DOCSLIB.ORG

Design and Synthesis of Fluoroquinophenoxazines That Interact with Human Telomeric G-Quadruplexes and Their Biological Effects1

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Design and Synthesis of Fluoroquinophenoxazines That Interact with Human Telomeric G-Quadruplexes and Their Biological Effects1 Vol. 1, 103–120, December 2001 Molecular Cancer Therapeutics 103 Design and Synthesis of Fluoroquinophenoxazines That Interact with Human Telomeric G-Quadruplexes and Their Biological Effects1 Wenhu Duan,2,3 Anupama Rangan,2 center of the external tetrad but within the loop region. Hariprasad Vankayalapati,2,3 Mu-Yong Kim,3 Molecular modeling using simulated annealing was 4 Qingping Zeng, Daekyu Sun, Haiyong Han, performed on the FQP-parallel G-quadruplex complex to 5 Oleg Yu. Fedoroff, David Nishioka, determine the optimum FQP orientation and key 6 Sun Young Rha, Elzbieta Izbicka, molecular interactions with the telomeric G-quadruplex Daniel D. Von Hoff, and Laurence H. Hurley3,7,8 structure. On the basis of the results of these studies, College of Pharmacy, The University of Texas, Austin, Texas 78712 two additional FQP analogues were synthesized, which [W. D., A. R., M-Y. K., Q. Z., O. Y. F., L. H. H.]; Institute for Drug Development, San Antonio, Texas 78245 [D. S., S. Y. R., E. I., were designed to test the importance of these key D. D. V. H.]; Department of Biology, Georgetown University, interactions. These analogues were evaluated in the Taq Washington, DC 20057 [D. N.]; and Arizona Cancer Center, Tucson, Arizona 85724 [H. H., D. D. V. H., L. H. H.] polymerase stop assay for G-quadruplex interaction. The data from this study and the biological evaluation of these three FQPs, using cytotoxicity and a sea urchin Abstract embryo system, were in accord with the predicted more In this study we have identified a new structural potent telomeric G-quadruplex interactions of the initial motif for a ligand with G-quadruplex interaction lead compound and one of the analogues. On the basis that results in biological effects associated with G- of these structural and biological studies, the design of quadruplex-interactive compounds. Fluoroquinolones more potent and selective telomeric G-quadruplex- have been reported to possess weak telomerase interactive compounds can be envisaged. inhibitory activity in addition to their better known bacterial gyrase poisoning. Starting with a Introduction fluoroquinobenzoxazine, which has modest potency Fluoroquinolones are best known therapeutically as bacterial in a human topoisomerase II assay, we have gyrase inhibitors (1, 2) but more recently have also been designed a more potent inhibitor of telomerase that demonstrated to be active against eukaryotic topoisomerase has lost its topoisomerase II poisoning activity. II, either as catalytic inhibitors or topoisomerase II poisons This fluoroquinophenoxazine (FQP) interacts with (3), or as telomerase inhibitors (4). One such group of com- G-quadruplex structures to inhibit the progression pounds, the quinobenzoxazines, typified by A-62176 of Taq polymerase in a G-quadruplex polymerase (Fig. 1B), has served as a starting point for the design of more 1 stop assay. In addition, we demonstrate by H NMR potent topoisomerase II inhibitors using a structure-based studies that this compound