DOCSLIB.ORG

Theoretical Study of Incorporating 6-Thioguanine Into a Guanine Tetrad and Their Influence on the Metal Ion–Guanine Tetrad

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Theoretical Study of Incorporating 6-Thioguanine Into a Guanine Tetrad and Their Influence on the Metal Ion–Guanine Tetrad http://www.paper.edu.cn Chemical Physics Letters 389 (2004) 421–426 Theoretical study of incorporating 6-thioguanine into a guanine tetrad and their influence on the metal ion–guanine tetrad Fancui Meng a,*, Weiren Xu a,b, Chengbu Liu a,* a Institute of Theoretical Chemistry, Shandong University, Jinan 250100, People’s Republic of China b Tianjin Institute of Pharmaceutical Research, Tianjin 300193, People’s Republic of China Received 15 January 2004; in final form 28 March 2004 Available online 20 April 2004 Abstract G-tetrad and other 6-thioguanine (SG) incorporated tetrads have been studied in this Letter. The geometries, energies, charge distributions have been discussed. The effects of different cations (Kþ and Naþ) on the various tetrads have also been studied. The outcomes show that as the SG number increases the tetrad becomes more and more unstable. The Naþ binds more tightly with the tetrad than that of Kþ without hydration correction, while considering hydration effects the stability sequence changes to Kþ >Naþ. Electrostatic potential map of the tetrads have been plotted and the binding sites of cations have been also shown. Ó 2004 Elsevier B.V. All rights reserved. 1. Introduction 6-Thioguanine (SG) is a known anti-cancer agent that is readily incorporated in place of guanine during DNA Guanine-rich oligonucleotides are inhibitors for fi- replication. The incorporation of SG nucleotides into brinogen action in thrombin and HIV viral mediated cell DNA and RNA by polymerases can lead to cell death. fusion [1]. Guanine-rich sequences, which occur in The replacement of oxygen by sulfur at the O6 position telomeres [2] at the ends of linear chromosomes, can of guanine has been proposed to hinder hydrogen form G quartets where multiple guanines are organized bonding necessary for normal G-tetrad formation and around a central cation in a four-stranded structure [3]. could lead to changes in telomere stability. Stefl et al. [15] The structural uniqueness of G-quadruplex DNA makes have performed large-scale molecular dynamics simula- it an ideal target for drug design [4]. Various small tions to investigate the ability of the four-stranded molecules have been found to bind to G-quadruplex guanine-DNA motif to incorporate nonstandard guan- DNA. Monovalent cations such as Kþ and Naþ have ine analogue bases, and they found that the incorpora- been shown to stabilize G-quadruplex structures, pre- tion of 6-thioguanine and 6-thiopurine sharply sumably by coordination with eight carbonyl oxygen destabilized four-stranded G-DNA structures. The metal atoms present between stacked tetrads. However, it is binding properties of thio and oxo guanines are different also known that Naþ and Kþ stabilize different G-tetrad [16]. structures in telomere sequences [5–7]. G-tetrads are structure subsets of G-quadruplex and have attracted considerable interests in both experimental [8,9] and 2. Calculation methods theoretical [10–14] chemistry. Perhaps the most inter- esting characteristic of these structures is their selective The initial structure of the G-tetrad has been gener- interaction with certain cations that fit well in the cavi- ated from the coordinates of the DNA telomere with ties formed by stacking of guanine tetrads. Protein Data Bank code 1KF1 [17]. The backbone has been deleted and the bases have been capped with * Corresponding authors. Fax: +86-531-856-4464 (Chengbu Liu). hydrogen atoms. It has been shown previous that E-mail address: [email protected] (C. Liu). the capping of bases has no significant influence on 转载 中国科技论文在线 http://www.paper.edu.cn 422 F. Meng et al. / Chemical Physics Letters 389 (2004) 421–426 H-bonding between the bases [18]. G-tetrad and SG- H H H2N N tetrad have been arranged to have C4h symmetry. The N H NN initial structures of the other tetrads have been obtained H N by replacing the O6 atom with sulfur atom, thus they all H N7 have Cs symmetry. N X 6 X6 H2 Conventional ab initio and DFT methods