Engineering Polymerases for Applications in Synthetic Biology
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Peptide Nucleic Acids, Morpholinos and Related Antisense Biomolecules
MEDICAL INTELLIGENCE UNIT Peptide Nucleic Acids, Morpholinos and Related Antisense Biomolecules Christopher G. Janson, M.D. Departments of Neurosurgery, Neurology and Molecular Genetics Cell and Gene Therapy Center UMDNJ-Robert Wood Johnson Medical School Camden, New Jersey, U.S.A. Matthew J. During, M.D., ScD. Department of Molecular Medicine and Pathology University of Auckland Auckland, New Zealand LANDES BIOSCIENCE / EUREKAH.COM KLUWER ACADEMIC / PLENUM PUBLISHERS GEORGETOWN, TEXAS NEW YORK, NEW YORK USA U.SA PEPTIDE NUCLEIC ACIDS, MORPHOLINOS AND RELATED ANTISENSE BIOMOLECULES Medical Intelligence Unit Landes Bioscience / Eurekah.com Kluwer Academic / Plenum Publishers Copyright ©2006 Eurekah.com and Kluwer Academic / Plenum Publishers All rights reserved. No part of this book may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher, vdth the exception of any material supplied specifically for the purpose of being entered and executed on a computer system; for exclusive use by the Purchaser of the work. Printed in the U.S.A. Kluwer Academic / Plenum PubHshers, 233 Spring Street, New York, New York, U.S.A. 10013 http ://www.wkap .nl/ Please address all inquiries to the Publishers: Landes Bioscience / Eurekah.com, 810 South Church Street, Georgetown, Texas, U.S.A. 78626 Phone: 512/ 863 7762; FAX: 512/ 863 0081 http ://v^^ww.eurekah. com http://www.landesbioscience.com Peptide -
(12) United States Patent (10) Patent No.: US 9,598.458 B2 Shimizu Et Al
USO09598458B2 (12) United States Patent (10) Patent No.: US 9,598.458 B2 Shimizu et al. (45) Date of Patent: Mar. 21, 2017 (54) ASYMMETRICAUXILLARY GROUP 3,687,808 A 8/1972 Merigan et al. 3,745,162 A 7/1973 Helsley 4,022,791 A 5/1977 Welch, Jr. (71) Applicant: NYTE SCIENCES JAPAN, 4,113,869 A 9, 1978 Gardner ... Kagoshima-shi (JP) 4.415,732 A 1 1/1983 Caruthers et al. 4,458,066 A 7/1984 Caruthers et al. (72) Inventors: Mamoru Shimizu, Uruma (JP); 4,500,707 A 2f1985 Caruthers et al. Takeshi Wada, Kashiwa (JP) 4,542,142 A 9, 1985 Martel et al. 4,659,774 A 4, 1987 Webb et al. 4,663,328 A 5, 1987 Lafon (73) Assignee: YESCIENCES JAPAN, 4,668,777. A 5/1987 Caruthers et al. ... Kagoshima-shi (JP) 4,725,677 A 2/1988 Koster et al. 4,735,949 A 4, 1988 Domagala et al. (*) Notice: Subject to any disclaimer, the term of this 4,840,956 A 6/1989 Domagala et al. patent is extended or adjusted under 35 3:38 A . 3. EthOester Phet al. et al. U.S.C. 154(b) by 17 days. 4,973,679 A 1 1/1990 Caruthers et al. 4,981,957 A 1/1991 Lebleu et al. (21) Appl. No.: 14/414,604 5,047,524. A 9/1991 Andrus et al. 5,118,800 A 6/1992 Smith et al. (22) PCT Filed: Jul. 12, 2013 5,130,302 A 7/1992 Spielvogel et al. -
(12) Patent Application Publication (10) Pub. No.: US 2013/0203610 A1 Meller Et Al
US 20130203610A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2013/0203610 A1 Meller et al. (43) Pub. Date: Aug. 8, 2013 (54) TOOLS AND METHOD FOR NANOPORES Related U.S. Application Data UNZIPPING-DEPENDENT NUCLECACID (60) Provisional application No. 61/318,872, filed on Mar. SEQUENCING 30, 2010. (75) Inventors: Amit Meller, Brookline, MA (US); Alon Publication Classification Singer, Brighton, MA (US) (51) Int. Cl. (73) Assignee: TRUSTEES OF BOSTON CI2O I/68 (2006.01) UNIVERSITY, Boston, MA (US) (52) U.S. Cl. CPC .................................... CI2O I/6874 (2013.01) (21) Appl. No.: 13/638,455 USPC ................................................. 506/6:506/16 (57) ABSTRACT (22) PCT Filed: Mar. 30, 2011 Provided herein is a library that comprises a plurality of molecular beacons (MBs), each MB having a detectable (86). PCT No.: PCT/US2O11AO3O430 label, a detectable label blocker and a modifier group. The S371 (c)(1), library is used in conjunction with nanopore unzipping-de (2), (4) Date: Apr. 17, 2013 pendent sequencing of nucleic acids. Patent Application Publication Aug. 8, 2013 Sheet 1 of 18 US 2013/020361.0 A1 . N s Patent Application Publication Aug. 8, 2013 Sheet 2 of 18 US 2013/020361.0 A1 I’9IAI ::::::::::: Dº3.modoueN Patent Application Publication Aug. 8, 2013 Sheet 3 of 18 US 2013/020361.0 A1 Z’9IAI ~~~~~~~~~);........ Patent Application Publication Aug. 8, 2013 Sheet 4 of 18 US 2013/020361.0 A1 s :·.{-zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz iii. 9 iii.338 lii &S Patent Application Publication Aug. 8, 2013 Sheet 5 of 18 US 2013/020361.0 A1 s r Patent Application Publication Aug. -