interacts with telomeric approach (5). The extended aromatic conjugation system of G-quadruplex structures by external stacking to the A-62176 suggested to us that quinobenzoxazines may also G-tetrad with both the unimolecular fold-over and the intercalate with the more expansive system of G-quadruplex parallel G-quadruplex structures. A photocleavage assay DNA and thereby be telomerase inhibitors in parallel with other confirms the FQP interaction site, which is located off G-quadruplex-interactive compounds, such as the anthraqui- nones (6–10), cationic porphyrins (11–13),9 piperazines (14), ethidium compounds, (15), and a pentacyclicacridinium com- pound (16). After we started this project, an independent report Received 8/17/01; revised 9/21/01; accepted 10/2/01. The costs of publication of this article were defrayed in part by the that bacterial quinolones may be weak telomerase inhibitors (4) payment of page charges. This article must therefore be hereby marked also supported the idea that a ring-extended fluoroquinolone advertisement in accordance with 18 U.S.C. Section 1734 solely to indi- would be a more potent telomerase inhibitor. cate this fact. 1 Supported by NIH Grants CA88310 and CA67760. G-quadruplexes (Fig. 1A) were first identified in 1962 (17); 2 These authors contributed equally to this paper. however, their possible biological significance was only sug- 3 Present address: College of Pharmacy, The University of Arizona, Tuc- son, AZ 85721. gested starting in the late 1980s (18–23), and they were first 4 Present address: Monsanto Co., St. Louis, MO 63167. proposed to be potential targets for drug design in 1989 (24). 5 Present address: Department of Biomolecular Sciences, University of The existence of chaperone proteins that facilitate their for- Manchester Institute of Science and Technology, Manchester M60 1QD, England. mation (25–27), G-quadruplex binding proteins that recog- 6 Present address: Cancer Metastasis Research Center, Yonsei University College of Medicine, Seoul, Korea. 7 Present address: College of Pharmacy and Department of Chemistry, The University of Arizona, Tucson, AZ 85721 and Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, AZ 85724. 9 D-F. Shi, R. T. Wheelhouse, D. Sun, and L. H. Hurley. Quadruplex- 8 To whom requests for reprints should be addressed, at Arizona Cancer interactive agents as telomerase inhibitors: synthesis of porphyrins and Center, 1515 N. Campbell Ave., Tucson, AZ 85724. Phone: 520-626-5622; structure-activity relationship for the inhibition of telomerase. J. Med. Fax: 520-626-5623; E-mail: [email protected]. Chem., in press, 2001. Downloaded from mct.aacrjournals.org on September 25, 2021. © 2001 American Association for Cancer Research. 104 FQP and G-Quadruplex Interactions Fig. 1. A, G-tetrad and G-quadru- plexes. Panel a, four guanine residues forming a planar structure G-tetrad through Hoogsteen hydrogen bond- ing. Panel b, a parallel G-quadruplex model. Panel c, an intermolecular anti- parallel G-quadruplex model. Panel d, an intramolecular basket G-quadru- plex model. Each parallelogram in panels b– d represents a G-tetrad. B, structures of the topoisomerase II-interactive compound (A-62176) and G-quadruplex-interactive com- pounds QQ58, QQ27, QQ28, and TMPyP4. nize these structures (25, 28–31), and