have been N + N H M H1 2 used to predicate the interactions between nucleic acid H2N H N1 bases [19–21] and have been proved to be useful since X 6 X6 they can get data that are not available by experiments, N N H such as information about the interaction energies and N H cooperative effects. Base tetrads are relatively large N N H N systems for quantum chemical calculations with inclu- N NH H 2 sion of electron correlation. Due to computer time and H size limitations, such calculations are limited to small Fig. 1. Structure and atom labels of the cation-G-tetrad complex. fragments without considering environment. DFT method has proved to be successful in the close agree- ment between calculated and experimental geometrical parameters and less time-consuming. In G-tetrad the donor groups are O6 and N7 atoms, The tetrad and also cation–tetrads have been opti- and the acceptor groups are H1 and H2. From Table 1 mized by analytic gradient techniques. The method used we could see that the two inter-base hydrogen bond is B3LYP, which is Becke’s three parameter hybrid lengths in G-tetrad are 1.802 and 1.990 A, respectively. functional using the Lee–Yang–Parr correlation func- As one of the Gs replaced by SG the hydrogen bond tional. The basis set used is the standard double-zeta with lengths changed. The most significant variation takes polarization functions, 6-31G*. All the calculations have place in the S6...H1 bond distance with a bond distance been performed using GAUSSIAN 98 package. The total of 2.234 A, which is increased by about 0.4 A. One of binding energy has been defined as the energy difference the O6 atoms forms a bifurcated structure with H1 and between the complex and the sum of the monomers. H2 atoms, and the bond distances are 1.885 and 2.060 A, respectively. The other two O6 atoms form hydrogen bonds that are shorter than that in G-tetrad. The bond 3. Results and discussions distances of N7...H2 are all increased in 3G-1SG as compared with those in G-tetrad. In this Letter, G-tetrad refers to guanine tetrad, 3G- 2G-2SG has two conformers, one is the tetrad with SG refers to guanine tetrad with one of the guanines two SGs in diagonal position and the other one is that replaced by 6-thioguanine, 2G-2SG-1 refers to the tetrad with two SGs in adjacent position. As to the adjacent that the two adjacent guanines changes to 6-thiogua- one, 2G-2SG-1, one of the S6 atom forms a bifurcated nines, 2G-2SG-2 refers to the two diagonal guanines structure and the two hydrogen bond lengths are 2.566 changed to 6-thioguanines, G-3SG is the tetrad that and 2.348 A, respectively. The other hydrogen bond three of guanines have been replaced by 6-thioguanines involving sulfur atom is 2.335 A. While as the two SGs and SG-tetrad refers to 6-thioguanine tetrad. in diagonal position, 2G-2SG-2, there exist two bifur- cated hydrogen bonds. Both of the two O atoms form a 3.1. Tetrads bifurcated structure between O6 and H1 or H2 atoms, and the bond distances are 1.949 and 1.939 A, respec- All of the aforementioned tetrads have been fully tively, while the hydrogen bonds involving sulfur are optimized and the atom labels are shown in Fig. 1. The 2.274 A long. optimized structures and geometric parameters are There are two bifurcated structures in G-3SG and the shown in Fig. 2 and Table 1, energy properties are listed distances of hydrogen bonds O6...H1 and O6...H2 are in Table 2, electrostatic potential maps are in Fig. 3. 2.512 and 2.394 A in one bifurcated H-bond structure and 2.029 and 1.901 A in the other. 3.1.1. Geometries As to SG-tetrad, the S6...H1 distance is 2.244 A and The N2–H2, N1–H1, C@O bond lengths of guanine N7...H2 distance is 2.627 A, while the corresponding monomer are 1.006, 1.014 and 1.218 A at B3LYP/6- distances in G-tetrad are 1.802 and 1.990 A. We could 31G* level, while the corresponding bond lengths in G- see that as O replaced by S the inter-base distances tetrad are all increased by about 0.02 A. The N2–H2, increased. The differences between the geometries of N1–H1, C@S bond lengths of SG monomer are 1.006, G-tetrad and SG incorporated tetrad all are due to the 1.015 and 1.665 A and the corresponding bond lengths larger radius of sulfur and thus we get less compact in tetrad are all elongated. structures. 