Telomerase Activity and Telomerase Subunits Gene Expression Patterns

Total Page:16

File Type:pdf, Size:1020Kb

Telomerase Activity and Telomerase Subunits Gene Expression Patterns Telomerase Activity and Telomerase Subunits Gene Expression Patterns in Neuroblastoma: A Molecular and Immunohistochemical Study Establishing Prognostic Tools for Fresh-Frozen and Paraffin-Embedded Tissues By Christopher Poremba, Christina Scheel, Barbara Hero, Holger Christiansen, Karl-Ludwig Schaefer, Jun-ichi Nakayama, Frank Berthold, Heribert Juergens, Werner Boecker, and Barbara Dockhorn-Dworniczak Purpose: We have recently demonstrated that te- Results: TA was present in a total of 39 (29.3%) of lomerase activity (TA) is an independent prognostic 133 neuroblastomas and in 31 (29.8%) of 104 initial factor in neuroblastomas. In the present study, the neuroblastomas without cytotoxic pretreatment. TA prognostic impact of TA and gene expression of the was significantly correlated with both event-free and three major telomerase subunits is evaluated by molec- overall survival (P < .0001). Furthermore, we found a ular and immunohistochemical techniques in fresh-fro- significant correlation between expression levels of TA zen and paraffin-embedded tissues. and hTRT (P < .0001) as well as hTR (P < .001). Multi- Patients and Methods: One hundred thirty-three variate analysis revealed only TA and tumor stage but neuroblastomas of all stages were analyzed for TA. The not serum lactate dehydrogenase, MYCN amplification, TA levels of 75 neuroblastoma cases were correlated or age at diagnosis as independent prognostic factors. with gene expression of telomerase subunits hTRT, hu- Conclusion: The significant correlation with clinical man telomerase RNA (hTR), and telomerase protein 1 outcome strongly recommends that analysis of TA be (TP1) by quantitative reverse transcriptase polymerase incorporated into the clinical investigation of each indi- chain reaction (RT-PCR), using an innovative approach vidual neuroblastoma at the time of diagnosis. Because on the LightCycler instrument (Roche Diagnostics, the mere presence or absence of TA without further Mannheim, Germany). For selected cases, the applica- quantification is sufficient basis for predicting disease bility of RT-PCR and immunohistochemistry for hTRT outcome, the telomeric repeat amplification protocol expression analysis was investigated in paraffin-em- assay could be complemented with but not replaced by bedded tissues. TA and subunit expression patterns analysis of hTRT or hTR expression. were correlated with traditional prognostic indicators J Clin Oncol 18:2582-2592. © 2000 by American and disease outcome. Society of Clinical Oncology. EUROBLASTOMA represents the third most com- outcome are age and stage, although an assessment of the N mon pediatric cancer and is the most common solid patient’s prognosis solely on the basis of clinical parameters extracranial neoplasm of infancy and childhood, responsible is limited because of diverse biologic tumor behavior and for approximately 15% of all childhood cancer deaths. The subsequent survival rates, even at distinct clinical stages.1,2 clinical hallmark of neuroblastoma is heterogeneity, which Therefore, the heterogeneity of this tumor entity requires is associated with a wide variety of likelihood of tumor cellular and molecular markers to distinguish the different progression. The most significant clinical predictors of biologic characteristics. Established molecular markers such as MYCN copy number and loss of heterozygosity for chromosome 1p32-36 may help in predicting poor outcome in all age and stage From the Gerhard-Domagk-Institute of Pathology and Department groups.3-7 Recent cytogenetic data also suggest that gain of of Pediatric Hematology and Oncology, Westfa¨lische Wilhelms-Uni- chromosome