DOCSLIB.ORG

RNA Kissing-Loop Interactions Supported by Bifacial Peptide Nucleic Acid

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
RNA Kissing-Loop Interactions Supported by Bifacial Peptide Nucleic Acid RNA kissing-loop interactions supported by bifacial peptide nucleic acid DISSERTATION Presented in Partial Fulfillment of the Requirements for the Degree Doctor of Philosophy in the Graduate School of The Ohio State University By Christopher Amedeo DeSantis Graduate Program in Chemistry The Ohio State University 2017 Dissertation Committee: Professor Dennis Bong, Advisor Professor Venkat Gopalan Professor Jovica Badjic Copyrighted by Christopher Amedeo DeSantis 2017 Abstract The dissertation to follow is an account of research efforts to utilize bifacial peptide nucleic acids (bPNA) triplexes to support kissing-loop complexes. A kissing-loop complex is composed of two nucleic acid stem-loops hybridized via Watson-Crick base pairing between their loop regions. For our studies, we employed two kissing-loop complexes in which a bPNA binding site, composed of ten sequential U-U mismatches, was inserted into the duplex stem of the interacting hairpins. The first system was a tRNA in which the anticodon stem was mutated with a 10-mer bPNA binding site and the loop region extended to nine nucleotides to facilitate a six-nucleotide loop-loop duplex during heterodimerization with a complementary tRNA mutant. The second system, based on the ColE1 plasmid replication control kissing-loop complex, involves two small hairpins which, after kissing complex formation, bind the protein Rop. The hairpins (RNAI-1 and RNAII-1) were mutated with a 10-mer bPNA binding site and have complementary seven- nucleotide loops. In the first part if this work, kissing-loop and Rop complex formation was analyzed in titration binding assays and native gel electrophoresis. tRNA duplex-triplex kissing complexes show a 5-fold decrease in affinity while omission of bPNA decreases affinity by a further 3-fold. Triplex-triplex tRNA mutant binding is 9-fold weaker compared to duplex kissing-loops and also show greater instability when bPNA is omitted. Triplex- duplex mutants in the ColE1 system show similar affinity to the wild type system with Rop ii present. Triplex-triplex kissing-loops bind 4-fold tighter than the wildtype system without the aid of Rop. Furthermore, Rop is able to bind to duplex-triplex and triplex-triplex kissing-loops; the first time a bPNA triplex has been installed at a protein-nucleic acid binding site without abolishing binding. In the latter part of this work, fluorescently-labeled bPNA were used to monitor kissing-loop formation in vitro. Triplex-triplex kissing-loop formation was monitored by FRET using Cy3- and Cy5-labeled bPNA triplexes. Competitive displacement of the U10 mutant tRNA by duplex tRNA in the triplex-triplex kissing-loop was observed via a decreased FRET signal. In the ColE1 system, Rop-catalyzed competitive displacement of a wild type hairpin by a U10 mutant in a WT-U10 kissing complex was monitored via increased FRET signal. In a separate study, fluorescence turn-on probes to detect the presence of a hairpin were developed. The fluorogen thiazole orange was conjugated to bPNA by several designed linkers and a series of synthetic RNA probes with a nine- nucleotide loop were tested for maximum fluorescence turn-on. A peptide with a 2-(2-(2- aminoethoxy)ethoxy)acetic acid linker combined with a probe in which the 1, 2 and 9 positions of the loop was mutated with propyl linkers provided 2.3-fold turn-on effect. In summary, we have shown that hairpins mutated with a bPNA triplex in the stem region are able to form kissing-loop complexes. Furthermore, proteins which interact with kissing-loops are still able to bind complexes with the triplex mutation. Using fluorescently labeled bPNA, we have proposed new technology to site selectively label and monitor RNA-RNA interactions. iii To my family. iv Acknowledgments First and foremost, I would like to thank my family. They were a constant source of support and love when I needed it most throughout this experience. Their sacrifices made moving all the way to Ohio for school possible and endurable. Their visits provided a welcomed reprieve and delicious Italian treats while reminding me what was most important in life. I love you Laura, Claudia, Mom, and Dad. Secondly, I would like to thank my friends Kendra Dewese, Laura Dzugan, Amanda Natter, Mike Davala, Johnny Wysocki, Dan Dilts, Emma Wei, and Nao Oda for reminding me to have fun. Their encouragement meant the world to me and lightened my heart on the toughest of days. Here is to many more home cooked meals together. I owe a debt of gratitude to Dr. Dennis Bong for the years of support as my advisor. Your constant encouragement and problem-solving discussions helped me when the projects stalled and progress