Deoxyribonucleic Acid Synthesis I. Effect of in Vivo Cyclophosphamide
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WO 2013/153359 Al 17 October 2013 (17.10.2013) P O P C T
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date WO 2013/153359 Al 17 October 2013 (17.10.2013) P O P C T (51) International Patent Classification: Edmund Cartwright House, 4 Robert Robinson Avenue, C07K 14/435 (2006.01) C12Q 1/00 (2006.01) Oxford Science Park, Oxford Oxfordshire OX4 4GA (GB). (21) International Application Number: (74) Agent: CHAPMAN, Lee Phillip; 14 South Square, Gray's PCT/GB20 13/050667 Inn, London Greater London WC1R 5JJ (GB). (22) International Filing Date: (81) Designated States (unless otherwise indicated, for every 15 March 2013 (15.03.2013) kind of national protection available): AE, AG, AL, AM, AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY, (25) Filing Language: English BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, (26) Publication Language: English DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (30) Priority Data: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, 61/622,174 10 April 2012 (10.04.2012) US ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, (71) Applicant: OXFORD NANOPORE TECHNOLOGIES NO, NZ, OM, PA, PE, PG, PH, PL, PT, QA, RO, RS, RU, LIMITED [GB/GB]; Edmund Cartwright House, 4 Robert RW, SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, Robinson Avenue, Oxford Science Park, Oxford Oxford TM, TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, shire OX4 4GA (GB). -
On-Demand Synthesis of Phosphoramidites
ARTICLE https://doi.org/10.1038/s41467-021-22945-z OPEN On-demand synthesis of phosphoramidites Alexander F. Sandahl1, Thuy J. D. Nguyen1, Rikke A. Hansen1, Martin B. Johansen 1, Troels Skrydstrup 1,2 & ✉ Kurt V. Gothelf 1,2 Automated chemical synthesis of oligonucleotides is of fundamental importance for the production of primers for the polymerase chain reaction (PCR), for oligonucleotide-based drugs, and for numerous other medical and biotechnological applications. The highly opti- mised automised chemical oligonucleotide synthesis relies upon phosphoramidites as the 1234567890():,; phosphate precursors and one of the drawbacks of this technology is the poor bench stability of phosphoramidites. Here, we report on the development of an on-demand flow synthesis of phosphoramidites from their corresponding alcohols, which is accomplished with short reaction times, near-quantitative yields and without the need of purification before being submitted directly to automated oligonucleotide synthesis. Sterically hindered as well as redox unstable phosphoramidites are synthesised using this methodology and the sub- sequent couplings are near-quantitative for all substrates. The vision for this technology is direct integration into DNA synthesisers thereby omitting manual synthesis and storage of phosphoramidites. 1 Interdisciplinary Nanoscience Center, iNANO, Aarhus University, Aarhus C, Denmark. 2 Department of Chemistry, Aarhus University, Aarhus C, Denmark. ✉ email: [email protected] NATURE COMMUNICATIONS | (2021) 12:2760 | https://doi.org/10.1038/s41467-021-22945-z | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | https://doi.org/10.1038/s41467-021-22945-z ynthetic oligonucleotides are essential for a range of dif- includetheuseofmechanochemistry11 or the use of P(V) chemistry Sferent areas and millions of oligonucleotides are synthesized to form the internucleosidic P–Obond12,13. -
Structure and Function Of
8/5/2019 DNA and RNA The Code of Life The Human Genome Project Gene Expression Genetic code The alphabet of the genetic code contains Genes are DNA sequences that encode proteins (the gene product) only four letters (A,T,G,C). Gene expression refers to the process A number of experiments confirmed that the whereby the information contained in genes genetic code is written in 3-letter words, each begins to have effects in the cell. of which codes for particular amino acid. DNA encodes and transmits the genetic A nucleic acid word (3 nucleotide letters) is information passed down from parents to offspring. referred to as a codon. 