DOCSLIB.ORG

RNA Structure and Dynamics: a Base Pairing Perspective

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
RNA Structure and Dynamics: a Base Pairing Perspective Progress in Biophysics and Molecular Biology xxx (2013) 1e20 Contents lists available at ScienceDirect Progress in Biophysics and Molecular Biology journal homepage: www.elsevier.com/locate/pbiomolbio Review RNA structure and dynamics: A base pairing perspective Sukanya Halder a, Dhananjay Bhattacharyya b,* a Biophysics division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064, India b Computational Science division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700 064, India article info abstract Article history: RNA is now known to possess various structural, regulatory and enzymatic functions for survival of Available online xxx cellular organisms. Functional RNA structures are generally created by three-dimensional organization of small structural motifs, formed by base pairing between self-complementary sequences from different Keywords: parts of the RNA chain. In addition to the canonical WatsoneCrick or wobble base pairs, several non- Non-canonical base pair canonical base pairs are found to be crucial to the structural organization of RNA molecules. They RNA secondary structure appear within different structural motifs and are found to stabilize the molecule through long-range Structural characterization of non-canonical intra-molecular interactions between basic structural motifs like double helices and loops. These base base pairs Detection of non-canonical base pairs pairs also impart functional variation to the minor groove of A-form RNA helices, thus forming anchoring site for metabolites and ligands. Non-canonical base pairs are formed by edge-to-edge hydrogen bonding interactions between the bases. A large number of theoretical studies have been done to detect and analyze these non-canonical base pairs within crystal or NMR derived structures of different functional RNA. Theoretical studies of these isolated base pairs using ab initio quantum chemical methods as well as molecular dynamics simulations of larger fragments have also established that many of these non- canonical base pairs are as stable as the canonical WatsoneCrick base pairs. This review focuses on the various structural aspects of non-canonical base pairs in the organization of RNA molecules and the possible applications of these base pairs in predicting RNA structures with more accuracy. Ó 2013 Elsevier Ltd. All rights reserved. Contents 1. Introduction . ................................................. 00 2. Studies on RNA structures . ................................................. 00 3. RNA structural organization through base pairing interactions . ..................... 00 4. Tools for RNA structure analysis . ............................................ 00 5. Structure and stability of non-canonical base pairs . .................................... 00 6. Structural organization of RNA: importance of non-canonical base pairs . ..................... 00 7. Functional importance of non-canonical base pairs . .................................... 00 8. Non-canonical base pairs in RNA structure prediction . .................................... 00 9. Structural stabilities of double helices containing non-canonical base pairs . ..................... 00 10. Conclusion . ................................................. 00 Acknowledgement . ....................... 00 References................................................................. ................................ ....................... 00 1. Introduction For years, RNA has been considered to be an intermediate stage between DNA and proteins. Until recently, RNA was only of in- * Corresponding author. Tel.: þ91 33 2337 0379x2252, fax: þ91 33 2337 4637. E-mail addresses: [email protected], [email protected] terest in its role as an intermediary in transcription and trans- (D. Bhattacharyya). lation, where genetic information of DNA is transferred to 0079-6107/$ e see front matter Ó 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.pbiomolbio.2013.07.003 Please cite this article in press as: Halder, S., Bhattacharyya, D., RNA structure and dynamics: A base pairing perspective, Progress in Biophysics and Molecular Biology (2013), http://dx.doi.org/10.1016/j.pbiomolbio.2013.07.003 2 S. Halder, D. Bhattacharyya / Progress in Biophysics and Molecular Biology xxx (2013) 1e20 messenger RNA (mRNA) through transcription and then translated several other purposes like house keeping, stress response, into protein with the help of transfer RNA (tRNA) and ribosomal virulence, quorum sensing etc. RNA (rRNA). However, it is now well established that commonly known 2. Studies on RNA structures functional RNAs like mRNA, tRNA