G-quadruplex-selec- G-quadruplex-interactive compounds have aroused tive helicases (32–34) that unwind these structures make more interest recently because it has been demonstrated their existence in vivo in human cells a real possibility. Re- that these compounds not only inhibit telomerase in cently their in vivo existence in ciliates has been supported cell-free (6, 9) and in in vitro systems (36) but also by antibody studies (35). cause telomere shortening and cell crisis in cancer cells Downloaded from mct.aacrjournals.org on September 25, 2021. © 2001 American Association for Cancer Research. Molecular Cancer Therapeutics 105 (14).10 A number of reviews on G-quadruplex and their targeting matography (ethyl acetate:hexane ϭ 2:1), yielding a bright 1 ␦ by small molecules have appeared recently (37–45). yellow powder (3.81 g; 83%). H NMR (CDCl3) (mixture of In this contribution we demonstrate that QQ58 (Fig. 1B), a isomers; multiplet, m; singlet, s) 1.17–1.26 (m, 3H), 2.95 (s, FQP11 that lacks bacterial gyrase or topoisomerase II poi- br, 1H), 4.10–4.25 (m, 2H), 7.05–7.20 (m, 1H), 7.33 (m, 2H), soning activity, is able to bind to G-quadruplex structures 7.43 (m, 1H), 7.52 (m, 3H), 7.85 (m, 1H), 8.69 (s, 0.7H), 8.74 and, by doing so, inhibit telomerase. Structural insight into (s, 0.3H); 19F NMR ␦ Ϫ156.2 (m, 1F), Ϫ154.5 (m, 0.75F), the interactions of this compound with both intermolecular Ϫ135.4 (m, 0.25F), Ϫ140.3 (m, 0.75F), Ϫ139.4 (m, 1F), 139.3 and intramolecular G-quadruplex structures has been obtained (m, 0.25F); and MS (CI): m/z 474 (M ϩ H). by one-dimensional 1H NMR molecular modeling and a photo- Ethyl 1,2-difluoro-4-oxo-4H-pyrido[3,2,1-k,l]-(3-amino- cleavage assay. We also demonstrate that this compound 2-hydroxydibenzofuranyl)[1,2-g]phenoxazine-5-carboxy- induces chromosomal effects and slowing of the division late (3). Ethyl 3-(2-hydroxydibenzofuran-3-amino)-2-[(2,3,4,5,- of sea urchin embryos typical of G-quadruplex-interactive tetrafluorophenyl)carbonyl] prop-2-enoate (2.32 g; 4.9 mmol) compounds. On the basis of molecular modeling studies, two and NaH (60% in mineral oil; 0.45 g; 11.3 mmol) were mixed additional analogues of this compound were designed and with freshly distilled tetrahydrofuran and stirred at Ϫ78°C for 15 synthesized (QQ27 and QQ28; Fig. 1B), and their interactions min. The mixture was allowed to warm to room temperature with G-quadruplex structures and biological effects were ex- gradually and then heated at 65°C for 30 min. The excess NaH amined. The maintenance or loss of biological potency paral- was quenched by addition of 30 ml of methanol. The solution leled their interactions with the G-quadruplex structure, and this was evaporated to dryness, and the product was purified was predicted on the basis of molecular modeling. through flash column chromatography, yielding a yellow pow- der (1.84 g; 89%): mp Ͼ229°C (decomposed); 1H NMR ␦ ϭ ϭ Materials and Methods (CDCl3) 9.01 (s, 1H), 7.90 (d, 1H, J 7.8 Hz), 7.80 (dd, 1H, J ϭ ϭ Synthesis of Extended Fluoroquinolones (QQ58, 7.8, 2.1 Hz), 7.39 (t, 1H, J 6.9 Hz), 4.48 (q, 2H, J 7.2 Hz), 19 QQ27, and QQ28 in Figure 2) 1.49 (t, 3H, J ϭ 7.2 Hz); F NMR Ϫ133.6 (dd, 1F, J ϭ 23, 10 Hz), Ϫ ϭ ϩ General. All of the melting points were recorded on a Tho- 1561.5 (dd, 1F, J 21, 9 Hz); and MS (CI): m/z 434 (M H).