looked bleak. By working in your group, I have become a better scientist and for this I thank you. I would also like to thank Jie Mao. My constant companion throughout grad school who was always ready with a friendly smile and encouraging words. My teachers, Xijun Piao, Xin Xia, and Zhun Zhou for putting up with my incessant questions and teaching me a myriad of lab skills. I would also like to thank the other lab group members for their helpful discussions. Finally, I would like to thank Dr. Gopalan and Dr. Badjic. v Vita 2007................................................................Hamilton High School East 2011................................................................B.A. Chemistry, Rutgers, the State University of New Jersey 2011 to present ..............................................Graduate Research Associate, The Ohio State University Publications Mao, J., DeSantis, C., and Bong, D.* (2017) “Small molecule recognition triggers secondary and tertiary interactions in DNA folding and hammerhead ribozyme catalysis.” J. Am. Chem. Soc., DOI: 10.1021/jacs.7b05448 Fields of Study Major Field: Chemistry vi Table of Contents Abstract ............................................................................................................................... ii Acknowledgments............................................................................................................... v Vita ..................................................................................................................................... vi Publications ........................................................................................................................ vi Fields of Study ................................................................................................................... vi Table of Contents .............................................................................................................. vii List of Tables .................................................................................................................... xii List of Figures .................................................................................................................. xiii Chapter 1: Structure of nucleic acids and their mimics ..................................................... 1 1.1.1 SECONDARY STRUCTURES OF NUCLEIC ACIDS: bulges and loops. ........ 6 1.1.2 SECONDARY STRUCTURES OF NUCLEIC ACIDS: junctions ...................... 8 1.1.3 SECONDARY STRUCTURES OF NUCLEIC ACIDS: G-quadruplex .............. 9 1.2 COMPONENTS OF TERTIARY STRUCTURE OF NUCLEIC ACIDS ............... 9 1.2.1 TERTIARY STRUCTURE OF NUCLEIC ACIDS: coaxial stacking. ........... 10 vii 1.2.2 COMPONENTS OF TERTIARY STRUCTURE OF NUCLEIC ACIDS: kissing-loops and pseudoknots .................................................................................. 11 1.2.3 COMPONENTS OF TERTIARY STRUCTURE OF NUCLEIC ACIDS: base triples. ........................................................................................................................ 12 1.2.4 COMPONENTS OF TERTIARY STRUCTURE OF NUCLEIC ACIDS: tetraloops ................................................................................................................... 13 1.2.5 COMPONENTS OF TERTIARY STRUCTURE OF NUCLEIC ACIDS: triplexes. .................................................................................................................... 14 1.3 MODIFICATIONS TO NUCLEIC ACIDS ............................................................ 16 1.3.1 MODIFICATIONS TO NUCLEIC ACIDS: natural modifications ................ 17 1.3.2 MODIFICATIONS TO NUCLEIC ACIDS: metal-coordinating bps. ............ 18 1.3.3 MODIFICATIONS TO NUCLEIC ACIDS: hydrogen bonding attenuation. 19 1.3.4 MODIFICATIONS TO NUCLEIC ACIDS: triplex promoting modifications. ................................................................................................................................... 20 1.3.5 MODIFICATIONS TO NUCLEIC ACIDS: triplex formation via Janus wedge. ........................................................................................................................ 21 1.4 MODIFICATIONS TO NUCLEIC ACID BACKBONES. .................................... 23 1.4.1 MODIFICATIONS TO NUCLEIC ACID BACKBONES: phosphodiester modifications. ............................................................................................................ 23 viii 1.4.2 MODIFICATIONS TO NUCLEIC ACID BACKBONES: ribose modifications. ............................................................................................................ 25 1.4.3 MODIFICATIONS TO NUCLEIC ACID BACKBONES: addressing backbone charge repulsion. ....................................................................................... 26 1.4.4 MODIFICATIONS TO NUCLEIC ACID BACKBONES: ribose substitutes.