arm 17q is associated with an adverse outcome versity, Mu¨nster, Germany; Departments of Pediatric Hematology and 8,9 Oncology, University of Ko¨ln, Ko¨ln, and University of Marburg, in neuroblastoma. A promising new marker is telomerase, Marburg, Germany; Cold Spring Harbor Laboratory, New York, NY; a multicomponent ribonucleoprotein enzyme, which has and Department of Life Science, Tokyo Institute of Technology, been implicated in cell immortalization and tumorigenesis Yokohama, Japan. in almost all human tumors, including neuroblastomas.9-14 Submitted October 12, 1999; accepted March 3, 2000. Supported in part by the German Research Foundation “Deutsche Recently, we have shown in multivariate analysis that Forschungsgemeinschaft DFG” (grant nos. Po. 529/4-1 and Po. 529/5-1). telomerase activity (TA) is an independent prognostic factor Address reprint requests to Barbara Dockhorn-Dworniczak, MD, in neuroblastoma, which may prove useful in conjunction with PhD, Gerhard-Domagk-Institute of Pathology, Westfa¨lische Wilhelms- established markers for assessing the individual patient’s prog- University, Domagkstrasse 17, 48149 Mu¨nster, Germany; email nosis.15 However, it is not known whether elevated TA in [email protected]. © 2000 by American Society of Clinical Oncology. neuroblastoma may simply be a marker of escape from cellular 0732-183X/00/1813-2582 senescence or whether markedly increased activity levels may 2582 Journal of Clinical Oncology, Vol 18, No 13 (July), 2000: pp 2582-2592 Downloaded from jco.ascopubs.org on June 3, 2010 . For personal use only. No other uses without permission. Copyright © 2000 by the American Society of Clinical Oncology. All rights reserved. TELOMERASE AS PROGNOSTIC MARKER IN NEUROBLASTOMA 2583 be associated with genomic instability and an increased like- adrenal gland and in the pelvic region. Metastatic sites in stage 4 cases lihood of further mutational events. Furthermore, to date, the were bone marrow in 35 patients, bone in 24, liver in 12, distant lymph frequency and location of telomerase-positive cells within nodes in 11, intracranial in five, and the gluteal muscle in one. In stage 4S patients, metastases were found in bone marrow in 10 patients, in neuroblastomas is not known. the liver in 15, in the skin in two, and the epididymis in two. Patients Recently, the catalytic subunit hTRT (or hTERT, hEST2, were treated according to the German Neuroblastoma Trial NB85 (n ϭ TP2) of human telomerase was cloned, and detection of 10), NB90 (n ϭ 113), NB95-S (n ϭ 5), or NB97 (n ϭ 5), with 22 hTRT expression by reverse transcriptase polymerase chain treatment stratification as described elsewhere. Surgery was per- ϭ ϭ reaction (RT-PCR) revealed a strong correlation with TA by formed either at diagnosis (n 104), after pretreatment (n 23), later in the course of disease in 4S patients without cytotoxic treatment (n ϭ the telomeric repeat amplification protocol (TRAP) assay in 4), or in recurrent tumor after cytotoxic pretreatment (n ϭ 2). Median the majority of tumors that have been examined thus follow-up was 5.2 years (range, 1.2 to 10.6 years). Five-year OS of all far.16-18 Other components of the telomerase holoenzyme patients was 0.77 Ϯ 0.04 (localized disease stages 1 to 3, 0.92 Ϯ 0.03; complex, such as human telomerase RNA (hTR) and stage 4, 0.29 Ϯ 0.09; stage 4S, 0.92 Ϯ 0.06). Five-year EFS was 0.69 Ϯ Ϯ Ϯ telomerase protein 1 (TP1, TLP1, hTEP1), seem to be 0.04 (localized disease, 0.88 0.04; stage 4, 0.26 0.09; stage 4S, 0.73 Ϯ 0.10). expressed in both normal and tumor tissues, and expression levels of these genes revealed no or only limited correlation Protein Preparation and Telomerase Assay 19-21 with TA. A more precise definition of the molecular Neuroblastoma specimens were derived from snap-frozen material mechanism of TA