Free ebooks ==> www.Ebook777.com RNA Technologies Stefan Jurga Volker A. Erdmann Jan Barciszewski Editors Modified Nucleic Acids in Biology and Medicine www.Ebook777.com Free ebooks ==> www.Ebook777.com RNA Technologies www.Ebook777.com More information about this series at http://www.springer.com/series/8619 Stefan Jurga • Volker A Erdmann • Jan Barciszewski Editors Modified Nucleic Acids in Biology and Medicine Free ebooks ==> www.Ebook777.com Editors Stefan Jurga Nanobiomedical Center Adam Mickiewicz University Poznan´ Poland Volker A Erdmann (Deceased) Formerly at Institute of Chemistry and Biochemistry Free University Berlin Berlin Germany Jan Barciszewski Institute of the Bioorganic Chemistry of the Polish Academy of Sciences Poznan´ Poland ISSN 2197-9731 ISSN 2197-9758 (electronic) RNA Technologies ISBN 978-3-319-34173-6 ISBN 978-3-319-34175-0 (eBook) DOI 10.1007/978-3-319-34175-0 Library of Congress Control Number: 2016944798 © Springer International Publishing Switzerland 2016 This work is subject to copyright All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed The use of general descriptive names, registered names, trademarks, service marks, etc in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG Switzerland www.Ebook777.com Preface The Power of Modified Nucleic Acids With this volume of the series RNA technologies, we aim to cover various aspects of nucleic acid modifications This is an interesting issue in the study of macromolecular components of cells DNA and RNA are key molecules of the cell The structure, function, and reactivity of DNA and RNA are central to molecular biology and are crucial for the understanding of complex biological processes For a long time DNA was considered as the most important molecule of all biology and the key of life However DNA is not the be all and end all of the living cell, but it appears as an important by-product of the RNA evolution Deoxyribonucleotides as DNA precursors are synthesized by specific enzymatic modification of ribonucleotides in which the 20 -hydroxyl group of the ribose moiety is replaced by 20 -hydrogen with ribonucleotide reductase One of these DNA bases, thymine, is produced by methylation of uracil There are a significant number of adenosines and cytidines in genomic DNA converted by spontaneous or enzymatic deamination to hypoxanthine and uracil, respectively Cytosine can be methylated to 5-methylcytosine derivative with not only a coding capacity but also a regulatory potential These data suggest that DNA looks similar to a modified RNA molecule although chemically more stable than RNA In the eukaryotic cell, all postreplicative modifications of DNA showed a few percent of all bases Cellular DNAs and RNAs can be chemically modified in more than 100 different ways Some of these modifications to nucleic acids are random or spontaneous and their formation requires significant energy from the cell The broad range of chemical modifications to nucleic acids is not restricted to simple nucleophilic substitution but extends to oxidative reactions and C–H activation by various agents The modifications might occur on DNA as well as different types of RNA such as transfer ribonucleic acids (tRNAs), ribosomal RNA (rRNA), messenger RNA (mRNA), and other noncodings (ncRNAs) Among them, tRNAs represent ca 15 % of the total cellular RNAs and are highly v vi Preface stable The primary role of tRNA is to deliver amino acids to the polypeptide chain during protein translation tRNA molecules 73–93 nucleotides long are heavily modified types of ribonucleic acid tRNA modifications (up to 25 %) are dynamic and adaptive to different environmental changes Modified nucleosides of tRNAs play an important role in the translation of the genetic code The modified nucleosides are utilized to fine tune nucleic acids structure and function These modifications are dynamic and participate in regulating diverse biological pathways They can also be used as specific markers of different states of cells and diseases or pathologies The process of RNAs turnover is directly correlated to their presence in the human Evaluation of modified nucleosides might become novel markers to facilitate early clinical diagnosis of cancer to improve human cancer risk assessment Nucleoside methylation and other nucleic acid modifications are of a great interest, prompted by the discovery of methylation and active demethylation of DNA and RNA In eukaryotic genomic DNA, 5-methylcytosine is a well-know epigenetic modification and is also known to exist in both rRNA and tRNA In response to oxidative stress caused by reactive oxidative species (ROS) as well as nutrient depletion and other growth arrest conditions, modified nucleotides are synthesized in the cell to serve various purposes Accidental non-enzymatic