1 8/5/2019 Nucleic acids Nucleotides Principle information molecule in the Nucleotides are the unit structure of cell. nucleic acids. Nucleotides composed of 3 All the genetic codes are carried out on components: the nucleic acids. Nitrogenous base (A, C, G, T or U) Pentose sugar Nucleic acid is a linear polymer of Phosphate nucleotides Nucleotides Nitrogenous bases There are four nitrogen bases making up four different nucleotides. There are 2 types: Purines(pyoo r-een): Adenine A Two ring structure Purines Adenine (A) and Guanine (G) Guanine G Pyrimidines(pahy-rim-i-deen,): N base Single ring structure Cytosine (C) and Thymine (T) or Uracil (U). Thymine T Pyrimidines Cytosine C 2 8/5/2019 A NUCLEOTIDE Nucleotide bases 1. Phosphate Group 2.3. 5Nitrogen-Carbon BaseSugar 1. Phosphate Group 2. 5-Carbon Sugar (Dexoyribose or Ribose) 3. (Dexoyribose or Ribose) 1. 3. Nitrogen Base 2. 3. Nucleotides, too O 1. -
Nucleotide Metabolism 22
Nucleotide Metabolism 22 For additional ancillary materials related to this chapter, please visit thePoint. I. OVERVIEW Ribonucleoside and deoxyribonucleoside phosphates (nucleotides) are essential for all cells. Without them, neither ribonucleic acid (RNA) nor deoxyribonucleic acid (DNA) can be produced, and, therefore, proteins cannot be synthesized or cells proliferate. Nucleotides also serve as carriers of activated intermediates in the synthesis of some carbohydrates, lipids, and conjugated proteins (for example, uridine diphosphate [UDP]-glucose and cytidine diphosphate [CDP]- choline) and are structural components of several essential coenzymes, such as coenzyme A, flavin adenine dinucleotide (FAD[H2]), nicotinamide adenine dinucleotide (NAD[H]), and nicotinamide adenine dinucleotide phosphate (NADP[H]). Nucleotides, such as cyclic adenosine monophosphate (cAMP) and cyclic guanosine monophosphate (cGMP), serve as second messengers in signal transduction pathways. In addition, nucleotides play an important role as energy sources in the cell. Finally, nucleotides are important regulatory compounds for many of the pathways of intermediary metabolism, inhibiting or activating key enzymes. The purine and pyrimidine bases found in nucleotides can be synthesized de novo or can be obtained through salvage pathways that allow the reuse of the preformed bases resulting from normal cell turnover. [Note: Little of the purines and pyrimidines supplied by diet is utilized and is degraded instead.] II. STRUCTURE Nucleotides are composed of a nitrogenous base; a pentose monosaccharide; and one, two, or three phosphate groups. The nitrogen-containing bases belong to two families of compounds: the purines and the pyrimidines. A. Purine and pyrimidine bases Both DNA and RNA contain the same purine bases: adenine (A) and guanine (G). -
European Patent Office *% a a N4 © Publication Number: 0 344 937 B1 Office Europeen Des Brevets
Europa,schesP_ MM M II M MM M MINI Ml M I II J European Patent Office *% A a n4 © Publication number: 0 344 937 B1 Office europeen des brevets © EUROPEAN PATENT SPECIFICATION © Date of publication of patent specification: 13.07.94 © Int. CI.5: C12P 19/38, C12P 17/12, C12N 1/20 © Application number: 89304820.7 @ Date of filing: 12.05.89 © Production of a deoxyrlbonucleoslde. ® Priority: 31.05.88 GB 8812846 (73) Proprietor: ZENECA LIMITED 22.03.89 GB 8906623 Imperial Chemical House, 9 Millbank London SW1P 3JF(GB) @ Date of publication of application: 06.12.89 Bulletin 89/49 @ Inventor: Naylor, Linda Anne Daphne House © Publication of the grant of the patent: 6 West Green 13.07.94 Bulletin 94/28 Helghlngton Village Newton Aye I if fe Co.Durham(GB) © Designated Contracting States: AT BE CH DE ES FR GB GR IT LI LU NL SE © Representative: Locke, Timothy John et al © References cited: ICI Group Patents Services Dept. FR-A- 2 126 437 PO Box 6 Shire Park Bessemer Road Welwyn Garden City Herts, AL7 1HD (GB) 00 IV CO Oi oo Note: Within nine months from the publication of the mention of the grant of the European patent, any person ® may give notice to the European Patent Office of opposition to the European patent granted. Notice of opposition CL shall be filed in a written reasoned statement. It shall not be deemed to have been filed until the opposition fee LU has been paid (Art. 99(1) European patent convention). Rank Xerox (UK) Business Services (3. -