and rRNA take additional re- sponsibility in post transcriptional regulation and translation The discovery of catalytic activity in RNA has prompted processes within the cellular machinery and thereby regulate serious attempts to decipher the mechanisms of their assembly gene expression levels. In the past few decades, RNA has been into functional native states starting from linear strands. Since shown to exhibit several other crucial functions also. The most the release of crystal structures of the ribosomal subunits in important one is their enzymatic activities similar to endonu- 2000e2001, determination of RNA structures have gained pace clease, nucleotidyltransferase, phosphodiesterase, phospho- remarkably, thanks to the advancements of various chemical and transferase and acid phosphatase (Zaug et al., 1983,1984,1986; biophysical methods. Elucidation of large and complex RNA Zaug and Cech, 1986a,b). Catalytic activity of Tetrahymena 26S structures like group I introns, riboswitches, RNA components of rRNA intervening sequence was first established with its self- both A-type and B-type RNaseP etc by X-ray crystallography has splicing role (Kruger et al., 1982). Endonuclease activity is also been possible. Improvements in techniques for the synthesis, imparted by the RNA component of RNaseP (Guerriertakada purification, crystallization and derivatization of large RNAs, as et al., 1983; Krasilnikov et al., 2003; Kazantsev et al., 2005). well as the development of advanced software, have been crucial This ribonuclease is among the first catalytic RNAs discovered for this advancement. In recent years nuclear magnetic reso- and is one of the only two known ribozymes conserved in all nance (NMR) spectroscopic technique has also improved signif- taxonomic kingdoms (Krasilnikov et al., 2004). Bacterial RNaseP icantly for structure determination of large macromolecules. can catalyze the hydrolysis of tRNA precursor by cleaving a Developments in other physical and chemical methods like phosphodiester bond even in the absence of protein-part in vitro single-particle cryo-electron microscopy, mass spectrometry and and results in 50-phosphorylated mature tRNA (Krasilnikov et al., structure-specific chemicals and enzymes have also helped in 2003; Kazantsev et al., 2005). Studies of the non-coding regions this exponential growth of structural data in the Protein Data of mRNA, or aptamers, have revealed their ability of recognition Bank (PDB) (Bernstein et al., 1977; Berman et al., 2000). The and binding to specific target molecules for genetic control determination of various RNA structures, such as the hammer- (Mironov et al., 2002; Szostak, 2002). These non-coding regions head ribozyme (Scott et al., 1995a,b), SRP RNA (Zwieb et al., 1999) assist in the signal transduction pathway and are required for and the 5S, 16S and 23S RNAs of ribosome (Ban et al. 2000)has translational regulation by sensing the level of a given metabo- greatly increased our knowledge of RNA folds and the three- lite. Another type of biotechnologically important gene regula- dimensional organization of RNA chains (Ferre-D’Amare et al., tory non-coding RNA is riboswitch, which are found in bacteria 1998; Batey et al., 1999; Hermann and Patel, 1999). Collectively, and fungi and not in higher organisms, making it target for cure these structures provide a large amount of information about in human. They can fold into unique shapes and have the ability RNA structural motifs (Moore, 1999). Similar exponential growth to shift its conformation to a different structure in presence or in number of crystal structures of proteins is also taking place in absence of specificmetabolite(Nudler and Mironov, 2004; the PDB. Considering the need of classification of these proteins, Vitreschak et al., 2004; Tucker and Breaker, 2005; Batey, 2006) there are a number of methods available, such as SCOP (Murzin for modulating protein synthesis process (Nahvi et al., 2002; et al., 1995; Hubbard et al., 1997), FSSP (Holm and Sander, Winkler et al., 2002a,b). Another functional aspect of RNA mol- 1997), Pisces (Wang and Dunbrack, 2005), BIPA (Lee and ecules is their role in peptide bond formation mediated by the 20- Blundell, 2009) etc. These methods can classify a protein struc- hydroxyl group of the 30-terminal ribose sugars of peptidyl tRNA ture based on its structural class, source organism, secondary (Das et al., 1999; Dorner et al. 2003; Strobel and Cochrane, 2007). structure content, resolution, etc. In a similar manner, it is also Recently, larger rRNA subunits of ribosomes in Eubacteria as necessary to organize the available RNA structures to determine well as plants and animals have been shown to possess chap- different structureefunction relationships. erone activity to assist protein folding (Samanta et al., 2008). The building blocks of nucleic acid structures
