DOCSLIB.ORG

An Atlas of RNA Base Pairs Involving Modified Nucleobases with Optimal Geometries and Accurate Energies

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
An Atlas of RNA Base Pairs Involving Modified Nucleobases with Optimal Geometries and Accurate Energies An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies Item Type Article Authors Chawla, Mohit; Oliva, R.; Bujnicki, J. M.; Cavallo, Luigi Citation An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies 2015 Nucleic Acids Research Eprint version Publisher's Version/PDF DOI 10.1093/nar/gkv606 Publisher Oxford University Press (OUP) Journal Nucleic Acids Research Rights This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http:// creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Download date 26/09/2021 02:06:18 Link to Item http://hdl.handle.net/10754/558768 Nucleic Acids Research Advance Access published June 27, 2015 Nucleic Acids Research, 2015 1 doi: 10.1093/nar/gkv606 An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies Mohit Chawla1, Romina Oliva2,*, Janusz M. Bujnicki3,4 and Luigi Cavallo1,* 1King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal 23955-6900, Saudi Arabia, 2Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, I-80143, Naples, Italy, 3Laboratory of Bioinformatics and Protein Downloaded from Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, 02-109 Warsaw, Poland and 4Laboratory of Bioinformatics, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland Received March 31, 2015; Revised May 27, 2015; Accepted May 28, 2015 http://nar.oxfordjournals.org/ ABSTRACT translational regulation, up to the tuning of cellular dif- ferentiation and development. It is particularly interesting Posttranscriptional modifications greatly enhance that the fraction of human genome that is cell-specifically the chemical information of RNA molecules, con- transcribed to generate these regulatory noncoding RNAs tributing to explain the diversity of their structures is larger that the fraction of it devoted to encode proteins and functions. A significant fraction of RNA experi- (1). at King Abdullah University of Science and Technology on July 1, 2015 mental structures available to date present modified RNA fulfills this striking variety of functions appar- nucleobases, with half of them being involved in H- ently based on a limited chemical diversity, established by bonding interactions with other bases, i.e. ‘modified only four nucleobases: adenine (A), guanine (G), cytosine base pairs’. Herein we present a systematic investi- (C), uracil (U). This apparent contradiction is solved when gation of modified base pairs, in the context of ex- thinking that RNA can take advantage of a large num- perimental RNA structures. To this end, we first com- ber of posttranscriptional modifications, greatly enhancing its chemical information. To date, more than 100 differ- piled an atlas of experimentally observed modified ent modifications have been reported in RNA molecules, base pairs, for which we recorded occurrences and ranging from simple additions or substitutions of chemi- structural context. Then, for each base pair, we se- cal groups as e.g. in methylations or deaminations, to com- lected a representative for subsequent quantum me- plex alterations, often comprising a series of reactions, some chanics calculations, to find out its optimal geometry of which even resulting in a different heterocyclic structure. and interaction energy. Our structural analyses show A complete catalogue of such modifications can be found that most of the modified base pairs are non Watson– in dedicated databases, such as the RNAmods database (2) Crick like and are involved in RNA tertiary structure and MODOMICS (3), with the latter database containing motifs. In addition, quantum mechanics calculations also information about RNA modification pathways and quantify and provide a rationale for the impact of the sites of modification in selected RNAs. different modifications on the geometry and stability While the highest concentration and diversity of post- transcriptional modifications has been till now reported in of the base pairs they participate in. tRNA molecules, they are also widespread in rRNA and mRNA, and more than a dozen of modifications have al- INTRODUCTION ready been reported in small, noncoding RNAs (2,4–8). As Discovery of various forms of noncoding RNAs in the a matter of fact, nowadays most if not all the major classes past two decades, besides the well-known coding messen- of RNA molecules in the cell are thought to possibly present ger RNA (mRNA), ribosomal RNA (rRNA) and transfer modified nucleotides. RNA (tRNA), has dramatically changed our view of the Specific modifications contribute to tRNA stability, favor RNA function. In addition to the transmission of genetic its recognition by the cognate aminoacyl synthetase and by information, it is indeed now clear that RNA molecules can mRNA, influence nuclear export of mRNA, protect it from fulfill a variety of other functions, including catalysis and degradation and regulate splicing, or can establish resis- *To whom correspondence should be addressed. Tel: +966 12 8087566; Fax +966 12 8089999; Email: [email protected] Correspondence may also be addressed to Romina Oliva. Tel: +39 081 5476541; Fax: +39 081 5476514; Email: [email protected] C The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. 