Rnase a Cleanup of DNA Samples Version Number: 1.0 Version 1.0 Date: 12/21/2016 Author(S): Yuko Yoshinaga, Eileen Dalin Reviewed/Revised By
SAMPLE MANAGEMENT STANDARD OPERATING PROCEDURE RNase A Cleanup of DNA Samples Version Number: 1.0 Version 1.0 Date: 12/21/2016 Author(s): Yuko Yoshinaga, Eileen Dalin Reviewed/Revised by: Summary RNase A treatment is used for the removal of RNA from genomic DNA samples. RNase A cleaves the phosphodiester bond between the 5'-ribose of a nucleotide and the phosphate group attached to the 3'- ribose of an adjacent pyrimidine nucleotide. The resulting 2', 3'-cyclic phosphate is hydrolyzed to the corresponding 3'-nucleoside phosphate. Materials & Reagents Materials Vendor Stock Number Disposables 1.5 ml microcentrifuge tubes Reagents TE Buffer, pH 8.0 Ambion 9849 RNase A, DNase and protease-free (10 mg/ml) ThermoFisher EN0531 Sodium acetate buffer solution (3M, pH 5.2) VWR 567422 Ethanol, 200 proof Pharmco-Aaper 111000200CSPP 50x TAE Buffer Life Technologies/ Invitrogen MRGF-4210 SYBR® Safe DNA gel stain (10,000x concentrate in Life Technologies/ Invitrogen S33102 DMSO) DNA Molecular Weight Marker II Sigma 10236250001 Gel Loading Dye, Blue (6x) New England BioLabs B7021S Equipment Centrifuge 4°C Heat block 37°C Gel electrophoresis device Gel Imager Bio-Rad EH&S PPE Requirements: 1.1 Safety glasses, lab coat, and nitrile gloves should be worn at all times while performing work in the lab during this protocol. 1.2 Ethanol is a highly flammable and irritating to the eyes. Vapors may cause drowsiness and dizziness. Keep containers closed and keep away from sources of ignition such as smoking. 1 SAMPLE MANAGEMENT STANDARD OPERATING PROCEDURE Avoid contact with skin and eyes. In case of contact with eyes, rinse immediately with plenty of water and seek medical advice. -
Secretariat of the CBD Technical Series No. 82 Convention on Biological Diversity
Secretariat of the CBD Technical Series No. 82 Convention on Biological Diversity 82 SYNTHETIC BIOLOGY FOREWORD To be added by SCBD at a later stage. 1 BACKGROUND 2 In decision X/13, the Conference of the Parties invited Parties, other Governments and relevant 3 organizations to submit information on, inter alia, synthetic biology for consideration by the Subsidiary 4 Body on Scientific, Technical and Technological Advice (SBSTTA), in accordance with the procedures 5 outlined in decision IX/29, while applying the precautionary approach to the field release of synthetic 6 life, cell or genome into the environment. 7 Following the consideration of information on synthetic biology during the sixteenth meeting of the 8 SBSTTA, the Conference of the Parties, in decision XI/11, noting the need to consider the potential 9 positive and negative impacts of components, organisms and products resulting from synthetic biology 10 techniques on the conservation and sustainable use of biodiversity, requested the Executive Secretary 11 to invite the submission of additional relevant information on this matter in a compiled and synthesised 12 manner. The Secretariat was also requested to consider possible gaps and overlaps with the applicable 13 provisions of the Convention, its Protocols and other relevant agreements. A synthesis of this 14 information was thus prepared, peer-reviewed and subsequently considered by the eighteenth meeting 15 of the SBSTTA. The documents were then further revised on the basis of comments from the SBSTTA 16 and peer review process, and submitted for consideration by the twelfth meeting of the Conference of 17 the Parties to the Convention on Biological Diversity. -