Load more

Recommended publications
  • An Introduction to Recurrent Nucleotide Interactions in RNA Blake A
    Overview An introduction to recurrent nucleotide interactions in RNA Blake A. Sweeney,1 Poorna Roy2 and Neocles B. Leontis2∗ RNA secondary structure diagrams familiar to molecular biologists summarize at a glance the folding of RNA chains to form Watson–Crick paired double helices. However, they can be misleading: First of all, they imply that the nucleotides in loops and linker segments, which can amount to 35% to 50% of a structured RNA, do not significantly interact with other nucleotides. Secondly, they give the impression that RNA molecules are loosely organized in three-dimensional (3D) space. In fact, structured RNAs are compactly folded as a result of numerous long-range, sequence-specific interactions, many of which involve loop or linker nucleotides. Here, we provide an introduction for students and researchers of RNA on the types, prevalence, and sequence variations of inter-nucleotide interactions that structure and stabilize RNA 3D motifs and architectures, using Escherichia coli (E. coli) 16S ribosomal RNA as a concrete example. The picture that emerges is that almost all nucleotides in structured RNA molecules, including those in nominally single-stranded loop or linker regions, form specific interactions that stabilize functional structures or mediate interactions with other molecules. The small number of noninteracting, ‘looped-out’ nucleotides make it possible for the RNA chain to form sharp turns. Base-pairing is the most specific interaction in RNA as it involves edge-to-edge hydrogen bonding (H-bonding) of the bases. Non-Watson–Crick base pairs are a significant fraction (30% or more) of base pairs in structured RNAs. © 2014 John Wiley & Sons, Ltd.
    [Show full text]
  • Review Article Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions
    SAGE-Hindawi Access to Research Journal of Nucleic Acids Volume 2011, Article ID 967098, 11 pages doi:10.4061/2011/967098 Review Article Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions Shu-ichi Nakano,1, 2 Masayuki Fujii,3, 4 and Naoki Sugimoto1, 2 1 Faculty of Frontiers of Innovative Research in Science and Technology, Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan 2 Frontier Institute for Biomolecular Engineering Research, Konan University, 7-1-20 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan 3 Department of Environmental and Biological Chemistry, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan 4 Molecular Engineering Institute, Kinki University, 11-6 Kayanomori, Iizuka, Fukuoka 820-8555, Japan Correspondence should be addressed to Shu-ichi Nakano, [email protected] and Naoki Sugimoto, [email protected] Received 14 April 2011; Accepted 2 May 2011 Academic Editor: Daisuke Miyoshi Copyright © 2011 Shu-ichi Nakano et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs.
    [Show full text]
  • Questions with Answers- Nucleotides & Nucleic Acids A. the Components
    Questions with Answers- Nucleotides & Nucleic Acids A. The components and structures of common nucleotides are compared. (Questions 1-5) 1._____ Which structural feature is shared by both uracil and thymine? a) Both contain two keto groups. b) Both contain one methyl group. c) Both contain a five-membered ring. d) Both contain three nitrogen atoms. 2._____ Which component is found in both adenosine and deoxycytidine? a) Both contain a pyranose. b) Both contain a 1,1’-N-glycosidic bond. c) Both contain a pyrimidine. d) Both contain a 3’-OH group. 3._____ Which property is shared by both GDP and AMP? a) Both contain the same charge at neutral pH. b) Both contain the same number of phosphate groups. c) Both contain the same purine. d) Both contain the same furanose. 4._____ Which characteristic is shared by purines and pyrimidines? a) Both contain two heterocyclic rings with aromatic character. b) Both can form multiple non-covalent hydrogen bonds. c) Both exist in planar configurations with a hemiacetal linkage. d) Both exist as neutral zwitterions under cellular conditions. 5._____ Which property is found in nucleosides and nucleotides? a) Both contain a nitrogenous base, a pentose, and at least one phosphate group. b) Both contain a covalent phosphodister bond that is broken in strong acid. c) Both contain an anomeric carbon atom that is part of a β-N-glycosidic bond. d) Both contain an aldose with hydroxyl groups that can tautomerize. ___________________________________________________________________________ B. The structures of nucleotides and their components are studied. (Questions 6-10) 6._____ Which characteristic is shared by both adenine and cytosine? a) Both contain one methyl group.
