Transcriptomic Study of Ciprofloxacin Resistance in Streptomyces Coelicolor A3(2)
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Restriction Endonucleases
Molecular Biology Problem Solver: A Laboratory Guide. Edited by Alan S. Gerstein Copyright © 2001 by Wiley-Liss, Inc. ISBNs: 0-471-37972-7 (Paper); 0-471-22390-5 (Electronic) 9 Restriction Endonucleases Derek Robinson, Paul R. Walsh, and Joseph A. Bonventre Background Information . 226 Which Restriction Enzymes Are Commercially Available? . 226 Why Are Some Enzymes More Expensive Than Others? . 227 What Can You Do to Reduce the Cost of Working with Restriction Enzymes? . 228 If You Could Select among Several Restriction Enzymes for Your Application, What Criteria Should You Consider to Make the Most Appropriate Choice? . 229 What Are the General Properties of Restriction Endonucleases? . 232 What Insight Is Provided by a Restriction Enzyme’s Quality Control Data? . 233 How Stable Are Restriction Enzymes? . 236 How Stable Are Diluted Restriction Enzymes? . 236 Simple Digests . 236 How Should You Set up a Simple Restriction Digest? . 236 Is It Wise to Modify the Suggested Reaction Conditions? . 237 Complex Restriction Digestions . 239 How Can a Substrate Affect the Restriction Digest? . 239 Should You Alter the Reaction Volume and DNA Concentration? . 241 Double Digests: Simultaneous or Sequential? . 242 225 Genomic Digests . 244 When Preparing Genomic DNA for Southern Blotting, How Can You Determine If Complete Digestion Has Been Obtained? . 244 What Are Your Options If You Must Create Additional Rare or Unique Restriction Sites? . 247 Troubleshooting . 255 What Can Cause a Simple Restriction Digest to Fail? . 255 The Volume of Enzyme in the Vial Appears Very Low. Did Leakage Occur during Shipment? . 259 The Enzyme Shipment Sat on the Shipping Dock for Two Days. -
Phosphate Steering by Flap Endonuclease 1 Promotes 50-flap Specificity and Incision to Prevent Genome Instability
ARTICLE Received 18 Jan 2017 | Accepted 5 May 2017 | Published 27 Jun 2017 DOI: 10.1038/ncomms15855 OPEN Phosphate steering by Flap Endonuclease 1 promotes 50-flap specificity and incision to prevent genome instability Susan E. Tsutakawa1,*, Mark J. Thompson2,*, Andrew S. Arvai3,*, Alexander J. Neil4,*, Steven J. Shaw2, Sana I. Algasaier2, Jane C. Kim4, L. David Finger2, Emma Jardine2, Victoria J.B. Gotham2, Altaf H. Sarker5, Mai Z. Her1, Fahad Rashid6, Samir M. Hamdan6, Sergei M. Mirkin4, Jane A. Grasby2 & John A. Tainer1,7 DNA replication and repair enzyme Flap Endonuclease 1 (FEN1) is vital for genome integrity, and FEN1 mutations arise in multiple cancers. FEN1 precisely cleaves single-stranded (ss) 50-flaps one nucleotide into duplex (ds) DNA. Yet, how FEN1 selects for but does not incise the ss 50-flap was enigmatic. Here we combine crystallographic, biochemical and genetic analyses to show that two dsDNA binding sites set the 50polarity and to reveal unexpected control of the DNA phosphodiester backbone by electrostatic interactions. Via ‘phosphate steering’, basic residues energetically steer an inverted ss 50-flap through a gateway over FEN1’s active site and shift dsDNA for catalysis. Mutations of these residues cause an 18,000-fold reduction in catalytic rate in vitro and large-scale trinucleotide (GAA)n repeat expansions in vivo, implying failed phosphate-steering promotes an unanticipated lagging-strand template-switch mechanism during replication. Thus, phosphate steering is an unappreciated FEN1 function that enforces 50-flap specificity and catalysis, preventing genomic instability. 1 Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. -
S1 Nuclease Degrades Single-Stranded Nucleic Acids, Releasing 5'-Phosphoryl Mono- Or Oligonucleotides