2 Nucleic Acids Research, 2015 tance to antibiotics in bacterial rRNA (9–14). Many more tive occurrences, and an accurate estimate of the effect of examples of the impact of modifications on the RNA func- each chemical modification on the structure and stability of tion and structure are reviewed in (8,13–17). Importantly, the corresponding H-bonded base pair. Notably, we found modifications also play a role in human diseases, partic- that the modified base pairs typically exhibit non canon- ularly tumors, myopathy, type-2 diabetes and obesity [re- ical geometries (i.e. different from the classical Watson– viewed in (18)]. Crick pairing) and are located in a variety of different RNA Chemical modifications that control the stability and molecules and structural motifs. This extends our under- proper folding of the RNA molecule are generally classi- standing of how posttranscriptional modifications act on fied as ‘structural’. The most efficient ways by which they the structure of RNA molecules to influence their function. can affect the RNA structure are hydrogen bonding, ␲- stacking and the coordination of metal ions, with the first MATERIALS AND METHODS one playing a major role. Chemical modifications may ac- Nomenclature Downloaded from tually occur at all the three edges used by nucleobases for H-bonding to other bases, i.e. the Watson–Crick, the Hoog- The adopted nomenclature for the geometry of the analysed steen and the sugar edge (see Figure 1). A modified nucle- H-bonded base pairs (Table 1) is based on that proposed by obase can thus exhibit significantly changed pairing prop- Leontis and Westhof (42,43) and extended by Lemieux and erties, as compared to the corresponding canonical one. If Major (44). In it, the interacting edges involved in the H- the Watson–Crick edge is affected, for instance, the canoni- bonding, i.e. Watson–Crick, Hoogsteen or sugar, and the http://nar.oxfordjournals.org/ cal Watson–Crick G-C/A-U pairing will be impaired, while two mutual orientations of the glycosidic bonds, i.e cis or non canonical base pairs, involving either of the other two trans are specified (42,43). A symbol ‘W’, ‘H’ or ‘S’, is given edges, may be favored. to indicate that the ‘Watson–Crick’, ‘Hoogsteen’ or ‘sugar’ To date, more than 3000 macromolecular structures have edge is involved in the base-base H-bonding interaction; been deposited in the wwPDB (19), which contain differ- ‘Bs’ is used for bifurcated base pairs involving the sugar side ent types of RNA molecules including not only tRNAs, amino/keto group (44). This is preceded by ‘c’ or ‘t’, indi- mRNAs, rRNAs, but also viral RNAs, riboswitches, ri- cating that the orientation of the glycosidic bonds is cis or bozymes and more recently discovered small non coding nu- trans, respectively. We added an ‘r’ in brackets after the edge clear and nucleolar RNAs. Remarkably, a significant frac- symbol when the corresponding ribose was also involved in at King Abdullah University of Science and Technology on July 1, 2015 tion of such structures present modified residues. There- H-bonding. The symbol for the edge H-bonding with the ri- fore, it is time to systematically investigate the structural ef- bose of the paired nucleoside was also reported in brackets, fect of chemical modifications in the context of experimen- if different from that involved in base-base pairing. Tradi- tal RNA structures. Herein we will focus on the modifica- tional abbreviations were adopted for the modified nucle- tions effect on H-bonded base pairs. To this end, we per- obases. For the non-natural modifications, after the num- formed a comprehensive search in the Protein Data Bank ber of the modified atom we reported the chemical symbol (19) to compile an atlas of experimentally observed ‘mod- of the halogen element substituting a hydrogen atom and ified base pairs’, i.e. H-bonded base pairs, with a given ge- the one-letter-code of the corresponding nucleobase. When ometry, involving at least one noncanonical nucleobase. For a base pair is characterized by only one H-bond, this is in- each specific combination of nucleobases and base pair ge- dicated by a ‘1’ after the edge symbols.