Load more

Recommended publications
  • Design of Nucleic Acid Strands with Long Low-Barrier Folding Pathways
    Nat Comput DOI 10.1007/s11047-016-9587-9 Design of nucleic acid strands with long low-barrier folding pathways Anne Condon1 · Bonnie Kirkpatrick2 · Ján Maˇnuch1 © The Author(s) 2017. This article is published with open access at Springerlink.com Abstract A major goal of natural computing is to design fully developed, that exploit base pairing interactions of biomolecules, such as nucleic acid sequences, that can be nucleic acids. Prominent examples include DNA strand dis- used to perform computations. We design sequences of placement systems (DSDs) (Seelig et al. 2006) and RNA nucleic acids that are “guaranteed” to have long folding origami systems (Geary and Andersen 2014). Our work here pathways relative to their length. This particular sequences is motivated by the goal of computing with a single RNA with high probability follow low-barrier folding pathways sequence as the nucleic acids of the sequence interact with that visit a large number of distinct structures. Long fold- each other. ing pathways are interesting, because they demonstrate that RNA sequences form folded structures in which pairs of natural computing can potentially support long and com- nucleic acids biochemically bond to each other. These bonds plex computations. Formally, we provide the first scalable change the physical energy of the sequence, and a given designs of molecules whose low-barrier folding pathways, sequence prefers to assume low-energy folded structures. with respect to a simple, stacked pair energy model, grow Folding is a dynamic process, constrained by kinetics, dur- superlinearly with the molecule length, but for which all sig- ing which an RNA sequence will move through a sequence nificantly shorter alternative folding pathways have an energy of structures with each differing from the previous one by barrier that is 2 − times that of the low-barrier pathway for the addition or removal of a single base pair.
    [Show full text]
  • Algorithms for Nucleic Acid Sequence Design
    Algorithms for Nucleic Acid Sequence Design Thesis by Joseph N. Zadeh In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy California Institute of Technology Pasadena, California 2010 (Defended December 8, 2009) ii © 2010 Joseph N. Zadeh All Rights Reserved iii Acknowledgements First and foremost, I thank Professor Niles Pierce for his mentorship and dedication to this work. He always goes to great lengths to make time for each member of his research group and ensures we have the best resources available. Professor Pierce has fostered a creative environment of learning, discussion, and curiosity with a particular emphasis on quality. I am grateful for the tremendously positive influence he has had on my life. I am fortunate to have had access to Professor Erik Winfree and his group. They have been very helpful in pushing the limits of our software and providing fun test cases. I am also honored to have two other distinguished researchers on my thesis committee: Stephen Mayo and Paul Rothemund. All of the work presented in this thesis is the result of collaboration with extremely talented individuals. Brian Wolfe and I codeveloped the multiobjective design algorithm (Chapter 3). Brian has also been instru- mental in finessing details of the single-complex algorithm (Chapter 2) and contributing to the parallelization of NUPACK’s core routines. I would also like to thank Conrad Steenberg, the NUPACK software engineer (Chapter 4), who has significantly improved the performance of the site and developed robust secondary structure drawing code. Another codeveloper on NUPACK, Justin Bois, has been a good friend, mentor, and reliable coding partner.
