Are Characterized by Faulty Condensin Loading after Replication Stress.

Cell Rep 2020 09;32(12):108177

MRC Human Genetics Unit, The University of Edinburgh, Crewe Rd South, Edinburgh EH4 2XU, UK. Electronic address:

Cells coordinate interphase-to-mitosis transition, but recurrent cytogenetic lesions appear at common fragile sites (CFSs), termed CFS expression, in a tissue-specific manner after replication stress, marking regions of instability in cancer. Despite such a distinct defect, no model fully provides a molecular explanation for CFSs. We show that CFSs are characterized by impaired chromatin folding, manifesting as disrupted mitotic structures visible with molecular fluorescence in situ hybridization (FISH) probes in the presence and absence of replication stress. Read More

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September 2020

Dual DNA binding mode of a turn-on red fluorescent probe thiazole coumarin.

PLoS One 2020 17;15(9):e0239145. Epub 2020 Sep 17.

Department of Biophysics, Bose Institute, Kolkata, India.

Turn-on fluorescent probes show enhanced emission upon DNA binding, advocating their importance in imaging cellular DNA. We have probed the DNA binding mode of thiazole-coumarin (TC) conjugate, a recently reported hemicyanine-based turn-on red fluorescent probe, using a number of biophysical techniques and a series of short oligonucleotides. TC exhibited increased fluorescence anisotropy and decreased absorbance (~50%) at low [DNA]/[TC] ratio. Read More

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November 2020