by quantitative detection of RNA and of primary tumor biopsy or surgical resection collected in a tumor bank protein subunit expression may therefore determine whether and stored at Ϫ80°C until use. A tumor content exceeding 70% was TA independently predicts for aggressive clinical behavior mandatory for all of the samples included in this study. Extractions of in neuroblastoma. cellular proteins of neuroblastoma tumor specimens were prepared as previously described.23 The extracts were rapidly frozen in liquid In the present study, we extended our previous studies and nitrogen and stored at Ϫ80°C until further use. The protein concentra- analyzed TA in 133 neuroblastoma tumors according to stage tions were measured by use of the Coomassie Protein Assay Reagent classification using our modified and highly specific TRAP (Bio-Rad Laboratories, Inc, Hercules, CA) on an enzyme-linked assay. Furthermore, TA levels were correlated with expression immunosorbent assay reader and adjusted to 2 ␮g/␮L. of the catalytic subunits by quantitative RT-PCR for 75 cases For in vitro detection of TA, a modified version of the TRAP assay was used, including an internal PCR-amplification control from a using an innovative approach for real-time, on-line detection of commercially available kit (TRAPeze telomerase detection kit; Oncor, reaction kinetics on the LightCycler instrument (Roche Diag- Gaithersburg, MD), resulting in a 36–base pair product that was nostics, Mannheim, Germany). For selected cases, the feasi- coamplified with telomerase-elongated products in a competitive man- bility of RT-PCR performed on RNA from formalin-fixed and ner. Each analysis included the telomerase-positive Ewing’s tumor cell paraffin-embedded tissues was analyzed for expression of the line VH64, a heat-inactivated control (telomerase-positive control incubated at 85°C for 10 minutes before reaction), and a negative catalytic subunit hTRT by using the TITAN system (Roche control (3-[3-cholamidopropyl-dimethylammonio]-1-propane-sulfo- Diagnostics). Finally, we report the successful in situ immu- nate lysis buffer
Recommended publications
  • Expand Reverse Transcriptase from Escherichia Coli: AP401 (K) Deoxynucleoside-Triphosphate:DNA Deoxynucleotidyl-Transferase (RNA Directed) E.C.2.7.7.49
    For life science research only. Not for use in diagnostic procedures. Expand Reverse Transcriptase from Escherichia coli: AP401 (k) Deoxynucleoside-triphosphate:DNA deoxynucleotidyl-transferase (RNA directed) E.C.2.7.7.49 Cat. No. 11 785 826 001 1 000 U y Version 13 Cat. No. 11 785 834 001 5 000 U Content version: March 2020 Store at Ϫ15 to Ϫ25°C Product overview General handling instructions Pack content RNA preparation For high quality eucaryotic mRNA preparations it is Vial Content necessary to minimize the activity of RNases liberated Expand Reverse • 1000 U (Cat. No. 11 785 826 001) during cell lysis by using inhibitors of RNases or meth- ods that disrupt cells and inactivate RNases simultane- Transcriptase • 5000 U (Cat. No. 11 785 834 001) ously. A good overview of the methods is given in (4) as Expand Reverse cDNA synthesis buffer (first-strand) well as in (5). Suitable reagents for the isolation of total Transcriptase 250 mM Tris-HCl, 200 mM KCl, 2) RNA/or mRNA are the mRNA Isolation Kit and TriPure Buffer, 5 × conc. 25 mM MgCl2, 2.5% Tween 20 Isolation Reagent. (v/v), pH 8.3 (25°C). Consequently, it is also important to avoid the acciden- Dithiothreitol 100 mM tal introduction of trace amounts of RNases from other (DTT) solution potential sources in the laboratory, like glassware, plasticware, contaminating solutions and contamina- Storage and The undiluted enzyme is stable at –15 to –25°C through tion of the investigators hands. stability the expiration date printed on the label. The product is shipped on dry ice.