methylation or oxidation of a base in a DNA and RNA, in addition to the normal enzymatic methylation processes, induces serious problems for living cells, especially for DNA, for which abnormal alkylation can be mutagenic To remove this type of modification, the cell has developed oxidative mechanisms in an indirect way The recent development of high-throughput sequencing technologies has enabled us to identify tRNA-derived RNA fragments It seems that they are not by-products from random degradation but rather functional molecules that can regulate translation and gene expression It takes a large effect to map RNA modifications globally as well as to identify the cellular function as writers, readers, and erasers for each modification Basic cellular pathways use ubiquitous metabolites and coenzymes to transfer methyl and amino acid groups, isoprenoids, sugars, phosphates, and various metabolite nucleic acid conjugates have been found that affect a functionality of their specific targets The turnover of nucleic acids increases when cell proliferation takes place Any disease or metabolic alteration affecting RNA turnover consequently results in altered nucleoside excretion patterns, leading to the hypothesis that RNA metabolites may be used as early indicators of disease In addition, increased RNA metabolism with altered nucleoside excretion patterns related to metabolic disorders such as cancer may be suitable markers to facilitate the monitoring of therapeutic intervention In this book we have collected work describing modified nucleosides, naturally occurring or chemically synthesized nucleic acids Their role in cell biology has huge potential for application in medicine Further research frontiers and new developments are also discussed Preface vii In total there are 18 chapters Five of them deal with tRNAs and their modifications in relation to biomedical applications Three discuss modified nucleosides including N6-methyladenosine and 8-hydroxyguanosine as well as 20 -O-methylated ribonucleotides A very interesting chapter describes the role of diadenosine tetraphosphate in health and disease Similar properties are described for circular RNAs and for modified therapeutic oligonucleotides Other chapters describe the properties of modified oligonucleotides Poznan´ Berlin Poznan´ January 2016 Stefan Jurga Volker A Erdmann Jan Barciszewski ThiS is a FM Blank Page Free ebooks ==> www.Ebook777.com RNA Around the Clock: Volker A Erdmann in Memoriam On September 11, 2015 we lost our colleague and dear friend Professor Volker A Erdmann from the Institute of ChemistryBiochemistry, Freie Universitaăt Berlin, Germany He was born on February 8, 1941 in Stettin (Germany, now Poland) and later became a U.S citizen In 1963 he earned his B.A in Chemistry and in 1966 an M.Sc in Biochemistry from the University of New Hampshire, Durham, N H., USA (advisor: Prof Dr E.J Herbst) From 1966 to 1969 at the Max-PlanckInstitut f€ ur experimentelle Medizin, Gottingen, Germany, and Technische Universitaăt Braunschweig, Germany, he obtained a Dr rer nat degree in Biochemistry with minors in Chemistry and Microbiology (advisor: Prof Dr F Cramer) After an NIH postdoctoral fellowship with Prof Dr M Nomura at University of Wisconsin, Madison, Wisc., USA, in 1971 he became a research group leader at the Max-Planck-Institut f€ur Molekulare Genetik in Berlin at the Department led by Prof Dr H.G Wittmann In 1978 Volker did Habilitation in Biochemistry and Molecular Biology at the Freie Universitaăt at Berlin, Germany ix www.Ebook777.com Polymerase Reactions that Involve Modified Nucleotides 439 Furthermore, in 2006, they designed a novel third base pair comprising 2-amino8-(20 -deoxy-β-D-erythro-pentofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (dP) and 6-amino-5-nitro-3-(10 -β-D-20 -deoxyribofuranosyl)-2(1H)-pyridone (dZ) (Yang et al 2006) PCR experiments using a 51-mer template containing a single dP residue showed high incorporation accuracies without using 2-thioTTP when dPTP and dZTP were used with the four natural dNTPs The estimated values for fidelity-per-round were 94.4 %, 97.5 %, and 97.5 %, respectively, when Taq, Vent (exo-), and Deep vent(exo-) DNA polymerases were used (Yang et al 2007) In the meantime, E T Kool, F E Romesberg, and I Hirao were independently designing and developing their own candidates for the third base pair In 1998, E T Kool and coworkers reported a F(2,4-difluorotoluene)–Z (4-methylbenzimidazole) base pair (Fig 4b), which does not form hydrogen bonds between the bases (Morales and Kool 1998) They demonstrated that efficiencies for a single incorporation of the Z residue opposite the F residue on a 28-mer DNA template were 130–1900-fold greater than those of the four natural dNs when KF (30 –50 exo-) was used Their