Description S1 Nuclease degrades single-stranded nucleic acids, releasing 5'-phosphoryl mono- or oligonucleotides. It is five times more active on DNA than on RNA (1). S1 Nuclease also cleaves dsDNA at the single-stranded region caused by a nick, gap, mismatch or loop. PRODUCT INFORMATION S1 Nuclease exhibits 3’-phosphomonoesterase activity. S1 Nuclease The enzyme is a glycoprotein with a carbohydrate content of 18%. Pub. No. MAN0013722 Applications Rev. Date 29 November 2016 (Rev. A.00) Removal of single-stranded overhangs of DNA #_ fragments (2). S1 transcript mapping (3, 4). Lot: _ Expiry Date: _ Cleavage of hairpin loops. Creation of unidirectional deletions in DNA fragments in Store at -20 °C conjunction with Exo III (5). Source Aspergillus oryzae cells. Components #EN0321 100 U/µL S1 Nuclease 10000 U 5X Reaction Buffer 2 1 mL www.thermofisher.com For Research Use Only. Not for use in diagnostic procedures. Definition of Activity Unit CERTIFICATE OF ANALYSIS One unit of the enzyme produces 1 µg of acid soluble S1 Nuclease was tested for the absence of deoxyribonucleotides in 1 min at 37 °C. contaminating double-stranded DNA specific nuclease Enzyme activity is assayed in the following mixture: activity. 30 mM sodium-acetate (pH 4.5), 50 mM NaCl, 0.1 mM ZnCl2, 5% (v/v) glycerol, 800 µg/mL heat Quality authorized by: Jurgita Zilinskiene denatured calf thymus DNA. Storage Buffer The enzyme is supplied in: 20 mM Tris-HCl (pH 7.5), 50 mM NaCl, 0.1 mM ZnCl2 and 50% (v/v) glycerol. 5X Reaction Buffer 200 mM sodium acetate (pH 4.5 at 25 °C), 1.5 M NaCl and 10 mM ZnSO4. -
Reduction of Pectinesterase Activity in a Commercial Enzyme Preparation
Journal of the Science of Food and Agriculture J Sci Food Agric 85:1613–1621 (2005) DOI: 10.1002/jsfa.2154 Reduction of pectinesterase activity in a commercial enzyme preparation by pulsed electric fields: comparison of inactivation kinetic models Joaquın´ Giner, Pascal Grouberman, Vicente Gimeno and Olga Martın´ ∗ Department of Food Technology, University of Lleida, CeRTA-UTPV, ETSEA, Avda Alcalde Rovira Roure 191, 25198-Lleida, Spain Abstract: The inactivation of pectinesterase (PE) in a commercial enzyme preparation (CEP) under high intensity pulsed electric fields (HIPEF) was studied. After desalting and water dilution of the raw CEP, samples were exposed to exponentially decay waveform pulses for up to 463 µs at electric field intensities ranging from 19 to 38 kV cm−1. Pulses were applied in monopolar mode. Experimental data were fitted to a first-order kinetic model as well as to models based on Fermi, Hulsheger¨ or Weibull equations to describe PE inactivation kinetics. Characteristic parameters for each model were calculated. Relationships between some of the parameters and process variables were obtained. The Weibull model yielded the best accuracy factor. The relationship between residual PE and input of electrical energy density was found to be that of exponential decay. 2005 Society of Chemical Industry Keywords: pulsed electric fields; kinetics; pectinesterase; model; inactivation INTRODUCTION It has become customary to use CEPs in fruit and Pectinesterase (PE; EC 3.1.1.11) is a pectic enzyme vegetable juice technology. Depending -
FAN1 Nuclease Activity Affects CAG Expansion and Age at Onset of Huntington's Disease
bioRxiv preprint doi: https://doi.org/10.1101/2021.04.13.439716; this version posted April 14, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. McAllister, Donaldson et al FAN1 nuclease activity affects CAG expansion and age at onset of Huntington's disease Branduff McAllister, PhD1+, Jasmine Donaldson, PhD1+, Caroline S. Binda, PhD1, Sophie Powell, BSc1, Uroosa Chughtai, BSc1, Gareth Edwards, PhD1, Joseph Stone, BA1, Sergey Lobanov, PhD1, Linda Elliston, MPhil1, Laura-Nadine Schuhmacher, PhD1, Elliott Rees, PhD1, Georgina Menzies, PhD2, Marc Ciosi, PhD3, Alastair Maxwell, PhD3, Michael J. Chao, PhD4, Eun Pyo Hong, PhD4, Diane Lucente, MS4, Vanessa Wheeler, PhD4, Jong-Min Lee, PhD4,5, Marcy E. MacDonald, PhD4,5, Jeffrey D. Long, PhD6, Elizabeth H. Aylward, PhD7, G. Bernhard Landwehrmeyer, MD PhD8, Anne E. Rosser, MB BChir, PhD9,10, REGISTRY Investigators of the European Huntington’s disease network11, Jane S. Paulsen, PhD12, PREDICT-HD Investigators of the Huntington Study Group13, Nigel M. Williams, PhD1, James F. Gusella, PhD4,5, Darren G. Monckton, PhD3, Nicholas D. Allen, PhD2, Peter Holmans, PhD1, Lesley Jones, PhD1,14* & Thomas H. Massey, BM BCh, DPhil1,15* 1 Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, CF24 4HQ, United Kingdom 2 School of Biosciences, Cardiff University, Cardiff, CF10 3AX, -
Type of the Paper (Article