    [Show full text]
  • Peptide Nucleic Acids, Morpholinos and Related Antisense Biomolecules
    MEDICAL INTELLIGENCE UNIT Peptide Nucleic Acids, Morpholinos and Related Antisense Biomolecules Christopher G. Janson, M.D. Departments of Neurosurgery, Neurology and Molecular Genetics Cell and Gene Therapy Center UMDNJ-Robert Wood Johnson Medical School Camden, New Jersey, U.S.A. Matthew J. During, M.D., ScD. Department of Molecular Medicine and Pathology University of Auckland Auckland, New Zealand LANDES BIOSCIENCE / EUREKAH.COM KLUWER ACADEMIC / PLENUM PUBLISHERS GEORGETOWN, TEXAS NEW YORK, NEW YORK USA U.SA PEPTIDE NUCLEIC ACIDS, MORPHOLINOS AND RELATED ANTISENSE BIOMOLECULES Medical Intelligence Unit Landes Bioscience / Eurekah.com Kluwer Academic / Plenum Publishers Copyright ©2006 Eurekah.com and Kluwer Academic / Plenum Publishers All rights reserved. No part of this book may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher, vdth the exception of any material supplied specifically for the purpose of being entered and executed on a computer system; for exclusive use by the Purchaser of the work. Printed in the U.S.A. Kluwer Academic / Plenum PubHshers, 233 Spring Street, New York, New York, U.S.A. 10013 http ://www.wkap .nl/ Please address all inquiries to the Publishers: Landes Bioscience / Eurekah.com, 810 South Church Street, Georgetown, Texas, U.S.A. 78626 Phone: 512/ 863 7762; FAX: 512/ 863 0081 http ://v^^ww.eurekah. com http://www.landesbioscience.com Peptide
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2013/0203610 A1 Meller Et Al
    US 20130203610A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2013/0203610 A1 Meller et al. (43) Pub. Date: Aug. 8, 2013 (54) TOOLS AND METHOD FOR NANOPORES Related U.S. Application Data UNZIPPING-DEPENDENT NUCLECACID (60) Provisional application No. 61/318,872, filed on Mar. SEQUENCING 30, 2010. (75) Inventors: Amit Meller, Brookline, MA (US); Alon Publication Classification Singer, Brighton, MA (US) (51) Int. Cl. (73) Assignee: TRUSTEES OF BOSTON CI2O I/68 (2006.01) UNIVERSITY, Boston, MA (US) (52) U.S. Cl. CPC .................................... CI2O I/6874 (2013.01) (21) Appl. No.: 13/638,455 USPC ................................................. 506/6:506/16 (57) ABSTRACT (22) PCT Filed: Mar. 30, 2011 Provided herein is a library that comprises a plurality of molecular beacons (MBs), each MB having a detectable (86). PCT No.: PCT/US2O11AO3O430 label, a detectable label blocker and a modifier group. The S371 (c)(1), library is used in conjunction with nanopore unzipping-de (2), (4) Date: Apr. 17, 2013 pendent sequencing of nucleic acids. Patent Application Publication Aug. 8, 2013 Sheet 1 of 18 US 2013/020361.0 A1 . N s Patent Application Publication Aug. 8, 2013 Sheet 2 of 18 US 2013/020361.0 A1 I’9IAI ::::::::::: Dº3.modoueN Patent Application Publication Aug. 8, 2013 Sheet 3 of 18 US 2013/020361.0 A1 Z’9IAI ~~~~~~~~~);........ Patent Application Publication Aug. 8, 2013 Sheet 4 of 18 US 2013/020361.0 A1 s :·.{-zzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzzz iii. 9 iii.338 lii &S Patent Application Publication Aug. 8, 2013 Sheet 5 of 18 US 2013/020361.0 A1 s r Patent Application Publication Aug.
    [Show full text]
  • Peptide Analogue of Glycol Nucleic Acid†
    Communications to the Editor Bull. Korean Chem. Soc. 2011, Vol. 32, No. 8 2863 DOI 10.5012/bkcs.2011.32.8.2863 γ3PNA: Peptide Analogue of Glycol Nucleic Acid† Taedong Ok, Joohee Lee, and Hee-Seung Lee* Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701 *E-mail: [email protected] Received February 7, 2011, Accepted February 9, 2011 Key Words : Peptide nucleic acids, GNA In the research of the chemical etiology of nucleic acid chemical yield were obtained with Mmt for γ3C and γ3G, Boc structure, the studies from Eschenmoser group1 and Nielsen for γ3A, respectively. In addition, the order of reactions at the group2 have demonstrated that the Watson-Crick base pairing initial steps turned out to be important for efficient synthesis. can be supported by various backbone derivatives. Inspired by For example, in case of γ3C, the protection of the amino groups the groundbreaking results, other researchers have devoted should be prior to the substitution reaction, whereas the other their attention to finding artificial nucleic acids that can form route worked better for the purine monomers (γ3A and γ3G). duplexes, in which both synthetic accessibility and new The detailed synthetic procedures are summarized in characteristics for potential therapeutic (or diagnostic) use are Scheme 1. The common intermediate bromide 1 was easily desirable aims.3 In this context, GNA (glycol nucleic acid, prepared from (S)-epichlorohydrin (> 99%ee) in three steps Figure 1A) is a promising artificial nucleic acid because it is (34% overall yield).6,7 For the synthesis of γ3A, the bromide 1 structurally very simple with a high atom economy and was reacted with unprotected adenine base in the presence of forms a duplex by Watson-Crick base pairing.4 sodium hydride in DMF for 48 hr at room temperature.