    [Show full text]
  • Basic Genetic Concepts & Terms
    Basic Genetic Concepts & Terms 1 Genetics: what is it? t• Wha is genetics? – “Genetics is the study of heredity, the process in which a parent passes certain genes onto their children.” (http://www.nlm.nih.gov/medlineplus/ency/article/002048. htm) t• Wha does that mean? – Children inherit their biological parents’ genes that express specific traits, such as some physical characteristics, natural talents, and genetic disorders. 2 Word Match Activity Match the genetic terms to their corresponding parts of the illustration. • base pair • cell • chromosome • DNA (Deoxyribonucleic Acid) • double helix* • genes • nucleus Illustration Source: Talking Glossary of Genetic Terms http://www.genome.gov/ glossary/ 3 Word Match Activity • base pair • cell • chromosome • DNA (Deoxyribonucleic Acid) • double helix* • genes • nucleus Illustration Source: Talking Glossary of Genetic Terms http://www.genome.gov/ glossary/ 4 Genetic Concepts • H describes how some traits are passed from parents to their children. • The traits are expressed by g , which are small sections of DNA that are coded for specific traits. • Genes are found on ch . • Humans have two sets of (hint: a number) chromosomes—one set from each parent. 5 Genetic Concepts • Heredity describes how some traits are passed from parents to their children. • The traits are expressed by genes, which are small sections of DNA that are coded for specific traits. • Genes are found on chromosomes. • Humans have two sets of 23 chromosomes— one set from each parent. 6 Genetic Terms Use library resources to define the following words and write their definitions using your own words. – allele: – genes: – dominant : – recessive: – homozygous: – heterozygous: – genotype: – phenotype: – Mendelian Inheritance: 7 Mendelian Inheritance • The inherited traits are determined by genes that are passed from parents to children.
    [Show full text]
  • A Standard Reference Frame for the Description of Nucleic Acid Base-Pair Geometry Wilma K
    doi:10.1006/jmbi.2001.4987 available online at http://www.idealibrary.com on J. Mol. Biol. (2001) 313, 229±237 NOMENCLATURE A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry Wilma K. Olson, Manju Bansal, Stephen K. Burley Richard E. Dickerson, Mark Gerstein, Stephen C. Harvey Udo Heinemann, Xiang-Jun Lu, Stephen Neidle, Zippora Shakked Heinz Sklenar, Masashi Suzuki, Chang-Shung Tung, Eric Westhof Cynthia Wolberger and Helen M. Berman # 2001 Academic Press Keywords: nucleic acid conformation; base-pair geometry; standard reference frame A common point of reference is needed to N1-C10 ÁÁÁC10 virtual angles consistent with values describe the three-dimensional arrangements of observed in the crystal structures of relevant small bases and base-pairs in nucleic acid structures. The molecules. Conformational analyses performed in different standards used in computer programs this reference frame lead to interpretations of local created for this purpose give rise to con¯icting helical structure that are essentially independent of interpretations of the same structure.1 For example, computational scheme. A compilation of base-pair parts of a structure that appear ``normal'' accord- parameters from representative A-DNA, B-DNA, ing to one computational scheme may be highly and protein-bound DNA structures from the unusual according to another and vice versa.Itis Nucleic Acid Database (NDB)4 provides useful thus dif®cult to carry out comprehensive compari- guidelines for understanding other nucleic acid sons of nucleic acid structures and to pinpoint structures. unique conformational features in individual struc- tures. In order to resolve these issues, a group of Base coordinates researchers who create and use the different soft- ware packages have proposed the standard base Models of the ®ve common bases (A, C, G, T reference frames outlined below for nucleic acid and U) were generated from searches of the crystal conformational analysis.