中国科技论文在线 http://www.paper.edu.cn F. Meng et al. / Chemical Physics Letters 389 (2004) 421–426 423 Fig. 2. Optimized geometries of various tetrads. Table 1 The optimized geometrical parameters of complexes at B3LYP/6-31G* level X6...H1 N7...H2 N2–H2 N1–H1 C@X6 G-tetrad 1.802 1.990 1.024 1.034 1.232 3G-1SG 2.234a 2.051 1.024 1.034 1.677 2.060/1.885b 1.022 1.022 1.241 1.723 2.117 1.022 1.034 1.232 1.789 2.000 1.025 1.035 1.232 2G-2SG-1 2.335 1.995 1.026 1.033 1.678 2.566/2.348 1.019 1.021 1.683 1.811 2.020 1.023 1.032 1.232 1.797 2.063 1.021 1.032 1.232 2G-2SG-2 2.274 2.103 1.023 1.031 1.675 1.949/1.939 1.022 1.024 1.241 2.274 2.103 1.023 1.031 1.675 1.949/1.939 1.022 1.031 1.673 G-3SG 2.358 2.027 1.025 1.030 1.676 2.512/2.394 1.019 1.021 1.683 2.275 2.054 1.024 1.032 1.672 2.029/1.901 1.022 1.023 1.241 SG-tetrad 2.244 2.627 1.016 1.031 1.673 a The hydrogen bonds are listed in clockwise sequence from the up one as shown in Fig.
Load more

Recommended publications
  • Specific Loop Modifications of the Thrombin Binding Aptamer Trigger the Formation of Parallel Structures
    “Specific loop modifications of the thrombin binding aptamer trigger the formation of parallel structures” Aviñó, A., Portella, G., Ferreira, R., Gargallo, R., Mazzini, S., Gabélica, V., Orozco, M., Eritja, R. The FEBS J., 281(4), 1085-1099 (2014). PMID: 24304855, doi: 10.1111/febs.12670 SPECIFIC LOOP MODIFICATIONS OF THE THROMBIN BINDING APTAMER TRIGGER THE FORMATION OF PARALLEL STRUCTURES Anna Aviñó1,#,Guillem Portella2,3,#, Ruben Ferreira1, Raimundo Gargallo5, Stefania Mazzini6, Valerie Gabélica7, Modesto Orozco,2,3,4*and Ramon Eritja1* 1Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Jordi Girona 18-26 08034 Barcelona, Spain. 2Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, 08028 Barcelona, Spain 3Joint IRB-BSC Program in Computational Biology, Barcelona, Spain 4Departament de Bioquímica i Biologia Molecular, Facultat de Biologia, University of Barcelona, 08028 Barcelona, Spain 5Department of Analytical Chemistry, University of Barcelona, 08028 Barcelona, Spain 6Department of Food, Environmental and Nutritional Sciences (DEFENS), Section of Chemical and Biomolecular Sciences, University of Milan, Via Celoria 2, 20133 Milan, Italy 7Physical Chemistry and Mass Spectrometry Laboratory, Department of Chemistry, University of Liège, Belgium. (Present addresses: (1) Univ. Bordeaux, IECB - ARNA laboratory, F-33600 Pessac, France, (2) INSERM, U869 - ARNA laboratory, F-33000 Bordeaux, France. * To whom correspondence should
    [Show full text]
  • Extensive Evaluation of Force Fields for G-Quadruplexes
    Extensive Evaluation of Force Fields for G-Quadruplexes Na Li1, Tong Zhu1,2* 1Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, People’s Republic of China. 2NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai, People’s Republic of China ABSTRACT G-Quadruplexes (GQs), folded by guanine-rich nucleic acid sequences, involve in gene expression processes and closely associated with the formation of tumors. So far, GQ has drawn widespread attention for its notable application of serving as potential anti-cancer target. Recently, theoretical studies for GQs have achieved significant progress, most of which are inseparable from molecular dynamics (MD) simulation. As a necessary tool to explore dynamics behavior of molecules, MD simulations strictly depend on force field parameters, which is a sticking point to obtain accurate results. Currently, many force fields for nucleic acids have been developed, but none of them have been accepted widely for GQs. In this paper, we selected five popular force fields, which are parmbsc0, parmbsc1, OL15, Drude2017 and AMOEBANUC17, and conducted explicit-solvent MD simulations on two DNA GQs respectively. We evaluated these force fields from many aspects in detail. Meanwhile, we compared conformational energy using quantum chemistry calculations. With the comprehensive evaluation, Drude2017 achieved better description for GQs, which we suggest that using Drude2017 force field should be taken into account first when investigating GQs by MD simulation. * To whom correspondence should be addressed. Email: [email protected]; [email protected] INTRODUCTION G-Quadruplexes (GQs)1 are folded by guanine-rich nucleic acid sequences.