    [Show full text]
  • For Improvement of Nucleic Acid Synthesis and Ampli
    Europäisches Patentamt *EP001088891B1* (19) European Patent Office Office européen des brevets (11) EP 1 088 891 B1 (12) EUROPEAN PATENT SPECIFICATION (45) Date of publication and mention (51) Int Cl.7: C12N 15/55, C12N 15/54, of the grant of the patent: C12N 9/22, C12N 9/12, 12.01.2005 Bulletin 2005/02 C12Q 1/68, C12P 19/34 (21) Application number: 99119268.3 (22) Date of filing: 28.09.1999 (54) Thermostable enzyme promoting the fidelity of thermostable DNA polymerases - for improvement of nucleic acid synthesis and amplification in vitro Thermostabiles Enzym welches die Genauigkeit thermostabiler DNA Polymerasen erhöht - zur Verbesserung der Nucleinsäuresynthese und in vitro Amplifikation Enzyme thermostable pour augmenter la fidélité de polymèrase d’ADN thermostable - pour l’amélioration de la synthèse des acides nucléiques et d’amplification in vitro (84) Designated Contracting States: • KLENK H-P ET AL: "The complete genome AT BE CH CY DE DK ES FI FR GB GR IE IT LI LU sequence of the hyperthermophilic, MC NL PT SE sulphate-reducing archaeon Archaeoglobus fulgidus" NATURE,GB,MACMILLAN JOURNALS (43) Date of publication of application: LTD. LONDON, vol. 390, 27 November 1997 04.04.2001 Bulletin 2001/14 (1997-11-27), pages 364-370, XP002091622 ISSN: 0028-0836 (73) Proprietor: Roche Diagnostics GmbH • KALUZ S ET AL: "DIRECTIONAL CLONING OF 68298 Mannheim (DE) PCR PRODUCTS USING EXONUCLEASE III" NUCLEIC ACIDS RESEARCH,GB,OXFORD (72) Inventors: UNIVERSITY PRESS, SURREY, vol. 20, no. 16, 1 • Dr.Waltraud Ankenbauer January 1992 (1992-01-01), pages 4369-4370, 82377 Penzberg (DE) XP002072726 ISSN: 0305-1048 • Franck Laue • BOOTH P M ET AL: "ASSEMBLY AND CLONING 82396 Paehl-Fischen (DE) OF CODING SEQUENCES FOR NEUROTROPHIC • Dr.Harald Sobek FACTORS DIRECTLY FROM GENOMIC DNA 82377 Penzberg (DE) USING POLYMERASE CHAIN REACTION AND • Michael Greif URACIL DNA GLYCOSYLASE" 83661 Lenggries (DE) GENE,NL,ELSEVIER BIOMEDICAL PRESS.
    [Show full text]
  • (10) Patent No.: US 8715987 B2
    US008715987B2 (12) United States Patent (10) Patent No.: US 8,715,987 B2 Johnson et al. (45) Date of Patent: May 6, 2014 (54) SOLUBILIZED PHOSPHOLIPIDS FOR WO WOO 132887 A1 5, 2001 STABILIZING NUCLECACID WO WO2O080 13885 A2 1, 2008 POLYMERASES WO WO2O08077O17 A2 6, 2008 OTHER PUBLICATIONS (75) Inventors: Donald Johnson, Brookline, MA (US); Thomas C. Evans, Jr., Topsfield, MA Manual Translation CN 101570792A, Nov. 2009.* Barnes, WM. “The fidelity of Taq polymerase catalyzing PCR is (US) improved by an N-terminal deletion”. Gene, 112(1):29-35, 1992. Cann, et al., “A heterodimeric DNA polymerase: evidence that mem (73) Assignee: New England Biolabs, Inc., Ipswich, bers of Euryarchaeota possess a distinct DNA polymerase.”. Proc. MA (US) Natl. Acad. Sci. USA,95: 14250-5, 1998. Capitani.etal, “Effect of phosphatidylcholine vesicles on the activity (*) Notice: Subject to any disclaimer, the term of this of DNA polymerase-O.", Mol and Cell Biochem 27:137-138, 1979. patent is extended or adjusted under 35 Chien, et al., “Deoxyribonucleic acid polymerase from the extreme U.S.C. 154(b) by 0 days. thermophile Thermus aquaticus”,Journal of Bacteriology, 127:1550, 1976. Diaz, et al., "Accuracy of replication in the polymerase chain reaction. (21) Appl. No.: 13/450,549 Comparison between Thermotoga maritima DNA polymerase and Thermus aquaticus DNA polymerase.”. Brazilian Journal of Medical (22) Filed: Apr. 19, 2012 and Biological Research, 31:1239, 1998. Eckert , et al. “The Fidelity of DNA Polymerases used in the (65) Prior Publication Data polymerase chain reactions'. Oxford University Press, New York, US 2012/O282669 A1 Nov.