    [Show full text]
  • Significance and Implications of Vitamin B-12 Reaction Shema- ETH ZURICH VARIANT: Mechanisms and Insights
    Taylor University Pillars at Taylor University Student Scholarship: Chemistry Chemistry and Biochemistry Fall 2019 Significance and Implications of Vitamin B-12 Reaction Shema- ETH ZURICH VARIANT: Mechanisms and Insights David Joshua Ferguson Follow this and additional works at: https://pillars.taylor.edu/chemistry-student Part of the Analytical Chemistry Commons, Inorganic Chemistry Commons, Organic Chemistry Commons, Other Chemistry Commons, and the Physical Chemistry Commons CHEMISTRY THESIS SIGNIFICANCE AND IMPLICATIONS OF VITAMIN B-12 REACTION SCHEMA- ETH ZURICH VARIANT: MECHANISMS AND INSIGHTS DAVID JOSHUA FERGUSON 2019 2 Table of Contents: Chapter 1 6 Chapter 2 17 Chapter 3 40 Chapter 4 59 Chapter 5 82 Chapter 6 118 Chapter 7 122 Appendix References 3 Chapter 1 A. INTRODUCTION. Vitamin B-12 otherwise known as cyanocobalamin is a compound with synthetic elegance. Considering how it is composed of an aromatic macrocyclic corrin there are key features of this molecule that are observed either in its synthesis of in the biochemical reactions it plays a role in whether they be isomerization reactions or transfer reactions. In this paper the focus for the discussion will be on the history, chemical significance and total synthesis of vitamin B12. Even more so the paper will be concentrated one of the two variants of the vitamin B-12 synthesis, namely the ETH Zurich variant spearheaded by Albert Eschenmoser.Examining the structure as a whole it is observed that a large portion of the vitamin B12 is a corrin structure with a cobalt ion in the center of the macrocyclic part, and that same cobalt ion has cyanide ligands.
    [Show full text]
  • Virus Research Frameshifting RNA Pseudoknots
    Virus Research 139 (2009) 193–208 Contents lists available at ScienceDirect Virus Research journal homepage: www.elsevier.com/locate/virusres Frameshifting RNA pseudoknots: Structure and mechanism David P. Giedroc a,∗, Peter V. Cornish b,∗∗ a Department of Chemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405-7102, USA b Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green Street, Urbana, IL 61801-3080, USA article info abstract Article history: Programmed ribosomal frameshifting (PRF) is one of the multiple translational recoding processes that Available online 25 July 2008 fundamentally alters triplet decoding of the messenger RNA by the elongating ribosome. The ability of the ribosome to change translational reading frames in the −1 direction (−1 PRF) is employed by many Keywords: positive strand RNA viruses, including economically important plant viruses and many human pathogens, Pseudoknot such as retroviruses, e.g., HIV-1, and coronaviruses, e.g., the causative agent of severe acute respiratory Ribosomal recoding syndrome (SARS), in order to properly express their genomes. −1 PRF is programmed by a bipartite signal Frameshifting embedded in the mRNA and includes a heptanucleotide “slip site” over which the paused ribosome “backs Translational regulation HIV-1 up” by one nucleotide, and a downstream stimulatory element, either an RNA pseudoknot or a very stable Luteovirus RNA stem–loop. These two elements are separated by six to eight nucleotides, a distance that places the NMR solution structure 5 edge of the downstream stimulatory element in direct contact with the mRNA entry channel of the Cryo-electron microscopy 30S ribosomal subunit. The precise mechanism by which the downstream RNA stimulates −1 PRF by the translocating ribosome remains unclear.