    [Show full text]
  • De Novo Nucleic Acids: a Review of Synthetic Alternatives to DNA and RNA That Could Act As † Bio-Information Storage Molecules
    life Review De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as y Bio-Information Storage Molecules Kevin G Devine 1 and Sohan Jheeta 2,* 1 School of Human Sciences, London Metropolitan University, 166-220 Holloway Rd, London N7 8BD, UK; [email protected] 2 Network of Researchers on the Chemical Evolution of Life (NoR CEL), Leeds LS7 3RB, UK * Correspondence: [email protected] This paper is dedicated to Professor Colin B Reese, Daniell Professor of Chemistry, Kings College London, y on the occasion of his 90th Birthday. Received: 17 November 2020; Accepted: 9 December 2020; Published: 11 December 2020 Abstract: Modern terran life uses several essential biopolymers like nucleic acids, proteins and polysaccharides. The nucleic acids, DNA and RNA are arguably life’s most important, acting as the stores and translators of genetic information contained in their base sequences, which ultimately manifest themselves in the amino acid sequences of proteins. But just what is it about their structures; an aromatic heterocyclic base appended to a (five-atom ring) sugar-phosphate backbone that enables them to carry out these functions with such high fidelity? In the past three decades, leading chemists have created in their laboratories synthetic analogues of nucleic acids which differ from their natural counterparts in three key areas as follows: (a) replacement of the phosphate moiety with an uncharged analogue, (b) replacement of the pentose sugars ribose and deoxyribose with alternative acyclic, pentose and hexose derivatives and, finally, (c) replacement of the two heterocyclic base pairs adenine/thymine and guanine/cytosine with non-standard analogues that obey the Watson–Crick pairing rules.
    [Show full text]
  • Glossary of Common Terms in Genetics
    Glossary of Common Terms in Genetics Acquired mutations Gene changes genetic information. DNA is held Multiplexing A sequencing approach that that arise within individual cells and together by weak bonds between base uses several pooled samples simultaneous­ accumulate throughout a person's life pairs of nucleotides: adenine, guanine, ly, greatly increasing sequencing speed. span. cytosine, and thymine. Mutation Any heritable change in DNA Alleles One of a group of genes that Gene The fundamental unit of heredi­ sequence. occur alternatively at a given locus. A ty. A gene is an ordered sequence of single allele is inherited separately from nucleotides located in a particular posi­ Nucleotide A subunit of DNA or RNA each parent (e.g., at a locus for eye tion on a particular chromosome that consisting of a nitrogenous base, a phos­ color, the allele might result in blue or encodes a specific functional product phate molecule, and a sugar molecule. brown eyes). (i.e., a protein or RNA molecule i. Thousands of nucleotides are linked to form a DNA or RNA molecule. Base pair Two nitrogenous bases (ade­ Gene expression The process by which nine and thymine or guanine and cyto- a gene's coded information is converted Oncogene One or more forms of a sine) held together by weak bonds. Two into the structures present and operat­ gene associated with cancer. strands of DNA are held together in the ing in the cell. shape of a double helix by the bonds Polygenic disorders Genetic disorders between base pairs. Gene mapping Determination of the resulting from the combined action of relative positions of genes on a DNA alleles of more than one gene (e.g., Carrier A person who has a recessive molecule and the distance between heart disease, diabetes, and some can­ mutated gene along with its normal them.