Supplementary Material A Proteomics Study on the Mechanism of Nutmeg-induced Hepatotoxicity Wei Xia 1, †, Zhipeng Cao 1, †, Xiaoyu Zhang 1 and Lina Gao 1,* 1 School of Forensic Medicine, China Medical University, Shenyang 110122, P. R. China; lessen- [email protected] (W.X.); [email protected] (Z.C.); [email protected] (X.Z.) † The authors contributed equally to this work. * Correspondence: [email protected] Figure S1. Table S1. Peptide fraction separation liquid chromatography elution gradient table. Time (min) Flow rate (mL/min) Mobile phase A (%) Mobile phase B (%) 0 1 97 3 10 1 95 5 30 1 80 20 48 1 60 40 50 1 50 50 53 1 30 70 54 1 0 100 1 Table 2. Liquid chromatography elution gradient table. Time (min) Flow rate (nL/min) Mobile phase A (%) Mobile phase B (%) 0 600 94 6 2 600 83 17 82 600 60 40 84 600 50 50 85 600 45 55 90 600 0 100 Table S3. The analysis parameter of Proteome Discoverer 2.2. Item Value Type of Quantification Reporter Quantification (TMT) Enzyme Trypsin Max.Missed Cleavage Sites 2 Precursor Mass Tolerance 10 ppm Fragment Mass Tolerance 0.02 Da Dynamic Modification Oxidation/+15.995 Da (M) and TMT /+229.163 Da (K,Y) N-Terminal Modification Acetyl/+42.011 Da (N-Terminal) and TMT /+229.163 Da (N-Terminal) Static Modification Carbamidomethyl/+57.021 Da (C) 2 Table S4. The DEPs between the low-dose group and the control group. Protein Gene Fold Change P value Trend mRNA H2-K1 0.380 0.010 down Glutamine synthetase 0.426 0.022 down Annexin Anxa6 0.447 0.032 down mRNA H2-D1 0.467 0.002 down Ribokinase Rbks 0.487 0.000 -
Download Product Insert (PDF)
PRODUCT INFORMATION Lysophospholipase D Polyclonal Antibody Item No. 10005375 Overview and Properties Contents: This vial contains 500 µl of peptide affinity-purified antibody. Synonyms: Autotaxin, ENPP2, lysoPLD Immunogen: Peptide from the C-terminal region of rat LysoPLD Species Reactivity: (+) Human, mouse, and rat; other species not tested Form: Liquid Storage: -20°C (as supplied) Stability: ≥1 year Storage Buffer: TBS, pH 7.4, with 50% glycerol, 0.1%l BSA, and 0.02% sodium azide Host: Rabbit Applications: Immunocytochemistry (ICC), Immunohistochemistry (IHC), and Western blot (WB); the recommended starting dilution for ICC is 1:500, 1:80 for IHC, and 1:200 for WB. Other applications were not tested, therefore optimal working concentration/dilution should be determined empirically. Images 1 · · · · · · · 104 kDa · · · · · · · 60 kDa Lane 1: Human cerebella supernatant (40 µg) Immunohistochemistry analysis of formalin-fixed, paraffin-embedded (FFPE) human cerebellum ǎssue aer heat-induced anǎgen retrieval in pH 6.0 citrate buffer. Aer incubaǎon with Lysophospholipase D Polyclonal Anǎbody (Item No. 10005375) at a 1:80 diluǎon, slides were incubated with bioǎnylated secondary anǎbody, followed by alkaline phosphatase-strepavidin and chromogen (DAB). WARNING CAYMAN CHEMICAL THIS PRODUCT IS FOR RESEARCH ONLY - NOT FOR HUMAN OR VETERINARY DIAGNOSTIC OR THERAPEUTIC USE. 1180 EAST ELLSWORTH RD SAFETY DATA ANN ARBOR, MI 48108 · USA This material should be considered hazardous until further information becomes available. Do not ingest, inhale, get in eyes, on skin, or on clothing. Wash thoroughly after handling. Before use, the user must review the complete Safety Data Sheet, which has been sent via email to your institution. PHONE: [800] 364-9897 WARRANTY AND LIMITATION OF REMEDY [734] 971-3335 Buyer agrees to purchase the material subject to Cayman’s Terms and Conditions. -
Structure and Function of Nucleases in DNA Repair: Shape, Grip and Blade of the DNA Scissors
Oncogene (2002) 21, 9022 – 9032 ª 2002 Nature Publishing Group All rights reserved 0950 – 9232/02 $25.00 www.nature.com/onc Structure and function of nucleases in DNA repair: shape, grip and blade of the DNA scissors Tatsuya Nishino1 and Kosuke Morikawa*,1 1Department of Structural Biology, Biomolecular Engineering Research Institute (BERI), 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan DNA nucleases catalyze the cleavage of phosphodiester mismatched nucleotides. They also recognize the bonds. These enzymes play crucial roles in various DNA replication or recombination intermediates to facilitate repair processes, which involve