    [Show full text]
  • Pwo DNA Polymerase Deoxynucleoside-Triphosphate: DNA Deoxynucleotidyl-Transferase (DNA-Directed); EC 2.7.7.7
    Version 060918 G:\products\productflyer\pcr\polymerasen\proof\descr_m3002_pwo_en.docx ENAXXON fon: +49(0)731 – 3608 123 X G fax: +49(0)731 – 3608 962 b i o s c i e n c e E-Mail: [email protected] Pwo DNA Polymerase Deoxynucleoside-triphosphate: DNA deoxynucleotidyl-transferase (DNA-directed); EC 2.7.7.7 Product Cat# Package size Pwo DNA Polymerase (proof-reading polymerase) M3002.0100 100 units Pwo DNA Polymerase (proof-reading polymerase) M3002.0500 2 x 250 units Pwo DNA Polymerase (proof-reading polymerase) M3002.1250 5 x 250 units Description The Genaxxon bioscience Pwo DNA Polymerase is a thermostable enzyme possessing 5‘-3‘ DNA polymerase and 3‘-5‘ proof reading exonuclease activities. It is isolated from the hyperthermophilic marine archae Pyroccocus woesei (Pwo). The enzyme provides extremely high fidelity. Whereas the enzyme is not able to amplify long fragments as efficiently as the Genaxxon Taq polymerase because of its very high exonuclease activity. To overcome this restriction we recommend to use the Genaxxon ReproFast DNA Polymerase, which will provide a more robust synthesis of longer amplification products (Barnes et al. (1994) Proc. Natl. Acad. Sci., USA 91, 2216-2220). Use of the Genaxxon Pwo DNA Polymerase in amplification results in blunt-ended products, which is not recommended for cloning into T/A vectors. Concentration: 2.5 units/µL Unit definition: One unit is defined as the amount of enzyme that incorporates 10nmoles of dNTPs into acid-insoluble form in 30 min at 72°C under the assay conditions (25mM TAPS (tris-(hydroxymethyl)methyl-amino-propane-sulphonic acid, sodium salt) pH9.3 (at 25°C), 50mM KCl, 2mM MgCl2, 1mM ß-mercaptoethanol) and activated calf thymus DNA as substrate.
    [Show full text]
  • Taq DNA Polymerase
    Polymerase Chain Reaction (PCR) • PCR is a technique which is used to amplify the number of copies of a specific region of DNA, in order to produce enough DNA to be adequately tested. • As a result, it now becomes possible to analyze and characterize DNA fragments found in minute quantities in different samples. Polymerase Chain Reaction (PCR) • PCR carry out for – DNA cloning – sequencing, – DNA-based phylogeny, or – functional analysis of genes; – the diagnosis of diseases; – genetic fingerprints and – the detection and diagnosis of infectious diseases. PROCEDURE ….. PCR Reagents • Template DNA (e.g., plasmid DNA, genomic DNA). • Forward and reverse PCR primers. • MgCl2 (25 mM). • dNTPs (a mixture of 2.5 mM dATP, dCTP, dGTP, and dTTP). • PCR buffer: 500 mM KCl, 100 mM Tris-HCl, pH 8.3, 25°C. PCR Reagents • Thermal stable DNA polymerase – DNA polymerases without 3′ → 5′ proofreading activity • Taq DNA polymerase • Tth DNA polymerase • Tfl DNA polymerase – DNA polymerases with 3′ → 5′ proofreading activity: • Pwo DNA polymerase • Pfu DNA polymerase • Tli DNA polymerase • Vent DNA polymerase PCR Reagents • Optional: PCR additives /cosolvents (optional; e.g., • betaine, glycerol, DMSO, formamide, bovine serum albumin, ammonium sulfate, polyethylene glycol, gelatin, Tween-20, Triton X-100, β-mercaptoethanol, or tetramethylammonium chloride). Polymerase Chain Reaction (PCR) • Initialization step: 94–96 °C (or 98 °C if extremely thermostable polymerases are used), for 1–9 minutes. – the complete separation of the DNA strands and unfolding secondary structures – This stage also required for DNA polymerases that require heat activation by hot-start PCR. Polymerase Chain Reaction (PCR) • Denaturation step: 94–98 °C for 20–30 seconds.