Load more

Recommended publications
  • 6.Start.Stop.07.Ppt [Read-Only]
    Accessory factors summary 1. DNA polymerase can’t replicate a genome. Solution ATP? No single stranded template Helicase + The ss template is unstable SSB (RPA (euks)) - No primer Primase (+) No 3’-->5’ polymerase Replication fork Too slow and distributive SSB and sliding clamp - Sliding clamp can’t get on Clamp loader (γ/RFC) + Lagging strand contains RNA Pol I 5’-->3’ exo, RNAseH - Lagging strand is nicked DNA ligase + Helicase introduces + supercoils Topoisomerase II + and products tangled 2. DNA replication is fast and processive DNA polymerase holoenzyme 1 Maturation of Okazaki fragments Topoisomerases control chromosome topology Catenanes/knots Topos Relaxed/disentangled •Major therapeutic target - chemotherapeutics/antibacterials •Type II topos transport one DNA through another 2 Starting and stopping summary 1. DNA replication is controlled at the initiation step. 2. DNA replication starts at specific sites in E. coli and yeast. 3. In E. coli, DnaA recognizes OriC and promotes loading of the DnaB helicase by DnaC (helicase loader) 4. DnaA and DnaC reactions are coupled to ATP hydrolysis. 5. Bacterial chromosomes are circular, and termination occurs opposite OriC. 6. In E. coli, the helicase inhibitor protein, tus, binds 7 ter DNA sites to trap the replisome at the end. 7. Eukaryotic chromosomes are linear, and the chromosome ends cannot be replicated by the replisome. 8. Telomerase extends the leading strand at the end. 9. Telomerase is a ribonucleoprotein (RNP) with RNA (template) and reverse-transcriptase subunits. Isolating DNA sequences that mediate initiation 3 Different origin sequences in different organisms E. Coli (bacteria) OriC Yeast ARS (Autonomously Replicating Sequences) Metazoans ???? Initiation in prokaryotes and eukaryotes Bacteria Eukaryotes ORC + other proteins load MCM hexameric helicases MCM (helicase) + RPA (ssbp) Primase + DNA pol α PCNA:pol δ + RFC MCM (helicase) + RPA (ssbp) PCNA:pol δ + RFC (clamp loader) Primase + DNA pol α PCNA:pol δ + DNA ligase 4 Crystal structure of DnaA:ATP revealed mechanism of origin assembly 1.
    [Show full text]
  • A DNA Gyrase-Binding Site at the Center of the Bacteriophage Mu Genome Is Required for Efficient Replicative Transposition (Supercoiling/Topoisomerases) MARTIN L
    Proc. Natl. Acad. Sci. USA Vol. 87, pp. 8716-8720, November 1990 Biochemistry A DNA gyrase-binding site at the center of the bacteriophage Mu genome is required for efficient replicative transposition (supercoiling/topoisomerases) MARTIN L. PATOtt§, MARTHA M. HOWE¶, AND N. PATRICK HIGGINS" tDepartment of Microbiology and Immunology, University of Colorado Health Sciences Center, Denver, CO 80262; tDepartment of Pediatrics, National Jewish Center for Immunology and Respiratory Medicine, Denver, CO 80206; $Department of Microbiology and Immunology, University of Tennessee, Memphis, TN 38163; and I'Department of Biochemistry, University of Alabama, Birmingham, AL 35294 Communicated by Nicholas R. Cozzarelli, August 15, 1990 ABSTRACT We have discovered a centrally located site genome for sequences that might enhance replication by that is required for efficient replication of bacteriophage Mu altering DNA supercoiling. Of particular usefulness in our DNA and identified it as a strong DNA gyrase-binding site. studies was a class of mutants of Mu called nuB (15). These Incubation of Mu DNA with gyrase and enoxacin revealed a mutant phage were isolated for their ability to grow on a host cleavage site 18.1 kilobases from the left end of the 37.2- gyrB mutant on which wild-type Mu does not grow. One kilobase genome. Two observations indicate a role for the site hypothesis to explain this phenotype was that the nuB in Mu replication: mutants of Mu, able to grow on an Esche- mutants have a gyrase-binding site with increased affinity for richia coli gyrB host that does not allow growth of wild-type the host enzyme.