results indicate that hydrogen bonding is not necessary for base pair formation, and, if anything, the size and shape of paired bases are more important to the adoption of artificial base pairs by an oligonucleotide duplex Indeed, thereafter, it was demonstrated that pyrene deoxynucleoside (dPyr) as a nonpolar base analog can selectively be incorporated opposite an abasic nucleoside (X) or a tetrahydrofuran abasic analog (ϕ) to form a dPyr–X/ϕ pair during PEX (Matray and Kool 1999) Moreover, they developed “yDNA” (an abbreviation of “wide DNA”), which involves benzopyrimidine deoxynucleosides (dyT and dyC) bearing size-expanded pyrimidines, i.e., yT and yC, designed to form yT–A and yC–G pairs (Lee and Kool 2005) They then examined whether or not dyT and dyC can store and transfer genetic information in vitro and in bacterial cells (Chelliserrykattil et al 2008) The results showed that the correct nucleotides could be inserted opposite yDNA residues in PEX using KF (30 –50 exo-) and Vent(exo-) DNA polymerases Furthermore, the first example of an encoding protein (GFP; green fluorescent protein) in a living organism, i.e., E coli, by unnatural DNA base pair architecture was exhibited in 2008 In 1999, F E Romesberg and coworkers reported that a stable 7-propynyl isocarbostyril nucleoside (dPICS) self-pair can be formed in duplex DNA (Fig 4c), and dPICS triphosphate can be incorporated opposite dPICS on the template by KF (30 –50 exo-) with reasonable efficiency (McMinn et al 1999) However, after the dPICS incorporation, synthesis proceeded inefficiently Thereafter, they determined the best pair from the 3600 (60 Â 60) combinations of unnatural DNA base analogs, i.e., dSICS–dMMO2 (Leconte et al 2008), and subsequently achieved d5SICS–dMMO2 and d5SICS–dNaM pairs, which exhibited the high values of 85.7–99.8 % for fidelity-per-round in PCR using Taq, Deep vent, and Phusion high-fidelity DNA polymerases (Seo et al 2009; Malyshev et al 2009) Recently, they finally managed to create a semisynthetic organism with an expanded genetic alphabet involving d5SICS–dNaM as the third base pair; the genetically engineered organism was E coli that expresses an algal nucleotide triphosphate transporter, which has the efficient uptake of the triphosphates of 440 M Kuwahara et al d5SICS and dNaM, and thereby accurately replicates a plasmid containing d5SICS–dNaM (Malyshev et al 2014) In 2000, I Hirao and coworkers designed and synthesized 2-amino-6-(N, Ndimethylamino)purine (denoted by x) and pyridin-2-one (denoted by y) deoxynucleoside analogs (Fig 4d) (Ishikawa et al 2000) They anticipated that the steric hindrance between the dimethyl at the N6 position of x and the 4-keto group of T would interfere with the formation of an x–T mismatch pair and, furthermore, that the unique pattern of hydrogen bonding between N1 and N2 on x and N1 and O2 on y would form a stable and specific x–y base pair In PEX, using KF and KF (30 –50 exo-), y was selectively incorporated opposite x on the template, which unfortunately was also erroneously incorporated opposites A and G A ribonucleoside-50 -triphosphate analog of y was also synthesized, and the single incorporation of y opposite x in transcription was assessed using T7 RNA polymerase (Ohtsuki et al 2001) As a result, y was incorporated opposite x with 95 % accuracy, while the erroneous incorporation of U opposite x was only occasionally observed ( www.Ebook777.com Polymerase Reactions that Involve Modified Nucleotides 453 Wolfe JL, Kawate T, Belenky A et al (2002) Synthesis and polymerase incorporation of 50 -amino20 ,50 -dideoxy-50 -N-triphosphate nucleotides Nucleic Acids Res 30:3739–3747 Yang Z, Hutter D, Sheng P et al (2006) Artificially expanded genetic information system: a new base pair with an alternative hydrogen bonding pattern Nucleic Acids Res 34:6095–6101 Yang Z, Sismour AM, Sheng P et al (2007) Enzymatic incorporation of a third nucleobase pair Nucleic Acids Res 35:4238–4249 Yu H, Zhang S, Chaput JC (2012) Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor Nat Chem 4:183–187 Zhang L, Yang Z, Sefah K et al (2015) Evolution of functional six-nucleotide DNA J Am Chem Soc 137:6734–6737 www.Ebook777.com ... pseudouridines increase the binding affinity of tRNA residues by inducing a C30 -endo sugar conformation, and dihydrouridines make these interactions more flexible by retaining the sugar pucker into... Suliman Boulos, Ehud Razin, Hovav Nechushtan, and Inbal Rachmin Thinking Small: Circulating microRNAs as Novel Biomarkers for Diagnosis, Prognosis, and Treatment Monitoring in Breast Cancer ... nucleosides including N6-methyladenosine and 8-hydroxyguanosine as well as 20 -O-methylated ribonucleotides A very interesting chapter describes the role of diadenosine tetraphosphate in health and disease