Excited State Dynamics of Isocytosine; a Hybrid Case of Canonical Nucleobase Photodynamics
The Journal of Physical Chemistry Letters This document is confidential and is proprietary to the American Chemical Society and its authors. Do not copy or disclose without written permission. If you have received this item in error, notify the sender and delete all copies. Excited State Dynamics of Isocytosine; a Hybrid Case of Canonical Nucleobase Photodynamics Journal: The Journal of Physical Chemistry Letters Manuscript ID jz-2017-020322.R1 Manuscript Type: Letter Date Submitted by the Author: n/a Complete List of Authors: Berenbeim, Jacob; UC Santa Barbara, Chemistry and Biochemistry Boldissar, Samuel; UCSB, Department of Chemistry Siouri, Faady; UCSB, Department of Chemistry Gate, Gregory; UCSB, Department of Chemistry Haggmark, Michael; UC Santa Barbara, Chemistry and Biochemistry Aboulache, Briana; University of California Santa Barbara Cohen, Trevor; UC Santa Barbara, Chemistry and Biochemistry De Vries, Mattanjah; UCSB, Department of Chemistry ACS Paragon Plus Environment Page 1 of 12 The Journal of Physical Chemistry Letters 1 2 3 4 Excited State Dynamics of Isocytosine; A Hybrid Case of Canonical 5 Nucleobase Photodynamics 6 7 Jacob A. Berenbeim, Samuel Boldissar, Faady M. Siouri, Gregory Gate, Michael R. 8 Haggmark, Briana Aboulache, Trevor Cohen, and Mattanjah S. de Vries* 9 10 Department of Chemistry and Biochemistry, University of California Santa 11 12 Barabara, CA 93106-9510 13 *E-mail: [email protected] 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 1 ACS Paragon Plus Environment The Journal of Physical Chemistry Letters Page 2 of 12 1 2 3 Abstract 4 5 We present resonant two-photon ionization (R2PI) spectra of isocytosine (isoC) and pump-probe 6 results on two of its tautomers. -
U6 Small Nuclear RNA Is Transcribed by RNA Polymerase III (Cloned Human U6 Gene/"TATA Box"/Intragenic Promoter/A-Amanitin/La Antigen) GARY R
Proc. Nati. Acad. Sci. USA Vol. 83, pp. 8575-8579, November 1986 Biochemistry U6 small nuclear RNA is transcribed by RNA polymerase III (cloned human U6 gene/"TATA box"/intragenic promoter/a-amanitin/La antigen) GARY R. KUNKEL*, ROBIN L. MASERt, JAMES P. CALVETt, AND THORU PEDERSON* *Cell Biology Group, Worcester Foundation for Experimental Biology, Shrewsbury, MA 01545; and tDepartment of Biochemistry, University of Kansas Medical Center, Kansas City, KS 66103 Communicated by Aaron J. Shatkin, August 7, 1986 ABSTRACT A DNA fragment homologous to U6 small 4A (20) was screened with a '251-labeled U6 RNA probe (21, nuclear RNA was isolated from a human genomic library and 22) using a modified in situ plaque hybridization protocol sequenced. The immediate 5'-flanking region of the U6 DNA (23). One of several positive clones was plaque-purified and clone had significant homology with a potential mouse U6 gene, subsequently shown by restriction mapping to contain a including a "TATA box" at a position 26-29 nucleotides 12-kilobase-pair (kbp) insert. A 3.7-kbp EcoRI fragment upstream from the transcription start site. Although this containing U6-hybridizing sequences was subcloned into sequence element is characteristic of RNA polymerase II pBR322 for further restriction mapping. An 800-base-pair promoters, the U6 gene also contained a polymerase III "box (bp) DNA fragment containing U6 homologous sequences A" intragenic control region and a typical run of five thymines was excised using Ava I and inserted into the Sma I site of at the 3' terminus (noncoding strand). The human U6 DNA M13mp8 replicative form DNA (M13/U6) (24). -
Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation
G C A T T A C G G C A T genes Review Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation Christian Diwo 1 and Nediljko Budisa 1,2,* 1 Institut für Chemie, Technische Universität Berlin Müller-Breslau-Straße 10, 10623 Berlin, Germany; [email protected] 2 Department of Chemistry, University of Manitoba, 144 Dysart Rd, 360 Parker Building, Winnipeg, MB R3T 2N2, Canada * Correspondence: [email protected] or [email protected]; Tel.: +49-30-314-28821 or +1-204-474-9178 Received: 27 November 2018; Accepted: 21 December 2018; Published: 28 December 2018 Abstract: The universal genetic code, which is the foundation of cellular organization for almost all organisms, has fostered the exchange of genetic information from very different paths of evolution. The result of this communication network of potentially beneficial traits can be observed as modern biodiversity. Today, the genetic modification techniques of synthetic biology allow for the design of specialized organisms and their employment as tools, creating an artificial biodiversity based on the same universal genetic code. As there is no natural barrier towards the proliferation of genetic information which confers an advantage for a certain species, the naturally evolved genetic pool could be irreversibly altered if modified genetic information is exchanged. We argue that an alien genetic code which is incompatible with nature is likely to assure the inhibition of all mechanisms of genetic information transfer in an open environment. The two conceivable routes to synthetic life are either de novo cellular design or the successive alienation of a complex biological organism through laboratory evolution. -
5-Fluorocytosine/Isocytosine Monohydrate. the First Example of Isomorphic and Isostructural Co-Crystal of Pyrimidine Nucleobases
crystals Article 5-Fluorocytosine/Isocytosine Monohydrate. The First Example of Isomorphic and Isostructural Co-Crystal of Pyrimidine Nucleobases Gustavo Portalone Department of Chemistry, ‘Sapienza’ University of Rome, 00185 Rome, Italy; [email protected]; Tel.: +396-4991-3715 Received: 1 October 2020; Accepted: 2 November 2020; Published: 3 November 2020 Abstract: To date, despite the crucial role played by cytosine, uracil, and thymine in the DNA/RNA replication process, no examples showing isomorphic and isostructural behavior among binary co-crystals of natural or modified pyrimidine nucleobases have been so far reported in the literature. In view of the relevance of biochemical and pharmaceutical compounds such as pyrimidine nucleobases and their 5-fluoroderivatives, co-crystals of the molecular complex formed by 5-fluorocytosine and isocytosine monohydrate, C H FN O C H N O H O, have been synthesized 4 4 3 · 4 5 3 · 2 by a reaction between 5-fluorocytosine and isocytosine. They represent the first example of isomorphic and isostructural binary co-crystals of pyrimidine nucleobases, as X-ray diffraction analysis shows structural similarities in the solid-state organization of molecules with that of the (1:1) 5-fluorocytosine/5-fluoroisocytosine monohydrate molecular complex, which differs solely in the H/F substitution at the C5 position of isocytosine. Molecules of 5-fluorocytosine and isocytosine are present in the crystal as 1H and 3H-ketoamino tautomers, respectively. They form almost coplanar WC base pairs through nucleobase-to-nucleobase DAA/ADD hydrogen bonding interactions, demonstrating that complementary binding enables the crystallization of specific tautomers. Additional peripheral hydrogen bonds involving all available H atom donor and acceptor sites of the water molecule give a three-dimensional polymeric structure. -
New Constrained Amino Acids and Peptide Nucleic Acid Building Blocks for the Construction of Bio-Polymers Alexandra Gresika
New constrained amino acids and peptide nucleic acid building blocks for the construction of bio-polymers Alexandra Gresika To cite this version: Alexandra Gresika. New constrained amino acids and peptide nucleic acid building blocks for the construction of bio-polymers. Other. Université Côte d’Azur, 2018. English. NNT : 2018AZUR4104. tel-02073232 HAL Id: tel-02073232 https://tel.archives-ouvertes.fr/tel-02073232 Submitted on 19 Mar 2019 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE DE DOCTORAT Nouveaux synthons contraints de type - amino acides et PNA en vue de l´élaboration de bio-foldamères New constrained amino acids and peptide