    [Show full text]
  • Antimycobacterial Activity of DNA Intercalator Inhibitors of Mycobacterium Tuberculosis Primase Dnag
    HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author J Antibiot Manuscript Author (Tokyo). Author Manuscript Author manuscript; available in PMC 2017 November 15. Published in final edited form as: J Antibiot (Tokyo). 2015 March ; 68(3): 153–157. doi:10.1038/ja.2014.131. Antimycobacterial activity of DNA intercalator inhibitors of Mycobacterium tuberculosis primase DnaG Chathurada Gajadeeraa,#, Melisa J. Willbyb,#, Keith D. Greena, Pazit Shaulc, Micha Fridmanc, Sylvie Garneau-Tsodikovaa,*, James E. Poseyb,*, and Oleg V. Tsodikova,* aDepartment of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, 40536-0596, USA bDivision of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA cSchool of Chemistry, Tel Aviv University, Tel Aviv, 66978, Israel Abstract Due to the rise in drug resistance in tuberculosis combined with the global spread of its causative pathogen, Mycobacterium tuberculosis (Mtb), innovative anti-mycobacterial agents are urgently needed. Recently, we developed a novel primase-pyrophosphatase assay and used it to discover inhibitors of an essential Mtb enzyme, primase DnaG (Mtb DnaG), a promising and unexplored potential target for novel anti-tuberculosis chemotherapeutics. Doxorubicin, an anthracycline antibiotic used as an anticancer drug, was found to be a potent inhibitor of Mtb DnaG. In this study, we investigated both inhibition of Mtb DnaG and the inhibitory activity against in vitro growth of Mtb and M. smegmatis (Msm) by other anthracyclines, daunorubicin and idarubicin, as well as by less cytotoxic DNA intercalators: aloe-emodin, rhein, and a mitoxantrone derivative. Generally, low-μM inhibition of Mtb DnaG by the anthracyclines was correlated with their low- μM minimum inhibitory concentrations.
    [Show full text]
  • DNA Replication
    Research Article Curr Trends Biomedical Eng & Biosci Volume 16 Issue 4 - September 2018 Copyright © All rights are reserved by Tariku Simion DOI: 10.19080/CTBEB.2018.16.555942 DNA Replication Tariku Simion* South Agricultura Research Institute, Arbaminch Agricultural Research Center, Ethopia Submission: June 06, 2018; Published: September 18, 2018 *Corresponding author: Tariku Simion, Southern Agricultural Research Institute, Arbaminch Agricultural Research Center, Arba Minch, Ethiopia, Email: Abstract Nearly every cell in a person’s body has the same DNA. Most DNA is located in the cell nucleus, but a small amount of DNA can also be found in the mitochondria. DNA was thought to be a simple molecule, consisting of nucleotides strung together like beads on a string.By the late 1940s biochemists knew that DNA was a very long polymer made up of millions of nucleotides. DNA is made up of two strands and each strand of the original DNA molecule serves as a template for the production of the complementary strand, a process referred to as semi conservative replication. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication. DNA usually exists as a todouble-stranded the four-nucleobase structure, adenine; with bothcytosine, strands guanine, coiled and together thymine, to form commonly the characteristic abbreviated double- as A, C, helix. G and Each T. This single review strand was of DNA assumed is a chain to have of four the historicaltypes of nucleotides. background Nucleotides of DNA replicationand in DNA contain major a deoxyriboseDNA replication sugar, steps a phosphate, and its function. and a nucleobase. The four types of nucleotide correspond Keywords: Nucleobase;Double- helix;Nucleus;Complementary and deoxyribose Introduction joined to one another in a chain by covalent bonds between the humans and almost all other organisms.
    [Show full text]
  • DNA Helicase-SSB Interactions Critical to the Regression and Restart of Stalled DNA Replication Forks in Escherichia Coli
    G C A T T A C G G C A T genes Review DNA Helicase-SSB Interactions Critical to the Regression and Restart of Stalled DNA Replication Forks in Escherichia coli Piero R. Bianco Center for Single Molecule Biophysics, University at Buffalo, SUNY, Buffalo, NY 14221, USA; pbianco@buffalo.edu; Tel.: +(716)-829-2599 Received: 31 March 2020; Accepted: 23 April 2020; Published: 26 April 2020 Abstract: In Escherichia coli, DNA replication forks stall on average once per cell cycle. When this occurs, replisome components disengage from the DNA, exposing an intact, or nearly intact fork. Consequently, the fork structure must be regressed away from the initial impediment so that repair can occur. Regression is catalyzed by the powerful, monomeric DNA helicase, RecG. During this reaction, the enzyme couples unwinding of fork arms to rewinding of duplex DNA resulting in the formation of a Holliday junction. RecG works against large opposing forces enabling it to clear the fork of bound proteins. Following subsequent processing of the extruded junction, the PriA helicase mediates reloading of the replicative helicase DnaB leading to the resumption of DNA replication. The single-strand binding protein (SSB) plays a key role in mediating PriA and RecG functions at forks. It binds to each enzyme via linker/OB-fold interactions and controls helicase-fork loading sites in a substrate-dependent manner that involves helicase remodeling. Finally, it is displaced by RecG during fork regression. The intimate and dynamic SSB-helicase interactions play key roles in ensuring fork regression and DNA replication restart. Keywords: RecG; single-strand binding protein (SSB); Stalled DNA replication fork; DNA repair; DNA replication; helicase; atomic force microscopy; OB-fold; SH3 domain; PXXP motif 1.