    [Show full text]
  • Transmissible Familial Creutzfeldt-Jakob Disease
    Proc. Natl. Acad. Sci. USA Vol. 88, pp. 10926-10930, December 1991 Medical Sciences Transmissible familial Creutzfeldt-Jakob disease associated with five, seven, and eight extra octapeptide coding repeats in the PRNP gene (amyloid precursor protein/prion protein) LEV G. GOLDFARB*, PAUL BROWN*, W. RICHARD MCCOMBIEt, DMITRY GOLDGABERt, GARY D. SWERGOLD§, PETER R. WILLS¶, LARISA CERVENAKOVAII, HENRY BARON**, C. J. GIBBS, JR.*, AND D. CARLETON GAIDUSEK* *Laboratory of Central Nervous System Studies, and tSection of Receptor Biochemistry and Molecular Biology, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892; 4Department of Psychiatry, State University of New York, Stony Brook, NY; §Laboratory of Biochemistry, Division of Cancer Biology and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892; IDepartment of Physics, University of Auckland, New Zealand; Institute of Preventive and Clinical Medicine, Bratislava, Czechoslovakia; and **Searle Pharmaceuticals, Paris, France Contributed by D. Carleton Gajdusek, September 6, 1991 ABSTRACT The PRNP gene, encoding the amyloid pre- MATERIALS AND METHODS cursor protein that is involved in centrally Creutzfeldt-Jakob The Tested Population. A total of 535 individuals were disease (CJD), has an unstable region of five variant tandem screened for extra repeats in the PRNP gene: 117 patients octapeptide coding repeats between codons 51 and 91. We with spongiform encephalopathies (including 60 familial cas- screened a total of 535 individuals for the presence of extra es); 159 first-degree relatives ofpatients with familial spongi- repeats in this region, including patients with sporadic and form encephalopathies; 39 patients with other neurological familial forms ofspongiform encephalopathy, members oftheir diseases; 16 patients with non-neurological diseases; and 204 families, other neurological and non-neurological patients, and normal controls.
    [Show full text]
  • A Global Sampling Approach to Designing and Reengineering RNA
    i “rnaensign” — 2017/7/1 — 22:02 — page 1 — #1 i i i Published online ?? Nucleic Acids Research, ??, Vol. ??, No. ?? 1–11 doi:10.1093/nar/gkn000 Aglobalsamplingapproachtodesigningandreengineering RNA secondary structures 1,2, 1, 3 1 1 Alex Levin ⇤,MieszkoLis ⇤,YannPonty ,CharlesW.O’Donnell ,SrinivasDevadas , 1,2, 1,2,4, Bonnie Berger †,J´erˆomeWaldisp¨uhl † 1 Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA 02139, USA. and 2 Department of Mathematics, MIT, Cambridge, MA 02139, USA. and 3 Laboratoire d’Informatique, Ecole´ Polytechnique, Palaiseau, France. and 4 School of Computer Science, McGill University, Montreal, QC H2A 3A7, Canada. Received ??; Revised ??; Accepted ?? ABSTRACT mechanisms (1), reprogramming cellular behavior (2), and designing logic circuits (3). The development of algorithms for designing artificial Here, we aim to design RNA sequences that fold into RNA sequences that fold into specific secondary structures specific secondary structures (a.k.a. inverse folding). Even has many potential biomedical and synthetic biology in this case, efficient computational formulations remain applications. To date, this problem remains computationally difficult, with no exact solutions known. Instead, the solutions difficult, and current strategies to address it resort available today rely on local search strategies and heuristics. to heuristics and stochastic search techniques. The Indeed, the computational difficulty of the RNA design most popular methods consist of two steps: First a problem was proven by M. Schnall-Levin et al. (4). random seed sequence is generated; next, this seed is One of the first and most widely known programs for progressively modified (i.e. mutated) to adopt the desired the RNA inverse folding problem is RNAinverse (5).