    [Show full text]
  • Structure and Function of Multimeric G-Quadruplexes
    molecules Review Structure and Function of Multimeric G-Quadruplexes Sofia Kolesnikova 1,2 and Edward A. Curtis 1,* 1 The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic 2 Department of Biochemistry and Microbiology, University of Chemistry and Technology, 166 28 Prague, Czech Republic * Correspondence: [email protected] Received: 13 August 2019; Accepted: 22 August 2019; Published: 24 August 2019 Abstract: G-quadruplexes are noncanonical nucleic acid structures formed from stacked guanine tetrads. They are frequently used as building blocks and functional elements in fields such as synthetic biology and also thought to play widespread biological roles. G-quadruplexes are often studied as monomers, but can also form a variety of higher-order structures. This increases the structural and functional diversity of G-quadruplexes, and recent evidence suggests that it could also be biologically important. In this review, we describe the types of multimeric topologies adopted by G-quadruplexes and highlight what is known about their sequence requirements. We also summarize the limited information available about potential biological roles of multimeric G-quadruplexes and suggest new approaches that could facilitate future studies of these structures. Keywords: G-quadruplex; dimer; tetramer; multimer; oligomer; telomere; promoter; R-loop; DNA:RNA hybrid 1. Introduction The B-form double helix is the most well known nucleic acid structure, but it is not the only one. Other examples include double helices with geometries that differ from that of classical B-form DNA, such as Z-DNA [1], triple helices [2], and even four-stranded structures in which canonical A-T and C-G base pairs are absent [3,4].
    [Show full text]
  • Thermodynamic Characterization of Tetraplex Dna Structures
    THERMODYNAMIC CHARACTERIZATION OF TETRAPLEX DNA STRUCTURES by BYUL KIM A thesis submitted in conformity with the requirements for the degree of Doctor of Philosophy Department of Pharmaceutical Sciences Leslie Dan Faculty of Pharmacy University of Toronto © Copyright by Byul Kim 2018 ABSTRACT Thermodynamic Characterization of Tetraplex DNA Structures Byul Kim Doctor of Philosophy Department of Pharmaceutical Sciences Leslie Dan Faculty of Pharmacy University of Toronto 2018 The role of counterion condensation as a dominant force governing the stability of DNA duplexes and triplexes is well established. In contrast, the effect of counterion condensation on the stability of G-quadrupex conformations is poorly understood. Unlike other ordered nucleic acid structures, G-quadruplexes exhibit a specific binding of counterions (typically, Na+ or K+) which are buried inside the central cavity and coordinated to the O6 carbonyls of the guanines forming the G-quartets. While it has been known that the G-quadruplex-to-coil transition temperature, TM, increases with an increase in the concentration of the stabilizing ion, the contributions of the specific (coordination in the central cavity) and nonspecific (condensation) ion binding have not been resolved. In the first part of the work performed in this dissertation, we used G-quadruplexes formed by four different sequences derived from the human telomeric region, c-MYC, and VEGF genes to separate the two ionic contributions. We studied the change + + in TM of preformed G-quadruplexes following the addition of nonstabilizing ions Li , Cs , and TMA+ (tetramethylammonium). Our data suggest that the stabilizing action of cations on the G- quadruplex conformation is, primarily, due to the central ions which act as specifically bound II ligands.