Load more

Recommended publications
  • SUPPLEMENTARY TABLE 1 Non-Destructive Characterisation Of
    Electronic Supplementary Material (ESI) for Analyst. This journal is © The Royal Society of Chemistry 2016 SUPPLEMENTARY TABLE 1 Non-destructive characterisation of mesenchymal stem cell differentiation using LC-MS-based metabolite footprinting Amal Surrati 1, Rob Linforth 2, Ian Fisk 2, VirginieSottile1*, Dong-Hyun Kim 3*. 1Wolfson Centre for Stem Cells, Tissue, Engineering and Modelling (STEM), School of Medicine, The University of Nottingham, CBS Building - University Park, Nottingham NG7 2RD (U.K.) 2Division of Food Sciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD (U.K.) 3Centre for Analytical Bioscience, Division of Molecular and Cellular Sciences, School of Pharmacy, The University of Nottingham, Nottingham, NG7 2RD (U.K.) *Correspondence to: Email: [email protected] Tel: +44 1158231235 Email: [email protected] Tel: +44 1157484697 Supplementary Table 1: Metabolites changed in MSC-conditioned medium compared to fresh medium (blank). ↑ indicates the metabolites that increased in all MSC-conditioned medium (control and OS) compared to their corresponding blanks, and ↓ indicates decreased metabolites. ID confidence: Metabolite identification level according to the metabolomics standards initiative 29,30 ; L1 – Level 1, L2 – Level 2. Change RT ID Identifier compared Exact mass Formula Putative metabolite (min) confidence (PubChem) to blank medium 179.0946 5.30 C10H13NO2 (-)-Salsolinol L2 91588 ↑ 358.1410 10.12 C20H22O6 (+)-Pinoresinol L2 7741 ↑ 148.0371
    [Show full text]
  • Unveiling Structural and Functional Divergences Of
    Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario Charles Bou-Nader, Hugo Montémont, Vincent Guérineau, Olivier Jean-Jean, Damien Brégeon, Djemel Hamdane To cite this version: Charles Bou-Nader, Hugo Montémont, Vincent Guérineau, Olivier Jean-Jean, Damien Brégeon, et al.. Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: per- spectives on the evolution scenario. Nucleic Acids Research, Oxford University Press, 2018, 46 (3), pp.1386-1394. 10.1093/nar/gkx1294. hal-01727508 HAL Id: hal-01727508 https://hal.sorbonne-universite.fr/hal-01727508 Submitted on 9 Mar 2018 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. Distributed under a Creative Commons Attribution| 4.0 International License 1386–1394 Nucleic Acids Research, 2018, Vol. 46, No. 3 Published online 27 December 2017 doi: 10.1093/nar/gkx1294 Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario Charles
    [Show full text]
  • N6-Methyladenosine (M6a) Is an Endogenous A3 Adenosine Receptor Ligand
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.21.391136; this version posted November 22, 2020. 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-NC-ND 4.0 International license. N6-methyladenosine (m6A) is an endogenous A3 adenosine receptor ligand Akiko Ogawa,1, 2, 3 Chisae Nagiri,4, 13 Wataru Shihoya,4, 13 Asuka Inoue,5, 6, 7, 13 Kouki Kawakami,5 Suzune Hiratsuka,5 Junken Aoki,7, 8 Yasuhiro Ito,3 Takeo Suzuki,9 Tsutomu Suzuki,9 Toshihiro Inoue,3 Osamu Nureki,4 Hidenobu Tanihara,10 Kazuhito Tomizawa,2, 11 Fan-Yan Wei1, 2, 12, 14 1Department of Modomics Biology & Medicine, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai 980-8575, Japan. 2Department of Molecular Physiology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan. 3Department of Ophthalmology, Faculty of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan. 4Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan. 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.21.391136; this version posted November 22, 2020. 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-NC-ND 4.0 International license. 5Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan.
    [Show full text]
  • Transcription-Wide Mapping of Dihydrouridine (D) Reveals That Mrna Dihydrouridylation Is Essential for Meiotic Chromosome Segregation
    Transcription-wide mapping of dihydrouridine (D) reveals that mRNA dihydrouridylation is essential for meiotic chromosome segregation Olivier Finet1, Carlo Yague-Sanz1, Lara Katharina Kruger2, Valérie Migeot1, Felix G.M. Ernst3, Denis L.J. Lafontaine3, Phong Tran2, Maxime Wery4, Antonin Morillon4, and Damien Hermand1,* 1 URPHYM-GEMO, The University of Namur, rue de Bruxelles, 61, Namur 5000 Belgium 2 Institut Curie, PSL Research University, CNRS, UMR 144, Paris, France. 3 RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S./FNRS), Université Libre de Bruxelles, Charleroi-Gosselies, Belgium2 4 ncRNA, epigenetic and genome fluidity, Institut Curie, PSL Research University, CNRS UMR 3244, Université Pierre et Marie Curie, Paris, France * Corresponding author: [email protected] 1 Electronic copy available at: https://ssrn.com/abstract=3569550 Summary Epitranscriptomic has emerged as a new fundamental layer of control of gene expression. Nevertheless, the determination of the transcriptome-wide occupancy and function of RNA modifications remains challenging. Here we have developed Rho- seq, an integrated pipeline detecting a range of modifications through differential modification-dependent Rhodamine labeling. Using Rho-seq, we confirm that the reduction of uridine to dihydrouridine by the Dus reductase enzymes family targets tRNAs in E. coli. Unexpectedly, we find that the D modification expands to mRNAs in fission yeast. The modified mRNAs are enriched for cytoskeleton-related encoding proteins. We show that the a-tubulin encoding mRNA nda2 undergoes dihydrouridylation, which affects its protein expression level. The absence of the modification onto the nda2 mRNA strongly impacts meiosis by inducing a metaphase delay or by completely preventing the formation of spindles during meiosis I and meiosis II, resulting in low gamete viability.