DNA replication, base the following reaction steps through the cleavage of excision repair, nucleotide excision repair, mismatch DNA strands (Table 1). repair, and double strand break repair. In recent years, Nucleases can be regarded as molecular scissors, new nucleases involved in various DNA repair processes which cleave phosphodiester bonds between the sugars have been reported, including the Mus81 : Mms4 (Eme1) and the phosphate moieties of DNA. They contain complex, which functions during the meiotic phase and conserved minimal motifs, which usually consist of the Artemis : DNA-PK complex, which processes a V(D)J acidic and basic residues forming the active site. recombination intermediate. Defects of these nucleases These active site residues coordinate catalytically cause genetic instability or severe immunodeficiency. essential divalent cations, such as magnesium, Thus, structural biology on various nuclease actions is calcium, manganese or zinc, as a cofactor. However, essential for the elucidation of the molecular mechanism the requirements for actual cleavage, such as the types of complex DNA repair machinery. Three-dimensional and the numbers of metals, are very complicated, but structural information of nucleases is also rapidly are not common among the nucleases. -
Flap DNA Unwinding and Incision by the Human FAN1 Dimer
ARTICLE Received 16 Aug 2014 | Accepted 30 Oct 2014 | Published 11 Dec 2014 DOI: 10.1038/ncomms6726 Structural insights into 50 flap DNA unwinding and incision by the human FAN1 dimer Qi Zhao1,*, Xiaoyu Xue1,*, Simonne Longerich1,*, Patrick Sung1 & Yong Xiong1 Human FANCD2-associated nuclease 1 (FAN1) is a DNA structure-specific nuclease involved in the processing of DNA interstrand crosslinks (ICLs). FAN1 maintains genomic stability and prevents tissue decline in multiple organs, yet it confers ICL-induced anti-cancer drug resistance in several cancer subtypes. Here we report three crystal structures of human FAN1 in complex with a 50 flap DNA substrate, showing that two FAN1 molecules form a head-to- tail dimer to locate the lesion, orient the DNA and unwind a 50 flap for subsequent incision. Biochemical experiments further validate our model for FAN1 action, as structure-informed mutations that disrupt protein dimerization, substrate orientation or flap unwinding impair the structure-specific nuclease activity. Our work elucidates essential aspects of FAN1-DNA lesion recognition and a unique mechanism of incision. These structural insights shed light on the cellular mechanisms underlying organ degeneration protection and cancer drug resistance mediated by FAN1. 1 Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA. * These authors contributed equally to this work. Correspondence and requests for materials should be addressed to P.S. (email: [email protected]) or to Y.X. (email: [email protected]). NATURE COMMUNICATIONS | 5:5726 | DOI: 10.1038/ncomms6726 | www.nature.com/naturecommunications 1 & 2014 Macmillan Publishers Limited. All rights reserved. -
Restriction Enzymes of Bac- Base Teria Combat Foreign Substances
Understanding Inheritance FESTRICT’K3N ENZYMES J ~ke the immune systems of vertebrate eukaryotes, the restriction enzymes of bac- Base teria combat foreign substances. In particu- Restriction Enzyme Source Organism Sequence of Restriction Site lar, restriction enzymes render the DNA of, BamH 1 Bacillus 5’- ATCC-3’ say, an invading bacteriophage harmless amyloliquefaciens 3’-CCTAG- -5’ by catalyzing its fragmentation, or, more precisely, by catalyzing the breaking of cer- ECORI Escherichia co/i 5’-G ATTC-3’ tain O-P–O– bridges in the backbones of 3’-CTTA5 -5’ each DNA strand. The evolution of restric- tion enzymes helped many species of bac- Hae[[I Haemophi/us aegyptius 5’-G c-3’ teria to survive; their discovery by humans 3’-CC% G-5’ helped precipitate the recombinant-DNA revolution, Hindl[ Haemophi/us influenza 5’-GT(C orT (A or G)AC-3’ 3’-CA(G orA ! (T or C) TG-5’ Three types of restriction enzymes are known, but the term “restriction enzyme” MboI Moraxeila bovis 5’ refers here and elsewhere in this issue to type II restriction endonucleases, the only type commonly used in the study of DNA. (A Notl Nocardia otitidis 5’-G GCCGC nuclease is an enzyme that catalyzes the 3’-CG”CCG% G brealking of -O–P–O- bridges in a string of deoxyribonucleotide or ribonucleotides; an Taql Thermus aquaticus 5’- GA endcmuclease catalyzes the breaking of 3’-AG% internal rather than terminal -O–P–O- bridges.) Many restriction enzymes have beer isolated; more than seventy are avail- man numeral denotes the order of its dis- a sample of human DNA and a sampie of able commercially. -