    [Show full text]
  • DNA Sequences That Interfere with Transcription: Implications for Genome Function and Stability † ‡ † Boris P
    Review pubs.acs.org/CR DNA Sequences That Interfere with Transcription: Implications for Genome Function and Stability † ‡ † Boris P. Belotserkovskii, Sergei M. Mirkin, and Philip C. Hanawalt*, † Department of Biology, Stanford University, Stanford, California 94305, United States ‡ Department of Biology, Tufts University, Medford, Massachusetts 02155, United States 1. INTRODUCTION The primary role of DNA-dependent RNA synthesis, or transcription, is to create components for the cellular machinery. The nascent RNA product of transcription is released from the DNA template and either serves as an intermediate message for protein synthesis or is used directly, as in the case of rRNA, tRNA, and various types of regulatory RNAs. Recently, a growing number of examples suggest that transcription per se, rather than its released product, could play a regulatory role in gene function or as a trigger for genomic modifications. The latter scenario is commonly attributed to anomalous progression of the RNA polymerase (RNAP), such as pausing CONTENTS or termination and/or retaining rather than releasing the nascent transcript. This has been implicated in class-switch 1. Introduction 8620 recombination and somatic hypermutation (reviewed in refs 1, − 2. Transcription Blockage Mechanisms 8621 2), telomere maintenance,3 and replication initiation.4 9 3. Effects of Unusual DNA Structures and DNA/RNA Anomalous transcription elongation has also been linked to Complexes on Transcription 8622 various deleterious phenomena, such as genomic instabilities, 3.1. General Introduction to DNA Structure and transcription−replication collisions, and transcription defi- DNA Supercoiling 8622 ciency in some hereditary human disorders (reviewed in refs 3.2. Overview of Unusual Structures and Their 10−14).
    [Show full text]
  • Structure, Properties, and Biological Relevance of the DNA and RNA G Quadruplexes: Overview 50 Years After Their Discovery
    ISSN 00062979, Biochemistry (Moscow), 2016, Vol. 81, No. 13, pp. 16021649. © Pleiades Publishing, Ltd., 2016. Original Russian Text © N. G. Dolinnaya, A. M. Ogloblina, M. G. Yakubovskaya, 2016, published in Uspekhi Biologicheskoi Khimii, 2016, Vol. 56, pp. 53154. REVIEW Structure, Properties, and Biological Relevance of the DNA and RNA GQuadruplexes: Overview 50 Years after Their Discovery N. G. Dolinnaya1*, A. M. Ogloblina2, and M. G. Yakubovskaya2 1Lomonosov Moscow State University, Department of Chemistry, 119991 Moscow, Russia; Email: [email protected] 2Blokhin Cancer Research Center, Institute of Carcinogenesis, Russian Academy of Medical Sciences, 115478 Moscow, Russia Received June 15, 2016 Abstract—Gquadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied noncanonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermo dynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conforma tional features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4specific smallmolecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of Gquadruplexes in cells.
    [Show full text]
  • A Novel G-Quadruplex-Forming GGA Repeat Region in the C-Myb Promoter Is a Critical Regulator of Promoter Activity Sunmi L
    Published online 5 February 2008 Nucleic Acids Research, 2008, Vol. 36, No. 6 1755–1769 doi:10.1093/nar/gkm1069 A novel G-quadruplex-forming GGA repeat region in the c-myb promoter is a critical regulator of promoter activity SunMi L. Palumbo1, Regan M. Memmott1, Diana J. Uribe1, Yulia Krotova-Khan1, Laurence H. Hurley1,2,3 and Scot W. Ebbinghaus1,* 1Arizona Cancer Center, University of Arizona, 1515 N. Campbell Ave., Tucson, AZ 85724-5024, 2College of Pharmacy, University of Arizona, 1295 N. Martin Ave., Tucson, AZ 85721 and 3BIO5 Institute, University of Arizona, 1657 E. Helen St., Tucson, AZ 85721, USA Received May 31, 2007; Revised and Accepted November 13, 2007 ABSTRACT encodes a critical transcription factor for proliferation, differentiation and survival of haematopoietic progenitor The c-myb promoter contains multiple GGA repeats cells (1). High levels of the gene product c-Myb prevent beginning 17 bp downstream of the transcription haematopoietic stem cells from both differentiation and initiation site. GGA repeats have been previously apoptosis (2,3). Because of the critical role of c-Myb in shown to form unusual DNA structures in solution. determining cell fate, c-Myb expression levels are tightly Results from chemical footprinting, circular dichro- controlled in normal cells, showing high levels in ism and RNA and DNA polymerase arrest assays on immature, proliferating haematopoietic cells and unde- oligonucleotides representing the GGA repeat region tectable levels in differentiated cells (4). c-Myb is over of the c-myb promoter demonstrate that the element expressed in many leukemias and some solid tumors, and is able to form tetrad:heptad:heptad:tetrad (T:H:H:T) plays a critical role in leukemogenesis by maintaining cells G-quadruplex structures by stacking two tetrad:hep- in a proliferative state and by preventing terminal tad G-quadruplexes formed by two of the three differentiation (5–7).