    [Show full text]
  • ABSTRACT CANTARA, WILLIAM ANTHONY. Arginyl-Trna Modifications Modulate Anticodon Domain Structure, Function and Dynamics in Esch
    ABSTRACT CANTARA, WILLIAM ANTHONY. Arginyl-tRNA Modifications Modulate Anticodon Domain Structure, Function and Dynamics in Escherichia coli. (Under the direction of Paul F. Agris) During ribosome-mediated protein synthesis, non-initiator tRNAs act as translating chaperones by transferring the correct amino acid to the ribosome through sequence-specific interactions with mRNA codons in the ribosomal A-site. To achieve uniformity in codon recognition ability between different tRNAs, the anticodon domains of all must adopt a singular conformation in the ribosomal decoding center. Since there is a necessary sequence variation for the three anticodon residues, innovative ways of attaining a constant loop structure are required. Nature has resolved this issue by introducing functional groups to the loop residues, changing the chemical environment and, thus, the conformation. In fact, there is a large diversity and number of these modifications found in tRNAs of all known life. Escherichia coli (E.coli) arginyl-tRNAs offer the opportunity to study these modifications in the context of six-fold degenerate codons that vary widely in their cellular usage. A single Arg1 Arg2 set of very similar isoacceptors, tRNA ICG and tRNA ICG, have anticodon domains that 2 differ only in the presence or absence of a very rare modification, 2-thiocytidine (s C32). 2 These tRNAs are particularly interesting not only because of the rare s C32 modification, but also through the wobble position modification I34, they are both responsible for decoding two very common codons CGU and CGC as well as the very rare CGA codon. Typically, the codon usage correlates with the tRNA content of the cell; however, in this instance, the tRNA content is high which does not match what would be expected for an isoacceptor that recognizes a rare codon.
    [Show full text]
  • Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post
    molecules Review Synthesis of Nucleobase-Modified RNA Oligonucleotides by Post-Synthetic Approach Karolina Bartosik , Katarzyna Debiec , Anna Czarnecka , Elzbieta Sochacka and Grazyna Leszczynska * Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland; [email protected] (K.B.); [email protected] (K.D.); [email protected] (A.C.); [email protected] (E.S.) * Correspondence: [email protected]; Tel.: +48-42-6313150 Academic Editor: Katherine Seley-Radtke Received: 20 June 2020; Accepted: 20 July 2020; Published: 23 July 2020 Abstract: The chemical synthesis of modified oligoribonucleotides represents a powerful approach to study the structure, stability, and biological activity of RNAs. Selected RNA modifications have been proven to enhance the drug-like properties of RNA oligomers providing the oligonucleotide-based therapeutic agents in the antisense and siRNA technologies. The important sites of RNA modification/functionalization are the nucleobase residues. Standard phosphoramidite RNA chemistry allows the site-specific incorporation of a large number of functional groups to the nucleobase structure if the building blocks are synthetically obtainable and stable under the conditions of oligonucleotide chemistry and work-up. Otherwise, the chemically modified RNAs are produced by post-synthetic oligoribonucleotide functionalization. This review highlights the post-synthetic RNA modification approach as a convenient and valuable method to introduce a wide variety of nucleobase modifications, including recently discovered native hypermodified functional groups, fluorescent dyes, photoreactive groups, disulfide crosslinks, and nitroxide spin labels. Keywords: phosphoramidite chemistry; RNA solid-phase synthesis; post-synthetic RNA modification; convertible nucleoside 1. Introduction Recently, a significant interest has been observed in the use of modified oligoribonucleotides in the fields of molecular biology, biochemistry, and medicine [1–3].