Diagnostic Value of Serum Enzymes-A Review on Laboratory Investigations
Review Article ISSN 2250-0480 VOL 5/ ISSUE 4/OCT 2015 DIAGNOSTIC VALUE OF SERUM ENZYMES-A REVIEW ON LABORATORY INVESTIGATIONS. 1VIDYA SAGAR, M.SC., 2DR. VANDANA BERRY, MD AND DR.ROHIT J. CHAUDHARY, MD 1Vice Principal, Institute of Allied Health Sciences, Christian Medical College, Ludhiana 2Professor & Ex-Head of Microbiology Christian Medical College, Ludhiana 3Assistant Professor Department of Biochemistry Christian Medical College, Ludhiana ABSTRACT Enzymes are produced intracellularly, and released into the plasma and body fluids, where their activities can be measured by their abilities to accelerate the particular chemical reactions they catalyze. But different serum enzymes are raised when different tissues are damaged. So serum enzyme determination can be used both to detect cellular damage and to suggest its location in situ. Some of the biochemical markers such as alanine aminotransferase, aspartate aminotransferase, alkaline phasphatase, gamma glutamyl transferase, nucleotidase, ceruloplasmin, alpha fetoprotein, amylase, lipase, creatine phosphokinase and lactate dehydrogenase are mentioned to evaluate diseases of liver, pancreas, skeletal muscle, bone, etc. Such enzyme test may assist the physician in diagnosis and treatment. KEYWORDS: Liver Function tests, Serum Amylase, Lipase, CPK and LDH. INTRODUCTION mitochondrial AST is seen in extensive tissue necrosis during myocardial infarction and also in chronic Liver diseases like liver tissue degeneration DIAGNOSTIC SERUM ENZYME and necrosis². But lesser amounts are found in Enzymes are very helpful in the diagnosis of brain, pancreas and lung. Although GPT is plentiful cardiac, hepatic, pancreatic, muscular, skeltal and in the liver and occurs only in the small amount in malignant disorders. Serum for all enzyme tests the other tissues. -
What Is Alkaline Phosphatase? What Are the Symptoms of Low ALP?
What is the treatment for HPP? In 2015, asfotase alfa (Strensiq™) was approved for use in the US, the European Union, and Canada for pediatric-onset HPP, and in Japan for HPP with onset at any age. The medication is an injection given multiple times per week underneath the skin (subcutaneous). It is a recombinant (factory-made) form of ALP that has a bone-targeting component. When patients take asfotase alfa, ALP levels measured in the blood are quite high (often in the multiple thousands). Therefore, measuring ALP levels is typically not helpful once a patient is on therapy. What is Alkaline Phosphatase? What are the symptoms of low ALP? For more information, please contact Patients with hypophosphatasia (HPP) have Low ALP can lead to multiple symptoms of HPP, the Soft Bones Foundation. a low blood alkaline phosphatase (ALP) level. including poor bone mineralization and rickets as well (866) 827-9937 – Toll Free as early tooth loss (prior to age 5 years). It is also (973) 453-3093 – Direct Line thought that PPi may build up in muscle tissue 121 Hawkins Place, #267 ALP is an enzyme (a protein that breaks down and may be responsible for the pain and muscle Boonton, New Jersey 07005 chemicals). Most health providers are aware that weakness that some patients with HPP experience. www.SoftBones.org high ALP levels may indicate medical problems, such as liver disease or other bone diseases besides HPP, but many providers may not recognize that low ALP levels can indicate HPP. Low ALP is important What questions should patients ask Written by because the inability to break down chemicals can their doctors about ALP? Jill Simmons, MD lead to elevated levels of these chemicals, which Associate Professor of Pediatrics, Ian Burr Division can cause multiple problems.