    [Show full text]
  • Structural Studies on DNA G-Quadrupiexes
    October 2006 Structural studies on DNA G-quadrupIexes Sarah Wallace Burge {née Rankin) A thesis submitted for the degree of Doctor of Philosophy of the University of London Cancer Research UK Biomolecular Structure Group The School of Pharmacy University of London ProQuest Number: 10104293 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest. ProQuest 10104293 Published by ProQuest LLC(2016). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States Code. Microform Edition © ProQuest LLC. ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 Acknowledgements This work is in part a testament to the advice and encouragement I have received from various quarters over the past three years. They are too numerous to include and these brief mentions are somewhat inadequate to express my gratitude for their forbearance, wisdom and friendship. My supervisor, Professor Stephen Neidle, provided excellent direction and advice which resulted in a fulfilling and productive three years. I extend my thanks also to Dr Gary Parkinson for his advice and to Dr Mire Zloh for his assistance with NMR data collection at the School of Pharmacy. The hospitality of Dr Anh Tuan Phan and Professor Dinshaw Patel at the Memorial Sloan Kettering Cancer Center, New York, made for a truly memorable visit; I am indebted to them for their assistance in the synthesis of the '^N labelled DNA and collection of the associated NMR spectra.
    [Show full text]
  • Gauri Misra Editor Basics of Biophysics
    Gauri Misra Editor Introduction to Biomolecular Structure and Biophysics Basics of Biophysics Introduction to Biomolecular Structure and Biophysics Gauri Misra Editor Introduction to Biomolecular Structure and Biophysics Basics of Biophysics Editor Gauri Misra Amity University Noida, Uttar Pradesh India ISBN 978-981-10-4967-5 ISBN 978-981-10-4968-2 (eBook) DOI 10.1007/978-981-10-4968-2 Library of Congress Control Number: 2017952062 # The Editor(s) (if applicable) and The Author(s) 2017 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. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
    [Show full text]
  • Molecular Dynamics Simulations Reveal the Balance of Forces Governing the Formation of a Guanine Tetrad––A Common Structural
    3020–3030 Nucleic Acids Research, 2016, Vol. 44, No. 7 Published online 14 March 2016 doi: 10.1093/nar/gkw160 Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad––a common structural unit of G-quadruplex DNA Mateusz Kogut, Cyprian Kleist and Jacek Czub* Department of Physical Chemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdansk, Poland Received January 20, 2016; Revised February 26, 2016; Accepted March 1, 2016 ABSTRACT mation of G4 motifs at the single-stranded telomeric 3- overhang leads to telomerase inhibition (10) and competes G-quadruplexes (G4) are nucleic acid conformations with the binding of the ssDNA overhang by POT1, a com- of guanine-rich sequences, in which guanines are ponent of shelterin protein complex protecting chromoso- arranged in the square-planar G-tetrads, stacked on mal ends (11–13). Accordingly, G4-stabilizing agents, such one another. G4 motifs form in vivo and are impli- as telomestatin, have been shown to impair telomere home- cated in regulation of such processes as gene ex- ostasis and thereby to induce growth arrest or apoptosis in pression and chromosome maintenance. The struc- cultured cells (14–16). As a result, G4 DNA is now consid- ture and stability of various G4 topologies were de- ered a promising target for anticancer therapy (17–19). G4- termined experimentally; however, the driving forces forming sequences are also found to be over-represented in for their formation are not fully understood at the other regulatory regions of the genome, including promot- molecular level. Here, we used all-atom molecular ers (20,21), introns (22), mitotic and meiotic double-strand break sites (6), immunoglobulin switch regions (9) and 5- dynamics to probe the microscopic origin of the G4 UTRs (23).