    [Show full text]
  • ST.25 Page: 3.25.1
    HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION Ref.: Standards – ST.25 page: 3.25.1 STANDARD ST.25 STANDARD FOR THE PRESENTATION OF NUCLEOTIDE AND AMINO ACID SEQUENCE LISTINGS IN PATENT APPLICATIONS Revision adopted by the SCIT Standards and Documentation Working Group at its eleventh session on October 30, 2009 It is recommended that Offices apply the provisions of the “Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in International Patent Applications Under the Patent Cooperation Treaty (PCT)” as set out in Annex C to the Administrative Instructions under the PCT, mutatis mutandis, to all patent applications other than the PCT international applications, noting that certain provisions specific to PCT procedures and requirements may not be applicable to patent applications other than PCT international applications(*). The text of that PCT Standard is reproduced on the following pages. (*) If, on July 1, 2009, the national law and practice applicable by an Office is not compatible with the provisions of paragraph 3(i) of the “Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in International Patent Applications Under the Patent Cooperation Treaty (PCT)” requiring that a sequence listing which is contained in the international application as filed “shall be presented as a separate part of the description, be placed at the end of the application, preferably be entitled ‘Sequence Listing’, begin on a new page and have independent page numbering”, that Office may choose not to follow those provisions for as long as that incompatibility continues. en / 03-25-01 Date: December 2009 HANDBOOK ON INDUSTRIAL PROPERTY INFORMATION AND DOCUMENTATION Ref.: Standards – ST.25 page: 3.25.2 ANNEX C STANDARD FOR THE PRESENTATION OF NUCLEOTIDE AND AMINO ACID SEQUENCE LISTINGS IN INTERNATIONAL PATENT APPLICATIONS UNDER THE PCT INTRODUCTION 1.
    [Show full text]
  • Characterizing the 3D Interactions of the Base-Pair Stems
    CHARACTERIZING THE 3D INTERACTIONS OF THE BASE-PAIR STEMS AND HELICES IN RNA MOLECULES BY ZAINAB MOHAMMED HASSAN FADHIL A thesis submitted to the The Graduate School- New Brunswick Rutgers, the state University of New Jersey In partial fulfillment of the requirements For the degree of Master of Science Graduate Program in Chemistry and Chemical Biology Written under the direction of Dr. Wilma K. Olson And approved By ………………………………… ………………………………… ………………………………… New Brunswick, New Jersey October 2017 ABSTRACT OF THE THESIS CHARACTERIZING THE 3D INTERACTIONS OF THE BASE-PAIR STEMS AND HELICES IN RNA MOLECULES By ZAINAB MOHAMMED HASSAN FADHIL Thesis Director: Wilma K. Olson Characterizing RNA structure experimentally is a challenging task. Computational methods complement experimental methods. In this thesis, we study, using software tools such as DSSR, Matlab, and Excel, the three-dimensional structures of a group of non-redundant RNA structures. These structures are those identifiers as Leontis and Zirbel at January 2017 [1], and the relevant coordinates for these structures downloaded from the Protein Data Bank (PDB) [2]. Specifically, we find the angles between all pairs of chemically linked double helical stems in each of the RNA structures, the distances between the mid points between all these stems, and the distributions for the calculated angles and distances. Additionally, we separate the above calculations to consider stems within the same helix. A helix is composed of at least two stacked base pairs and these base pairs are not necessarily chemically linked. The third part contains these calculations separated for stems in different helices. Based on these calculations, the stems in the same helix can be classified into two groups.
    [Show full text]
  • Structural Landscape of Base Pairs Containing Post-Transcriptional
    bioRxiv preprint doi: https://doi.org/10.1101/098871; this version posted January 6, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Structural landscape of base pairs containing post- transcriptional modifications in RNA PREETHI S.P,1 PURSHOTAM SHARMA2,* and ABHIJIT MITRA1,* 1Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology Hyderabad (IIIT-H), Gachibowli, Hyderabad, Telangana, 500032, India. 2Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India. Corresponding authors: [email protected], [email protected] ABSTRACT Base pairs involving post-transcriptionally modified nucleobases are believed to play important roles in a wide variety of functional RNAs. Here we present our attempts towards understanding the structural and functional role of naturally occurring modified base pairs by analyzing their distribution in different RNA classes, with the help of crystal structure and sequence database analyses. In addition, we quantify the variation in geometrical features of modified base pairs within RNA structures, and characterize their optimum geometries and binding energies using advanced quantum chemical methods. Further comparison of modified base pairs with their unmodified counterparts illustrates the effect of steric and electronic structure alterations due to base modifications. Analysis of specific structural contexts of modified base pairs in RNA crystal structures revealed several interesting scenarios, including those at the tRNA:rRNA interface, antibiotic-binding site and the three-way junctions within tRNA, which when analyzed in context of available experimental data, allowed us to correlate the occurrence and strength of modified base pairs with the specific functional roles they play in context of RNA macromolecules.