1/05661 1 Al
(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT) (19) World Intellectual Property Organization International Bureau (10) International Publication Number (43) International Publication Date _ . ... - 12 May 2011 (12.05.2011) W 2 11/05661 1 Al (51) International Patent Classification: (81) Designated States (unless otherwise indicated, for every C12Q 1/00 (2006.0 1) C12Q 1/48 (2006.0 1) kind of national protection available): AE, AG, AL, AM, C12Q 1/42 (2006.01) AO, AT, AU, AZ, BA, BB, BG, BH, BR, BW, BY, BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM, DO, (21) Number: International Application DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT, PCT/US20 10/054171 HN, HR, HU, ID, IL, IN, IS, JP, KE, KG, KM, KN, KP, (22) International Filing Date: KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD, 26 October 2010 (26.10.2010) ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI, NO, NZ, OM, PE, PG, PH, PL, PT, RO, RS, RU, SC, SD, (25) Filing Language: English SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM, TN, TR, (26) Publication Language: English TT, TZ, UA, UG, US, UZ, VC, VN, ZA, ZM, ZW. (30) Priority Data: (84) Designated States (unless otherwise indicated, for every 61/255,068 26 October 2009 (26.10.2009) US kind of regional protection available): ARIPO (BW, GH, GM, KE, LR, LS, MW, MZ, NA, SD, SL, SZ, TZ, UG, (71) Applicant (for all designated States except US): ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, MD, RU, TJ, MYREXIS, INC. -
Nucleotide Metabolism Pathway: the Achilles' Heel for Bacterial Pathogens
REVIEW ARTICLES Nucleotide metabolism pathway: the achilles’ heel for bacterial pathogens Sujata Kumari1,2,* and Prajna Tripathi1,3 1National Institute of Immunology, New Delhi 110 067, India 2Present address: Department of Zoology, Magadh Mahila College, Patna University, Patna 800 001, India 3Present address: Institute of Molecular Medicine, Jamia Hamdard, New Delhi 110 062, India de novo pathway, the nucleotides are synthesized from Pathogens exploit their host to extract nutrients for their survival. They occupy a diverse range of host simple precursor molecules. In the salvage pathway, the niches during infection which offer variable nutrients preformed nucleobases or nucleosides which are present accessibility. To cause a successful infection a patho- in the cell or transported from external environmental gen must be able to acquire these nutrients from the milieu to the cell are utilized to form nucleotides. host as well as be able to synthesize the nutrients on its own, if required. Nucleotides are the essential me- tabolite for a pathogen and also affect the pathophysi- Purine biosynthesis pathway ology of infection. This article focuses on the role of nucleotide metabolism of pathogens during infection The purine biosynthesis pathway is universally conserved in a host. Nucleotide metabolism and disease pathoge- in living organisms (Figure 1). As an example, we here nesis are closely related in various pathogens. Nucleo- present the pathway derived from well-studied Gram- tides, purines and pyrimidines, are biosynthesized by positive bacteria Lactococcus lactis. In the de novo the de novo and salvage pathways. Whether the patho- pathway the purine nucleotides are synthesized from sim- gen will employ the de novo or salvage pathway dur- ple molecules such as phosphoribosyl pyrophosphate ing infection is dependent on various factors, like (PRPP), amino acids, CO2 and NH3 by a series of enzy- availability of nucleotides, energy condition and pres- matic reactions. -
Chemoenzymatic Synthesis of Nucleoside Analogs As Potential Medicinal Agents