    [Show full text]
  • Replication (Prepriming/Protein N'/Dtaab Protein/Primase/Supercoiling) ROBERT L
    Proc. NatL Acad. SciL USA Vol. 78, No. 3, pp. 1436-1440, March 1981 Biochemistry Conservation of the primosome in successive -stages of 4X'174 DNA- replication (prepriming/protein n'/dtaaB protein/primase/supercoiling) ROBERT L. Low, KEN-ICHI ARAI*, AND ARTHUR KORNBERG Department of Biochemistry, Stanford University'School of Medicine, Stanford, California 94305 Contributed by Arthur Kornberg, November 17, 1980 ABSTRACT Synthesis of a complementary strand to- match by primosome action of a ssDNA -- RF system identical to that the single-stranded, circular, viral (+) DNA.strand of phage used to initiate synthesis of the parental RF (16). 4+X174 creates a parental duplex circle (replicative form, RF). This synthesis is initiated by the assembly and action of a priming In this study, we have obtained physical and functional evi- system, called the primosome [Arai, K. &Kornberg, A (1981) Proc. dence that major components of the primosome (i.e., n' pro- NatL Acad. Sci USA'78, 69-73; Arai, K.,.Low, R. L. & Kornberg, tein, dnaB protein, and primase) isolated by gel filtration are A. (1981) Proc. NatL Acud. Sci. USA 78, 707-711]. Of the seven stably retained with the parental RF and function during RF proteins that participate in the assembly and function of the pri- duplication upon addition of proteins i, n", and dnaC. An even mosome, most all of the components remain even after the DNA more intact primosome isolated by sedimentation requires ad- duplex is completed and covalently sealed. Remarkably, the pri- mosome in the isolated RF obviates the need for superciling of dition ofonly protein i.
    [Show full text]
  • DNA Replication
    DNA replication: • Copying genetic information for transmission to the next generation • Occurs in S phase of cell cycle • Process of DNA duplicating itself • Begins with the unwinding of the double helix to expose the bases in each strand of DNA • Each unpaired nucleotide will attract a complementary nucleotide from the medium – will form base pairing via hydrogen bonding. • Enzymes link the aligned nucleotides by phosphodiester bonds to form a continuous strand. 1 DNA replication: – First question asked was whether duplication was semiconservative or conservative • Meselson and Stahl expt • Semiconservative - – one strand from parent in each new strand • Conservative- – both strands from parent and other is all new strands 2 DNA replication: • Complementary base pairing produces semiconservative replication – Double helix unwinds – Each strand acts as template – Complementary base pairing ensures that T signals addition of A on new strand, and G signals addition of C – Two daughter helices produced after replication 3 4 Experimental proof of semiconservative replication – three possible models • Semiconservative replication – – Watson and Crick model • Conservative replication: – The parental double helix remains intact; – both strands of the daughter double helix are newly synthesized • Dispersive replication: – At completion, both strands of both double helices contain both original and newly synthesized material. 5 6 Meselson-Stahl experiments confirm semiconservative replication • Experiment allowed differentiation of parental and newly formed DNA. • Bacteria were grown in media containing either normal isotope of nitrogen (14N) or the heavy isotope (15N). • DNA banded after equilibrium density gradient centrifugation at a position which matched the density of the DNA: – heavy DNA was at a higher density than normal DNA.