    [Show full text]
  • Glycine Trna Mutants with Normal Anticodon Loop Size Cause -1 Frameshifting (Protein Synthesis/Translocation/Frameshift Suppressor/Acceptor Stem/TFC Loop) DANIEL J
    Proc. Nati. Acad. Sci. USA Vol. 86, pp. 7979-7983, October 1989 Genetics Glycine tRNA mutants with normal anticodon loop size cause -1 frameshifting (protein synthesis/translocation/frameshift suppressor/acceptor stem/TFC loop) DANIEL J. O'MAHONY*t, BETSY H. MIMSt, SHAHLA THOMPSONt, EMANUEL J. MURGOLAt, AND JOHN F. ATKINS*§ *Department of Biochemistry, University College, Cork, Ireland; tDepartment of Genetics, Trinity College, Dublin 2, Ireland; tDepartment of Molecular Genetics, The University of Texas, M. D. Anderson Cancer Center, Houston, TX 77030; and §Department of Human Genetics and Howard Hughes Medical Institute, University of Utah Medical Center, Salt Lake City, UT 84132 Communicated by John Carbon, July 17, 1989 (receivedfor review May 5, 1989) ABSTRACT Mutations in the acceptor stem, the 5- frameshift mutations. Many suppressors of + 1 frameshift methyluridine-pseudouridine-cytidine (TFC) arm, and the an- mutations in both bacteria and yeast have been characterized ticodon ofSalmonella tRNAG'Y can cause -1 frameshifting. The as tRNAs with increased anticodon loop size (refs. 12-14 and potential for standard base pairing between acceptor stem the references therein). In contrast, few -1 frameshift mutant positions 1 and 72 is disrupted in the mutant sujS627. This suppressors have been described (15-20). The weaker -1 disruption may interfere with the interaction of the tRNA with suppressors previously characterized are mutants ofprotein- elongation factor-Tu-GTP or an as-yet-unspecified domain of coding genes (see ref. 20). Some ofthem, the tufclasses (17), the ribosome. The potential for standard base pairing in part carry alleles of either gene for elongation factor Tu. Two of the TFC stem is disrupted in mutant suJS625.
    [Show full text]
  • Doubling the DNA Alphabet: Implications for Life in the Universe and DNA Storage
    Science Highlight – March 2019 Doubling the DNA Alphabet: Implications for Life in the Universe and DNA Storage Life on Earth is dictated by the DNA alphabet comprised of only four DNA bases or letters: A, T, G and C. It has long been of interest to understand whether there is something very special about the four letters that comprise DNA and whether this is the only code that could support life. At a basic level, this question can be addressed by examining an expanded alphabet and determining the properties of DNA including additional synthetic letters. This study impacts our current understanding of terrestrial DNA and suggests that extraterrestrial life forms could have evolved using a different genetic code than found here on Earth. The work has immediate applications in synthetic biology for the creation of new molecules and greatly expands the ability to store information in DNA. Now, in breakthrough work, funded by NASA, NSF and NIGMS, Dr. Steven Benner at the Foundation for Applied Molecular Evolution, in collaboration with Dr. Millie Georgiadis at the Indiana University School of Medicine, and colleagues at biotechnology companies and other universities, have provided evidence that the standard DNA code can be expanded to include eight letters forming “hachimoji DNA” (“hachi” eight and “moji” letter in Japanese) using four novel synthetic nucleobases (B, S, P and Z) in addition to A, T, C and G and still retain critical features of natural DNA1,2. Structurally, hachimoji DNA can adopt a standard double helical form of DNA and retain Watson-Crick complementary base pairing, which allows the expanded DNA to be faithfully replicated and transcribed by polymerases to produce hachimoji DNA copies and hachimoji Figure.
    [Show full text]
  • Dynamic DNA Kit© Assembly Instructions
    ...where molecules become real TM DYNAMIC DNA KIT© © Assembly Instructions DYNAMIC DNA KIT Why aren’t all my nucleotides assembled? By assembly the nucleotides you will become familiar with the features and capabilities of the nucleotides in the Dynamic DNA Kit. We believe this will help you determine the best use of Dynamic DNA in your various courses, based on your students and curriculum. (We discovered some teachers didn’t realize the nucleotides in our previous DNA Discovery Kit could be separated into their three component groups.) We think your students will enjoy discovering how Nucleotide components to assemble the nitrogenous base, sugar and phosphate groups, the way Francis Crick and James Watson did when they determined the structure of DNA with their metal plates and connecting pieces! Assembling Nucleotides Please note: the post and hole fittings between the nitrogenous base and sugar group is distinctly different than the post and hole fitting between the sugar group and phosphate groups. No magnets are used in assembling the components of each nucleotide bases. Magnets are used to simulate the bond connections between the A-T and G-C nucleotides. 1. Insert the post on the nucleotide base into the hole in the sugar. Hold the blue swivel part tightly and line up the post with the hole in the sugar. Make sure the orientation of the two shapes match before you insert. You will need to push hard. Hold the swivel post tightly. Note the distinct shapes of the post and hole and line them up before insertion. Push firmly to insert the post.