Chemoenzymatic synthesis of nucleoside analogs as potential medicinal agents vorgelegt von M. Sc. Heba Yehia Mohamed ORCID: 0000-0002-3238-0939 von der Fakultät III-Prozesswissenschaften der Technischen Universität Berlin zur Erlangung des akademischen Grades Doktorin der Naturwissenschaften - Dr. rer. nat. – genehmigte Dissertation Promotionsausschuss: Vorsitzender: Prof. Dr. Roland Lauster, Medical Biotechnology, TU Berlin, Berlin Gutachter: Prof. Dr. Peter Neubauer, Bioprocess Engineering, TU Berlin, Berlin Gutachter: Prof. Dr. Jens Kurreck, Applied Biochemistry, TU Berlin, Berlin Gutachter: Prof. Dr. Vlada B. Urlacher, Biochemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf Tag der wissenschaftlichen Aussprache: 16. Juli 2019 Berlin, 2019 Heba Y. Mohamed Synthesis of nucleoside analogs as potential medicinal agents Abstract Modified nucleosides are important drugs used to treat cancer, viral or bacterial infections. They also serve as precursors for the synthesis of modified oligonucleotides (antisense oligonucleotides (ASOs) or short interfering RNAs (siRNAs)), a novel and effective class of therapeutics. While the chemical synthesis of nucleoside analogs is challenging due to multi-step procedures and low selectivity, enzymatic synthesis offers an environmentally friendly alternative. However, current challenges for the enzymatic synthesis of nucleoside analogs are the availability of suitable enzymes or the high costs of enzymes production. To address these challenges, this work focuses on the application of thermostable purine and pyrimidine nucleoside phosphorylases for the chemo-enzymatic synthesis of nucleoside analogs. These enzymes catalyze the reversible phosphorolysis of nucleosides into the corresponding nucleobase and pentofuranose-1-phosphate and have already been successfully used for the synthesis of modified nucleosides in small scale. So far, the production of sugar-modified nucleosides has been a major challenge. -
Increased Cytotoxicity of Herpes Simplex Virus Thymidine Kinase Expression in Human Induced Pluripotent Stem Cells
International Journal of Molecular Sciences Article Increased Cytotoxicity of Herpes Simplex Virus Thymidine Kinase Expression in Human Induced Pluripotent Stem Cells Chizuru Iwasawa 1, Ryota Tamura 2, Yuki Sugiura 3, Sadafumi Suzuki 4, Naoko Kuzumaki 1, Minoru Narita 1, Makoto Suematsu 3, Masaya Nakamura 5, Kazunari Yoshida 2, Masahiro Toda 2, Hideyuki Okano 4,* and Hiroyuki Miyoshi 4,* 1 Department of Pharmacology, Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41, Ebara, Shinagawa-ku, Tokyo 142-8501, Japan; [email protected] (C.I.); [email protected] (N.K.); [email protected] (M.N.) 2 Department of Neurosurgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; [email protected] (R.T.); [email protected] (K.Y.); [email protected] (M.T.) 3 Department of Biochemistry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; [email protected] (Y.S.); [email protected] (M.S.) 4 Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; [email protected] 5 Department of Orthopedic Surgery, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan; [email protected] * Correspondence: [email protected] (H.O.); [email protected] (H.M.); Tel.: +81-3-5363-3747 (H.O. & H.M.); Fax: +81-3-3357-5445 (H.O. & H.M.) Received: 19 November 2018; Accepted: 11 February 2019; Published: 14 February 2019 Abstract: Human induced pluripotent stem cells (iPSCs) hold enormous promise for regenerative medicine. The major safety concern is the tumorigenicity of transplanted cells derived from iPSCs. -
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research papers 7-Iodo-5-aza-7-deazaguanine ribonucleoside: crystal structure, physical properties, base-pair stability and functionalization ISSN 2053-2296 Dasharath Kondhare,a Simone Budow-Busse,a Constantin Daniliucb and Frank Seelaa,c* Received 19 February 2020 aLaboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Accepted 3 April 2020 Mu¨nster, Germany, bOrganisch-Chemisches Institut, Westfa¨lische Wilhelms-Universita¨tMu¨nster, Corrensstrasse 40, 48149 Mu¨nster, Germany, and cLaboratorium fu¨r Organische und Bioorganische Chemie, Institut fu¨r Chemie, Universita¨t Edited by D. S. Yufit, University of Durham, Osnabru¨ck, Barbarastrasse 7, 49069 Osnabru¨ck, Germany. *Correspondence e-mail: [email protected] England Keywords: 7-iodo-5-aza-7-deazaguanosine; The positional change of nitrogen-7 of the RNA constituent guanosine to the ribonucleoside; crystal structure; Hirshfeld bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-deaza- surface analysis; base-pair prediction; crystal guanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base packing; all-purine RNA; pKa values. pairs and the Watson–Crick proton donor site N3—H becomes a proton- acceptor site. This causes changes in nucleobase recognition in nucleic acids and CCDC reference: 1950946 has been used to construct stable ‘all-purine’ DNA and DNA with silver- Supporting information: this article has mediated base pairs. The present work reports the single-crystal X-ray structure supporting information at journals.iucr.org/c of 7-iodo-5-aza-7-deazaguanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O40- endo) for the ribose moiety, with an antiperiplanar orientation of the 50-hydroxy group. -