    [Show full text]
  • Possible Regulatory Roles of Promoter G-Quadruplexes in Cardiac Function-Related Genes – Human Tnic As a Model
    Possible Regulatory Roles of Promoter G-Quadruplexes in Cardiac Function-Related Genes – Human TnIc as a Model Wenhua Zhou1, Kogularamanan Suntharalingam2, Nigel J. Brand3, Paul J. R. Barton3,4, Ramon Vilar2, Liming Ying1* 1 Molecular Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom, 2 Department of Chemistry, Imperial College London, London, United Kingdom, 3 Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Middlesex, United Kingdom, 4 NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, United Kingdom Abstract G-quadruplexes (G4s) are four-stranded DNA secondary structures, which are involved in a diverse range of biological processes. Although the anti-cancer potential of G4s in oncogene promoters has been thoroughly investigated, the functions of promoter G4s in non-cancer-related genes are not well understood. We have explored the possible regulatory roles of promoter G4s in cardiac function-related genes using both computational and a wide range of experimental approaches. According to our bioinformatics results, it was found that potential G4-forming sequences are particularly enriched in the transcription regulatory regions (TRRs) of cardiac function-related genes. Subsequently, the promoter of human cardiac troponin I (TnIc) was chosen as a model, and G4s found in this region were subjected to biophysical characterisations. The chromosome 19 specific minisatellite G4 sequence (MNSG4) and near transcription start site (TSS) G4 sequence (280 G4) adopt anti-parallel and parallel structures respectively in 100 mM KCl, with stabilities comparable to those of oncogene G4s. It was also found that TnIc G4s act cooperatively as enhancers in gene expression regulation in HEK293 cells, when stabilised by a synthetic G4-binding ligand.
    [Show full text]
  • Genomic Deoxyuracil: Targeting, Regulation and Repair
    Illinois State University ISU ReD: Research and eData Theses and Dissertations 9-25-2015 Genomic Deoxyuracil: Targeting, Regulation And Repair Nate Warren Holton Illinois State University, [email protected] Follow this and additional works at: https://ir.library.illinoisstate.edu/etd Part of the Molecular Biology Commons Recommended Citation Holton, Nate Warren, "Genomic Deoxyuracil: Targeting, Regulation And Repair" (2015). Theses and Dissertations. 468. https://ir.library.illinoisstate.edu/etd/468 This Dissertation is brought to you for free and open access by ISU ReD: Research and eData. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of ISU ReD: Research and eData. For more information, please contact [email protected]. GENOMIC DEOXYURACIL: TARGETING, REGULATION AND REPAIR Nate W. Holton 127 pages Maintaining genomic integrity is critical to avoid sequence mutations and genetic disease. However the immune system requires genomic rearrangements in order to produce novel antibodies and elicit a full immunological response. The expression of DNA modifying enzymes is essential for antibody production but the off target effects are not well understood. The work presented here was performed to elucidate molecular mechanisms responsible for the regulation and targeting of DNA editing enzymes, as well as characterize repair of these lesions at off target loci. KEYWORDS: Activation Induced Cytosine Deaminase, AID, miRNA, miR155, miR93, G-quadruplex, G4, Uracil DNA Glycosylase, UDG, UNG GENOMIC DEOXYURACIL: TARGETING, REGULATION AND REPAIR NATE W. HOLTON A Dissertation Submitted in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY School of Biological Sciences ILLINOIS STATE UNIVERSITY 2015 Copyright 2015 Nate W.
    [Show full text]