    [Show full text]
  • Topoisomerase VI Is a Chirally-Selective, Preferential DNA Decatenase Shannon J
    bioRxiv preprint doi: https://doi.org/10.1101/2021.02.15.431225; this version posted February 16, 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 4.0 International license. McKie et al., 2020 Thursday, 28 January 2021 Topoisomerase VI is a chirally-selective, preferential DNA decatenase Shannon J. McKie1,2, Parth Desai1, Yeonee Seol1, Anthony Maxwell2 and Keir Neuman1 1Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA 2Dept. Biological Chemistry, John Innes Centre, Norwich NR4 7UH, UK Abstract DNA topoisomerase VI (topo VI) is a type IIB DNA topoisomerase found predominantly in archaea and some bacteria, but also in plants and algae. Since its discovery, topo VI has been proposed to be a DNA decatenase, however robust evidence and a mechanism for its preferential decatenation activity was lacking. Using single-molecule magnetic tweezers measurements and supporting ensemble biochemistry, we demonstrate that Methanosarcina mazei topo VI preferentially unlinks, or decatenates, DNA crossings, in comparison to relaxing supercoils, through a preference for certain DNA crossing geometries. In addition, topo VI demonstrates a dramatic increase in ATPase activity, DNA binding and rate of strand passage, with increasing DNA writhe, providing further evidence that topo VI is a DNA crossing sensor. Our study strongly suggests that topo VI has evolved an intrinsic preference for the unknotting and decatenation of interlinked chromosomes by sensing and preferentially unlinking DNA crossings with geometries close to 90°.
    [Show full text]
  • Genetic Functions Promoting Homologous Recombination in Escherichia Coli: a Study of Inversions in Phage X
    Copyright 0 1987 by the Genetics Society of America Genetic Functions Promoting Homologous Recombination in Escherichia coli: A Study of Inversions in Phage X Don G. Ennis,*$'Susan K. Amundsen+**and Gerald R. "Institute of Molecular Biology, University of Oregon, Eugene, Oregon 97403, and TFred Hutchinson Cancer Research Center, 1124 Columbia Street, Seattle, Washington 98104 Manuscript received June 19, 1986 Revised copy accepted September 13, 1986 ABSTRACT We have studied homologous recombination in a derivative of phage X containing two 1.4-kb repeats in inverted orientation. Inversion of the intervening 2.5-kb segment occurred efficiently by the Escherichia coli RecBC pathway but markedly less efficiently by the X Red pathway or the E. coli RecE or RecF pathways. Inversion by the RecBCD pathway was stimulated by Chi sites located to the right of the invertible segment; this stimulation decreased exponentially by a factor of about 2 for each 2.2 kb between the invertible segment and the Chi site. In addition to RecA protein and RecBCD enzyme, inversion by the RecBC pathway required single-stranded DNA binding protein, DNA gyrase, DNA polymerase I and DNA ligase. Inversion appeared to occur either intra- or intermolec- ularly. These results are discussed in the framework of a current molecular model for the RecBC pathway of homologous recombination. 0 elucidate the molecular mechanism of homol- 1974, 1975). KLECKNERand ROSS(1980) described a T ogous recombination it is important to identify derivative of phage X that has the potential to undergo the genetic functions that promote recombination. homologous intramolecular recombination. This The major pathway of recombination associated with phage contains three copies of ISIO, the terminal 1.4 conjugation and generalized transduction in Esche- kb of transposon TnlO (Figure 1).