Interrelations Between Substrate Cycles and De Novo
Proc. Nati. Acad. Sci. USA Vol. 83, pp. 986-990, February 1986 Cell Biology Interrelations between substrate cycles and de novo synthesis of pyrimidine deoxyribonucleoside triphosphates in 3T6 cells (hydroxyurea/nucleoside incorporation/metabolic flux) VERA BIANCHI, ELISABET PONTIS, AND PETER REICHARD* Medical Nobel Institute, Department of Biochemistry I, Karolinska Institutet, Box 60400, S104 01 Stockholm, Sweden Contributed by Peter Reichard, September 23, 1985 ABSTRACT Degradation of pyrimidine deoxyribonucleo- but also resulted in a continued uptake and net phosphoryl- side triphosphates plays a major role in the regulation of their ation of deoxyuridine. This effect was secondary to a large pool sizes in 3T6 cells. During normal growth, these cells drop in the intracellular dUMP pool. We propose that excrete deoxyribonucleosides (mostly deoxyuridine) into the deoxyuridine and dUMP form a substrate cycle and that the medium. When DNA strand elongation is inhibited, de novo operative direction of this cycle is regulated by the intracel- synthesis of dCTP and dTTP continues, followed by degrada- lular concentration of dUMP. tion of the deoxyribonucleotides. We now demonstrate that inhibition of de novo synthesis with hydroxyurea stops degra- AND dation of deoxyribonucleotides and leads to an influx of MATERIALS METHODS deoxyuridine from the medium. This effect appears to be Materials. Deoxy[6-3H]uridine (21 Ci/mmol; l Ci = 37 caused by a large drop in the size of the intracellular dUMP GBq) was from New England Nuclear Dupont, and [5- pool. We propose that substrate cycles, involving phosphoryl- 3H]cytidine (25-30 Ci/mmol) and [3H]dNTPs and [a-32P]- ation of deoxyribonucleosides by kinases and dephosphoryla- dNTPs were from Amersham. -
Activities of DNA Nucleotidyltransferases and Other Enzymes in Cell-Free Preparations from Hepatomas of Different Growth Rates1
(CANCER RESEARCH 26 Part 1, 2470-2480, December 196«) Activities of DNA Nucleotidyltransferases and Other Enzymes in Cell-free Preparations from Hepatomas of Different Growth Rates1 GLYNN P. WHEELER, JO ANN ALEXANDER, DOROTHY D. HILL, AND HAROLD P. MORRIS Kettering-Meyer Laboratory? Southern Research Institute, Birmingham, Alabama, and Laboratory of Hiockemistry, National Cancer Institute, NIH, Bethesda, Maryland Summary by liver and hepatomas, namely: (a) de novo synthesis of purine ribonucleotides; (6) catabolism of purine nudeotides and of Cell-free preparations were made from host livers and the purines; and (c) utilization of ribonucleotides for the eventual following rat hepatomas, which are listed in the order of increas formation of DNA. In the present investigation, cell-free prepa ing rates of growth: Morris Hepatoma 5123-C, Reuber Hepatoma H-35, Morris Hepatoma 7288-C, Morris Hepatoma 3683, and rations from adult liver and from several types of hepatomas were used to obtain additional information relating to b and c. Novikoff hepatoma. These preparations were assayed for rep licative DNA nucleotidyltransferase and terminal DNA nucleo- As these crude preparations are multienzyme systems, a number of processes occur simultaneously, and the observed synthesis of tidyltransf erase by using them in incubation mixtures containing MC-labeled deoxyribonucleoside phosphates in the presence and DNA is the net result of anabolic and catabolic processes. Chart 1 shows the relationships of some of these processes. The use of absence of the other 3 nonradioactive deoxyribonucleoside phos radioactive deoxyribonucleoside monophosphates or triphos phates. Both the monophosphates and the triphosphates were phates as substrates in these exi>eriments yielded information used as substrates.