    [Show full text]
  • 1 Chapter 1 Chemistry on the Pyrimidine Ring Introduction
    Chapter 1 Chemistry On The Pyrimidine Ring Introduction Pyrimidines are 6-membered heterocyclic ring compounds composed of nitrogen and carbon. They are present throughout nature in various forms and are the building blocks of numerous natural compounds from antibiotics to vitamins and liposacharides. The most commonly recognized pyrimidines are the bases of RNA and DNA, the most abundant being cytosine, thymine or uracil. The origin of the term pyrimidine dates back to 1884 when Pinner coined the term from a combination of the words pyridine and amidine because of the structural similarity to those compounds (1). Since these initial investigations hundreds of pyrimidine-containing compounds have been found in biochemistry. The numerous modifications upon this scaffold and its relative importance in nature make it an interesting area of study. Here we have chosen to explore some of the general mechanisms nature has employed to create and modify pyrimidines. Mechanistically related metabolic and catabolic enzymes involved in ring opening/closure and oxidation/reduction of pyrimidines will be examined. Enzymes involved in the methylation, thiolation and amination of the pyrimidine ring will also be compared. 1 Biosynthetic Origin The majority of organisms synthesize pyrimidines through a de novo pathway, and a minority, depend on a uracil salvage pathway (2). The de novo pyrimidine biosynthetic pathway starts with bicarbonate and ammonia, often derived from glutamine, to form uridine-5’-monophosphate (Figure 1.1). There are six enzymes in the de novo biosynthetic pathway: carbamoyl-phosphate synthetase, aspartate carbamoyltransferase, dihydroorotase, dihydroorotate dehydrogenase, orotate phosphoribosyltransferase, and orotidine-5’-phosphate decarboxylase. In most prokaryotes each of these enzymes is a separate protein, whereas in eukaryotes the first three steps of this pathway are catalyzed by a single enzyme formed from a single polypeptide chain (3).
    [Show full text]
  • Molecular Recognition of Inhibitors, Metal Ions and Substrates by Ribonuclease P
    MOLECULAR RECOGNITION OF INHIBITORS, METAL IONS AND SUBSTRATES BY RIBONUCLEASE P by Xin Liu A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy (Chemistry) in the University of Michigan 2013 Doctoral Committee: Professor Carol A. Fierke, Chair Professor David R. Engelke Professor George A. Garcia Professor Anna K. Mapp Professor Nils G. Walter © Xin Liu 2013 DEDICATION To Lei Shi (石磊) Lei, you believe in me and listen to my wildest dreams. You bring out the best in me. Thank you for your endless love, patience and support! 愛你的馨! ii ACKNOWLEDGEMENTS This work would not be possible without support from many mentors, friends and family members. First of all, I want to thank my advisor Professor Carol Fierke for her great guidance and enormous patience for the past few years. Without her encouragement and critical suggestions, I would have not been able to learn such a great deal of experimental and analytical methods and to finish this dissertation. Carol has set a role model for me as an extraordinary scientist and inspiring mentor that I hope to learn from in my future careers. I would also like to thank my committee members who have been patient and helped me in many different ways. Prof. David Engelke helped me to think and communicate my research more clearly during the monthly RNase P meetings. Prof. Ann Mapp allowed me to use the TECAN instruments in her laboratory and wrote letters for supporting my various fellowship applications. I have learned about many different research projects when attending the Midwest enzyme mechanism conference organized by Prof.
    [Show full text]
  • A Database of Experimentally Validated Chemically Modified Sirnas
    www.nature.com/scientificreports OPEN siRNAmod: A database of experimentally validated chemically modified siRNAs Received: 02 October 2015 Showkat Ahmad Dar, Anamika Thakur, Abid Qureshi & Manoj Kumar Accepted: 21 December 2015 Small interfering RNA (siRNA) technology has vast potential for functional genomics and development Published: 28 January 2016 of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod. RNA interference (RNAi) phenomenon was described by A. Fire and coworkers in Caenorhabditis elegans1. They injected double stranded RNA that potentially and specifically interfere with the endogenous gene at mRNA level leading to its silencing1.
    [Show full text]