    [Show full text]
  • The Architecture of the Protein Domain Universe
    The architecture of the protein domain universe Nikolay V. Dokholyan Department of Biochemistry and Biophysics, The University of North Carolina at Chapel Hill, School of Medicine, Chapel Hill, NC 27599 ABSTRACT Understanding the design of the universe of protein structures may provide insights into protein evolution. We study the architecture of the protein domain universe, which has been found to poses peculiar scale-free properties (Dokholyan et al., Proc. Natl. Acad. Sci. USA 99: 14132-14136 (2002)). We examine the origin of these scale-free properties of the graph of protein domain structures (PDUG) and determine that that the PDUG is not modular, i.e. it does not consist of modules with uniform properties. Instead, we find the PDUG to be self-similar at all scales. We further characterize the PDUG architecture by studying the properties of the hub nodes that are responsible for the scale-free connectivity of the PDUG. We introduce a measure of the betweenness centrality of protein domains in the PDUG and find a power-law distribution of the betweenness centrality values. The scale-free distribution of hubs in the protein universe suggests that a set of specific statistical mechanics models, such as the self-organized criticality model, can potentially identify the principal driving forces of molecular evolution. We also find a gatekeeper protein domain, removal of which partitions the largest cluster into two large sub- clusters. We suggest that the loss of such gatekeeper protein domains in the course of evolution is responsible for the creation of new fold families. INTRODUCTION The principles of molecular evolution remain elusive despite fundamental breakthroughs on the theoretical front 1-5 and a growing amount of genomic and proteomic data, over 23,000 solved protein structures 6 and protein functional annotations 7-9.
    [Show full text]
  • 3.1.4 Droplet-Based Microfluidics
    Rodriguez Garcia, Marc (2016) Engineering the transition from non-living to living matter. PhD thesis. https://theses.gla.ac.uk/7605/ Copyright and moral rights for this work are retained by the author A copy can be downloaded for personal non-commercial research or study, without prior permission or charge This work cannot be reproduced or quoted extensively from without first obtaining permission in writing from the author The content must not be changed in any way or sold commercially in any format or medium without the formal permission of the author When referring to this work, full bibliographic details including the author, title, awarding institution and date of the thesis must be given Enlighten: Theses https://theses.gla.ac.uk/ [email protected] Engineering the transition from non-living to living matter Marc Rodríguez Garcia A thesis submitted to the University of Glasgow for the degree of Doctor of Philosophy School of Chemistry College of Science and Engineering August 2016 A tota la meva família, per haver-me ajudat a arribar fins aquí. Però sobretot als meus pares, per estar tant a prop malgrat la distància. I en especial a la Nuria, per ser el motiu que em fa tirar endavant. “The good thing about science is that it's true whether or not you believe in it.” -Neil deGrasse Tyson Acknowledgements 1 Acknowledgements This project was carried out between September 2012 and June 2016 in the group of Prof Leroy Cronin in the School of Chemistry at the University of Glasgow. I have received much help and support from many colleagues and friends.
    [Show full text]
  • Chapter 23 Nucleic Acids
    7-9/99 Neuman Chapter 23 Chapter 23 Nucleic Acids from Organic Chemistry by Robert C. Neuman, Jr. Professor of Chemistry, emeritus University of California, Riverside [email protected] <http://web.chem.ucsb.edu/~neuman/orgchembyneuman/> Chapter Outline of the Book ************************************************************************************** I. Foundations 1. Organic Molecules and Chemical Bonding 2. Alkanes and Cycloalkanes 3. Haloalkanes, Alcohols, Ethers, and Amines 4. Stereochemistry 5. Organic Spectrometry II. Reactions, Mechanisms, Multiple Bonds 6. Organic Reactions *(Not yet Posted) 7. Reactions of Haloalkanes, Alcohols, and Amines. Nucleophilic Substitution 8. Alkenes and Alkynes 9. Formation of Alkenes and Alkynes. Elimination Reactions 10. Alkenes and Alkynes. Addition Reactions 11. Free Radical Addition and Substitution Reactions III. Conjugation, Electronic Effects, Carbonyl Groups 12. Conjugated and Aromatic Molecules 13. Carbonyl Compounds. Ketones, Aldehydes, and Carboxylic Acids 14. Substituent Effects 15. Carbonyl Compounds. Esters, Amides, and Related Molecules IV. Carbonyl and Pericyclic Reactions and Mechanisms 16. Carbonyl Compounds. Addition and Substitution Reactions 17. Oxidation and Reduction Reactions 18. Reactions of Enolate Ions and Enols 19. Cyclization and Pericyclic Reactions *(Not yet Posted) V. Bioorganic Compounds 20. Carbohydrates 21. Lipids 22. Peptides, Proteins, and α−Amino Acids 23. Nucleic Acids **************************************************************************************
    [Show full text]