    [Show full text]
  • Thermodynamic and Structural Contributions of the 6-Thioguanosine
    www.nature.com/scientificreports OPEN Thermodynamic and structural contributions of the 6-thioguanosine residue to helical Received: 15 November 2018 Accepted: 21 February 2019 properties of RNA Published: xx xx xxxx Michał Gładysz , Witold Andrałojć , Tomasz Czapik , Zofa Gdaniec & Ryszard Kierzek Thionucleotides, especially 4-thiouridine and 6-thioguanosine, are photosensitive molecules that photocrosslink to both proteins and nucleic acids, and this feature is a major reason for their application in various investigations. To get insight into the thermodynamic and structural contributions of 6-thioguanosine to the properties of RNA duplexes a systematic study was performed. In a series of RNA duplexes, selected guanosine residues located in G-C base pairs, mismatches (G-G, G-U, and G-A), or 5′ and 3′-dangling ends were replaced with 6-thioguanosine. Generally, the presence of 6-thioguanosine diminishes the thermodynamic stability of RNA duplexes. This efect depends on its position within duplexes and the sequence of adjacent base pairs. However, when placed at a dangling end a 6-thioguanosine residue actually exerts a weak stabilizing efect. Furthermore, the structural efect of 6-thioguanosine substitution appears to be minimal based on NMR and Circular Dichroism (CD) data. RNA contains many modifed nucleotides performing various biological functions, and thionucleotides con- stitute one group of these modified nucleotides. The following thionucleotides can be found among the 112 entries of the RNA modification database (http://mods.rna.albany.edu): 2-thiocytidine, 2-thiouridine, 4-thiouridine, 5-methyl-2-thiouridine, 2-thio-2′-O-methyluridine, 5-methoxycarbonylmethyl-2 -thiouridine, 5-aminomethyl-2-thiouridine, 5-methylaminomethyl-2-thiouridine, 5-(isopente- nyl aminomethyl)-2-thiouridine, geranylated 5-methylaminomethyl-2-thiouridine and geranylated 5-carboxymethylaminomethyl-2-thiouridine.
    [Show full text]
  • Unnatural Base Pairs for Specific Transcription
    Unnatural base pairs for specific transcription Takashi Ohtsuki*, Michiko Kimoto†, Masahide Ishikawa‡, Tsuneo Mitsui‡, Ichiro Hirao‡§, and Shigeyuki Yokoyama*†‡§ *Genomic Sciences Center, and ‡Yokoyama CytoLogic Project, Exploratory Research for Advanced Technology (ERATO), Japan Science and Technology Corporation (JST), Institute of Physical and Chemical Research (RIKEN), 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan; and †Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan Edited by Leslie Orgel, The Salk Institute for Biological Studies, San Diego, CA, and approved February 22, 2001 (received for review November 7, 2000) An unnatural base pair of 2-amino-6-(N,N-dimethylamino)purine On the other hand, the new type of unnatural base pairs, in (designated as x) and pyridin-2-one (designated as y) has been which pairing is mediated by hydrophobicity and complemen- developed for specific transcription. The ribonucleoside triphos- tarity of shape, has been more quantitatively tested for replica- phates of y and a modified y, 5-methylpyridin-2-one, are selectively tion efficiency and fidelity (20–27). The hydrophobic base pairs, incorporated into RNA opposite x in the templates by T7 RNA such as 4-methylbenzimidazole⅐difluorotoluene, can replace the polymerase. In addition, the sequences of the DNA templates natural hydrogen-bonded base pairs in replication and are containing x can be confirmed by a dideoxynucleotide chain- enzymatically incorporated into DNA. Studies of non-hydrogen- terminator method supplemented with the deoxynucleoside bonded base pairs have shown the importance of the shape triphosphate of y. The bulky dimethylamino group of x in the complementarity between pairing bases for replication fidelity.
    [Show full text]