nucleic acid building blocks for the construction of biopolymers Alexandra Gresika Molécules Bioactives Présentée en vue de l’obtention Devant le jury, composé de : du grade de docteur en Chimie Muriel Amblard, Directrice de Recherche d’Université Côte d’Azur CNRS, IBMM UMR 5247, Université de Dirigée par : Nadia Patino Montpellier Karine Alvarez, Chargée de Recherche Soutenue le : 16.11.2018 CNRS, AFBM UMR 7257, Université Aix- Marseille Mohamed Mehiri, Maître de Conférences, ICN UMR 7272, Université Côte d’Azur Nadia Patino, Professeur des Universités, ICN UMR 7272, Université Côte d’Azur 1 New constrained amino acids and peptide nucleic acid building blocks for the construction of bio-polymers. -
Durham Research Online
Durham Research Online Deposited in DRO: 04 January 2019 Version of attached le: Published Version Peer-review status of attached le: Peer-reviewed Citation for published item: Pohl, Radek and Socha, Ond§rejand Slav¡§cek,Petr and S¡ala,Michal§ and Hodgkinson, Paul and Dra§c¡nsk¡y, Martin (2018) 'Proton transfer in guaninecytosine base pair analogues studied by NMR spectroscopy and PIMD simulations.', Faraday discussions., 212 . pp. 331-344. Further information on publisher's website: https://doi.org/10.1039/C8FD00070K Publisher's copyright statement: This article is licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported Licence. Additional information: Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full DRO policy for further details. Durham University Library, Stockton Road, Durham DH1 3LY, United Kingdom Tel : +44 (0)191 334 3042 | Fax : +44 (0)191 334 2971 https://dro.dur.ac.uk Faraday Discussions Cite this: Faraday Discuss.,2018,212,331 View Article Online PAPER View Journal | View Issue Proton transfer in guanine–cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations† a a b a Radek Pohl, Ondˇrej Socha, Petr Slav´ıcek,ˇ Michal Sˇala,´ c a Paul Hodgkinson and Martin Dracˇ´ınsky´ * Received 28th March 2018, Accepted 1st May 2018 DOI: 10.1039/c8fd00070k It has been hypothesised that proton tunnelling between paired nucleobases significantly enhances the formation of rare tautomeric forms and hence leads to errors in DNA Creative Commons Attribution-NonCommercial 3.0 Unported Licence. -
Threose Nucleic Acid
2/23/11! Something else…! •" Neither the chicken nor the egg came first! Alternative Ideas! •" Transitional forms that were later discarded! Or was it the “egkin”?! Some experiments with peptide nucleic acid! Threose Nucleic Acid (TNA)! (PNA).! PNA: Peptide backbone with bases! •" Threose is one of two sugars with a four- sided ring! Can act as template for polymerization of RNA! •" Fewer issues with incorrect linkages, From activated nucleotides! selection of correct handedness! (Böhler, et al., Nature, 376, 578! •" Replace ribose sugar in RNA with threose! & comments by Piccirilli, pg. 548 17 Aug. 1995! •" Can base pair with RNA! •" Could have preceded RNA! PNA could be simpler to form under prebiotic conditions! Main point is that a simpler thing (not necessarily PNA) ! could have preceded RNA! 1! 2/23/11! Focus on Energy! Membranes! G. Wächtershäuser! Inorganic - organic connection! •" Membranes provide enclosure! FeS2 ! (Iron pyrite)! –"Also fundamental for metabolism! Attracts negatively charged molecules ! •" Membranes never arise from scratch! Surface catalysis provides energy via formation from! –"Always passed down and added to! FeS + H2S! –"All derived from ancestral cell! •" T. Cavalier-Smith proposes membranes! Scene is hot sulfur vents on sea floor! –"Plus nucleic acid formed “ob-cell”! Some successes in simulations! Amino acids formed peptide bonds! –"Merger of 2 ob-cells formed first cell! Thioester World! H O 1." Need precursor to RNA world! H H S H O Thioester! S C. de Duve! C C O 2. !Need energy conversion! In Vital Dust! O !Protometabolism! Thiol + Carboxyl! Background:! H O H H O H O Ester! O Thiols involved in metabolism, particularly in ancient ! C C pathways! O O Hydroxyl + Carboxyl! Also can catalyze ester formation by group transfer! Reactions! e.g.