    [Show full text]
  • Roche Applied Science
    FNR498_PCR_RZ 02.06.2006 14:55 Uhr Seite 1 C M Y CM MY CY CMY K PCR Applications Manual 3rd edition www.roche-applied-science.com Probedruck Acknowledgement We would like to thank all contributors and editors for their diligent efforts. Without their work, this project would not have been possible. Impressum Editorial Management: Degen, Hans-Joachim, Ph.D. Deufel, Annette, Ph.D. Eisel, Doris Grünewald-Janho, Stefanie Keesey, Joe, Ph.D. Art Direction: Fanz & Neumayer, Schifferstadt Layout Design and Typesetting: Active Artware GmbH, Saarbrücken © 2006 by Roche Diagnostics GmbH, Mannheim All rights reserved. No part of this booklet may be reproduced in any form without written permission of the publishers. Printed in Germany. www.roche-applied-science.com Table of Contents 1 Introduction Page 1.1 Principles of PCR and RT-PCR ........................................................................................................................... 9 1.2 The Evolution of PCR ..........................................................................................................................................11 1.3 Purpose of this PCR Applications Manual...................................................................................................15 2 General Guidelines Page 2.1 Preventing Contamination in the PCR Laboratory....................................................................................19 2.1.1 Setting Up the PCR Laboratory Space Correctly.......................................................................................20
    [Show full text]
  • Sigma-Aldrich Biochemical Reagents
    Expanding access to our Biochemical Reagent products New distribution agreement with Sigma-Aldrich Material No. SKU name Material No. SKU name 10148334001 2.3-Diphosphoglycerate Test Kit 11816594001 Agarose MS, 500 g 11051466001 2’-Deoxy-guanosine-5’-TP Solution 10171832001 Aldehyde Dehydrogenase from Yeast 10127833001 3-HBDH, Grade II 03359123001 Alkaline Phosphatase, recomb. 10127841001 3-HBDH, Grade II 10602442001 alpha-2 -Macroglobulin 03353621001 5’/3’ RACE Kit, 2nd generation 10102814001 alpha-Amylase (pig pancreas) 11296736001 5-Bromo-2´-dU Labeling/Detection Kit I 11742027001 alpha-Glucosidase Assay, 1 pc 11299964001 5-Bromo-2´-dU Labeling/Detection Kit II 10835269001 Ampicillin, 50 g 11444611001 5-Bromo-2´-dU Labeling/Detection Kit III 10835242001 Ampicillin, 5 g 10280879001 5-Bromo-2’-deoxy-uridine 10102857001 Amyloglucosidase from Aspergillus niger 10988537001 7-Deaza-2’-deoxy-GTP, Di-Li 11202367001 Amyloglucosidase from Aspergillus niger 10102946001 ABTS 11202332001 Amyloglucosidase, Lyo., SQ (500 U) 11204530001 ABTS Buffer, 125 ml 11858777001 Annexin V Fluos Staining Kit 11112597001 ABTS Buffer, 16.7 g 11828681001 Annexin-V-Fluos 11684302001 ABTS Solution 11988549001 Annexin-V-Fluos Staining Kit 11204521001 ABTS Tablets, 5 mg 11170376001 Anti-BRDU, Formalin Grade 11112422001 ABTS Tablets, 50 mg 11202693001 Anti-BRDU-Flourescein, Formalin Grade 10101893001 Acetyl-CoA, 10 mg 11585860001 Anti-BRDU-Peroxidase, Formalin Grade 11585371001 Acetyl-CoA, 200 mg 11667149001 Anti-c-myc, 200 ug 10101907001 Acetyl-CoA, 50 mg 11667203001 Anti-c-myc, 5 mg 11498045910 Actin RNA Probe, DIG, 2 ug 11814150001 Anti-c-myc-Peroxidase 10102105001 Adenosine Deaminase (ADA), 10 mg 11093274910 Anti-Digoxigenin AP-conjugate 10102121001 Adenosine Deaminase (ADA), susp. 11333062910 Anti-Digoxigenin MAB 10102547001 Adenylyl-imidodiphosphate (AMP-PNP), Li4 11207733910 Anti-Digoxigenin POD-conjugate 10127558001 ADH, susp.