    [Show full text]
  • Architecture and Conservation of the Bacterial DNA Replication Machinery, an Underexploited Drug Target
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Research Online University of Wollongong Research Online Faculty of Science - Papers (Archive) Faculty of Science, Medicine and Health 2012 Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target Andrew Robinson University of Wollongong, [email protected] Rebecca J. Causer University of Wollongong, [email protected] Nicholas E. Dixon University of Wollongong, [email protected] Follow this and additional works at: https://ro.uow.edu.au/scipapers Part of the Life Sciences Commons, Physical Sciences and Mathematics Commons, and the Social and Behavioral Sciences Commons Recommended Citation Robinson, Andrew; Causer, Rebecca J.; and Dixon, Nicholas E.: Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target 2012, 352-372. https://ro.uow.edu.au/scipapers/2996 Research Online is the open access institutional repository for the University of Wollongong. For further information contact the UOW Library: [email protected] Architecture and conservation of the bacterial DNA replication machinery, an underexploited drug target Abstract "New antibiotics with novel modes of action are required to combat the growing threat posed by multi- drug resistant bacteria. Over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. We can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of new broad- spectrum antibacterials.
    [Show full text]
  • A Topoisomerase from Escherichia Coli Related to DNA Gyrase (DNA Relaxation/Supercoiling/Nalidixic Acid/Subunits/Site-Specific DNA Cleavage) PATRICK 0
    Proc. Natl. Acad. Sci. USA Vol. 76, No. 12, pp. 6110-6114, December 1979 Biochemistry A topoisomerase from Escherichia coli related to DNA gyrase (DNA relaxation/supercoiling/nalidixic acid/subunits/site-specific DNA cleavage) PATRICK 0. BROWN*, CRAIG L. PEEBLESt*, AND NICHOLAS R. COZZARELLI*t Departments of *Biochemistry and of tBiophysics and Theoretical Biology, The University of Chicago, Chicago, Illinois 60637 Communicated by Bernard Roizman, August 27,1979 ABSTRACT We have identified a topoisomerase activity We have identified and purified this enzyme, which we from Escherichia coli related to DNA gyrase (topoisomerase designate topo II'. It was constructed from subunit A and a II); we designate it topoisomerase II'. It was constructed of two v appears to be related to subunits, which were purified separately. One is the product 50,000-dalton subunit we call that of the gyrA (formerly nalU) gene and is identical to subunit A subunit B. The subunits of topo II' were resolved early in the of DNA gyrase. The other is a 50,000-dalton protein, which we purification and were purified separately; neither subunit alone have purified to homogeneity and call v. v may be a processed had any detectable activity. Topo II' resembled gyrase in that form of the much larger gyrase subunit B or may be derived both enzymes relaxed negative supercoils, apparently wrapped from a transcript of part of the subunit B structural gene, be- their DNA substrate around them in a positive coil (6, 10), and cause preliminary peptide maps of the two subunits are similar. in Topoisomerase II' relaxes negatively supercoiled DNA and, carried out an aborted reaction which double-strand breaks uniquely among E.
    [Show full text]
  • Polymerase Chain Reaction (PCR)
    Polymerase Chain Reaction (PCR) Objectives In this laboratory you will carry out the Polymerase Chain Reaction (PCR) technique to amplify a specific DNA sequence from a small amount of DNA template. You will then analyze the resulting PCR products by agarose gel electrophoresis. Introduction The Polymerase Chain Reaction (PCR) technique is essentially DNA replication in vitro targeted to a very specific region of a DNA sample. As a result, the DNA in the target region is amplified exponentially due to repeated rounds of DNA replication. For example, consider that the human genome consists of ~3 billion base pairs of DNA. PCR makes it possible to take a sample of human DNA and selectively amplify any desired portion of it provided it is no larger than several thousand base pairs. The remaining DNA is more or less ignored by the replication machinery. The importance of PCR cannot be overstated. It has completely revolutionized biological research, forensics, diagnostic testing, and any other field that involves DNA analysis. So how does PCR accomplish the selective amplification of a relatively small portion a complex DNA sample? To answer this question you need to understand how DNA replication works. Recall that DNA replication in bacteria requires the following components: DNA template* deoxyribonucleotide triphosphates (dNTPs)* origin of replication helicase DNA gyrase (topoisomerase) RNA primase DNA polymerase III* DNA polymerase I DNA ligase * all that is required for PCR All of these components and more are required for a bacterial cell to completely copy a very large piece of DNA, the bacterial chromosome which in E. coli is ~4 million base pairs.
    [Show full text]