    [Show full text]
  • Overview of Thermostable DNA Polymerases for Classical PCR Applications: from Molecular and Biochemical Fundamentals to Commercial Systems
    Appl Microbiol Biotechnol (2013) 97:10243–10254 DOI 10.1007/s00253-013-5290-2 MINI-REVIEW Overview of thermostable DNA polymerases for classical PCR applications: from molecular and biochemical fundamentals to commercial systems Kay Terpe Received: 22 July 2013 /Revised: 20 September 2013 /Accepted: 22 September 2013 /Published online: 1 November 2013 # Springer-Verlag Berlin Heidelberg 2013 Abstract During the genomics era, the use of thermostable before becoming standard. Time and temperature of denaturing DNA polymerases increased greatly. Many were identified and can deactivate the polymerase more or less depending on the described—mainly of the genera Thermus, Thermococcus and used enzyme. Factors like DNA origin, primer and product Pyrococcus. Each polymerase has different features, resulting length as well as guanine–cytosine content should have a direct from origin and genetic modification. However, the rational influence on the choice of polymerase (Wu et al. 1991). Salt, choice of the adequate polymerase depends on the application magnesium and deoxyribonucleotide triphosphate (dNTP) con- itself. This review gives an overview of the most commonly centrations can greatly affect the PCR (Ling et al. 1991; used DNA polymerases used for PCR application: KOD, Pab Owczarzy et al. 2008). Additives like BSA (Al-Soud and (Isis™), Pfu, Pst (Deep Vent™), Pwo, Taq, Tbr, Tca, Tfi, Tfl, Rådström 2001), dimethylsulfoxide (Chester and Marshak Tfu, Tgo, Tli (Vent™), Tma (UITma™), Tne, Tth and others. 1993), formamide (Sarkar et al. 1990), betaine (Henke et al. 1997; Rees et al. 1993), ethylene glycol and 1,2-propanediol Keywords Thermostable DNA polymerase . Polymerase (Zhang et al. 2009), and others (Al-Soud and Rådström 2000; chain reaction (PCR) .
    [Show full text]
  • ROCHE PRODUCTS for Distribution by Sigma-Aldrich
    ROCHE PRODUCTS For Distribution by Sigma-Aldrich Researchers will soon be able to turn to Sigma-Aldrich as an Sigma-Aldrich and Roche are currently working on processes to ensure a seamless transition for customers. It is expected that easy, single source supplier of well-respected, high quality Roche products will be available to purchase through the award- winning Sigma-Aldrich website in mid-2015. Until then, customers genomics, proteomics and cell analysis reagents and kits should continue to purchase products through their standard from Roche. Roche channels. The products listed below are complementary to Sigma-Aldrich's biology offer and industry-leading levels of service. Together, we will provide researchers with global access to key materials across For more information, visit their workflow. sigmaaldrich.com/roche Roche Product List Cat. No. Product Description Cat. No. Product Description 10148334001 2.3-Diphosphoglycerate Test kit 10127558001 ADH, susp. 1g (34ml) 11051466001 2'-Deoxy-guanosine-5'-TP Solution 11685660001 Agarose LE, 100g 10127833001 3-HBDH, Grade II 11685678001 Agarose LE, 500g 10127841001 3-HBDH, Grade II 11388983001 Agarose MP, 100g 03353621001 5'/3' RACE Kit, 2nd generation 11388991001 Agarose MP, 500g 11296736001 5-Bromo-2´-dU Labeling/Detection Kit I 11816586001 Agarose MS, 100 g 11299964001 5-Bromo-2´-dU Labeling/Detection Kit II 11816594001 Agarose MS, 500 g 11444611001 5-Bromo-2´-dU Labeling/Detection Kit III 10171832001 Aldehyde Dehydrogenase from Yeast 10280879001 5-Bromo-2'-deoxy-uridine 03359123001
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2017/0002401 A1 TRINH Et Al
    US 2017.0002401A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2017/0002401 A1 TRINH et al. (43) Pub. Date: Jan.5, 2017 (54) COMPOSITIONS, KITS AND METHODS FOR (60) Provisional application No. 61/357,031, filed on Jun. SYNTHESIS AND/OR DETECTION OF 21, 2010. NUCLEC ACDS (71) Applicant: LIFE TECHNOLOGIES Publication Classification CORPORATION, Carlsbad, CA (US) (51) Int. Cl. (72) Inventors: Christopher TRINH, San Jose, CA CI2O I/68 (2006.01) (US); Tom XU, Castro Valley, CA (52) U.S. Cl. (US); Yating SHI, San Leandro, CA CPC ....... CI2O I/686 (2013.01); C12Y 207/07007 (US); Ferrier LE, San Jose, CA (US); Claire MARJORIBANKS, Campbell, (2013.01); C12O 1/6848 (2013.01) CA (US) (21) Appl. No.: 15/198,689 (57) ABSTRACT (22) Filed: Jun. 30, 2016 A composition comprising a thermostable DNA polymerase; Related U.S. Application Data and a PCR inhibitor blocking agent, wherein the PCR (62) Division of application No. 13/165,571, filed on Jun. inhibitor blocking agent is present in an amount effective to 21, 2011, now Pat. No. 9,410,194. enhance tolerance of an assembled PCR to a PCR inhibitor. Patent Application Publication Jan. 5, 2017. Sheet 1 of 13 US 2017/0002401 A1 37.5 Assay Pane O ACADV. A. APOE 35 v ASB7 C2 KXED3 32.5 WSF3 27.5 25 22.5 Taqian(8) Fast Advanced Taqiang Universal PCR ?iaster fix Master ?ix FG. 1 Patent Application Publication Jan. 5, 2017. Sheet 2 of 13 US 2017/0002401 A1 OOO ...i. --- 2 3 4 5 6 F 8 20 222 23 24 25 26 27 28 29 303 Cycle Number FG.
    [Show full text]
  • SUPPORTING INFORMATION Deoxynucleoside Triphosphates
    Electronic Supplementary Material (ESI) for Organic & Biomolecular Chemistry This journal is © The Royal Society of Chemistry 2013 SUPPORTING INFORMATION Deoxynucleoside triphosphates bearing histamine, carboxylic acid, and hydroxyl residues – Synthesis and biochemical characterization Marcel Hollenstein* Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland. Table of Contents: 1. General procedures 1 2. Synthesis of compounds S1-S3 3-5 3. Oligonucleotides 5 4. Additional primer extension reactions 7-9 5. Conversion of modified DNA to unmodified DNA 10-11 6. Sequencing reactions 12-15 7. References 16 1 Electronic Supplementary Material (ESI) for Organic & Biomolecular Chemistry This journal is © The Royal Society of Chemistry 2013 1. General procedures: All reactions were performed under Ar in flame-dried glassware. Anhydrous solvents for reactions were obtained by filtration through activated aluminum oxide, or by storage over 4Å activated molecular sieves. Flash chromatography was performed using silica gel (230–400 mesh) from Silicycle. Thin layer chromatography was carried out on precoated glass-backed plates of silica gel (0.25mm, UV254) from Macherey-Nagel. All chemicals and solvents used were purchased from Sigma-Aldrich, unless stated otherwise. 4-pentynoic acid methyl ester was synthesized following a literature procedure.1 5-iodo-2'-deoxyuridine was purchased from AK Scientific and 5-iodo-2'-deoxycytidine was purchased from Carbosynth. NMR spectra were recorded on a Bruker DRX-400 or a Bruker AC-300 spectrometer (400 or 300 MHz for 1H, 101 or 75.5 MHz for 13C, 121.4 MHz for 31P, and 376.5 MHz for 19F) and all spectra were referenced to the signals of the corresponding solvent.
    [Show full text]
  • UPF1 Promotes the Formation of R Loops to Stimulate DNA Double-Strand Break Repair ✉ Greg H
    ARTICLE https://doi.org/10.1038/s41467-021-24201-w OPEN UPF1 promotes the formation of R loops to stimulate DNA double-strand break repair ✉ Greg H. P. Ngo 1, Julia W. Grimstead1 & Duncan M. Baird 1 DNA-RNA hybrid structures have been detected at the vicinity of DNA double-strand breaks (DSBs) occurring within transcriptional active regions of the genome. The induction of DNA- RNA hybrids strongly affects the repair of these DSBs, but the nature of these structures and 1234567890():,; how they are formed remain poorly understood. Here we provide evidence that R loops, three-stranded structures containing DNA-RNA hybrids and the displaced single-stranded DNA (ssDNA) can form at sub-telomeric DSBs. These R loops are generated independently of DNA resection but are induced alongside two-stranded DNA-RNA hybrids that form on ssDNA generated by DNA resection. We further identified UPF1, an RNA/DNA helicase, as a crucial factor that drives the formation of these R loops and DNA-RNA hybrids to stimulate DNA resection, homologous recombination, microhomology-mediated end joining and DNA damage checkpoint activation. Our data show that R loops and DNA-RNA hybrids are actively generated at DSBs to facilitate DNA repair. 1 Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK. ✉email: [email protected] NATURE COMMUNICATIONS | (2021) 12:3849 | https://doi.org/10.1038/s41467-021-24201-w | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-021-24201-w elomeres are nucleoprotein structures at the end of linear Results Tchromosomes that protect the DNA from being recognized DNA resection contributes to deletion formation at telomere as DNA double-strand breaks (DSBs).
    [Show full text]