DOCSLIB.ORG

Coevolution Predicts Direct Interactions Between Mtdna-Encoded and Ndna-Encoded Subunits of Oxidative Phosphorylation Complex I

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Coevolution Predicts Direct Interactions Between Mtdna-Encoded and Ndna-Encoded Subunits of Oxidative Phosphorylation Complex I doi:10.1016/j.jmb.2010.09.029 J. Mol. Biol. (2010) 404, 158–171 Contents lists available at www.sciencedirect.com Journal of Molecular Biology journal homepage: http://ees.elsevier.com.jmb Coevolution Predicts Direct Interactions between mtDNA-Encoded and nDNA-Encoded Subunits of Oxidative Phosphorylation Complex I Moran Gershoni1†, Angelika Fuchs2†, Naama Shani1, Yearit Fridman1, Marisol Corral-Debrinski3, Amir Aharoni1, Dmitrij Frishman2⁎ and Dan Mishmar1⁎ 1Department of Life Sciences and the Nation Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel 2Technische Universität München, Wissenschaftszentrum Weihenstephan, Am Forum 1, 85354 Freising, Germany 3Institut de la Vision, Université Pierre et Marie Curie Paris 6, Unité Mixte de Recherche, S 592, 17 rue Moreau, Paris F-75012, France Received 29 October 2009; Despite years of research, the structure of the largest mammalian received in revised form oxidative phosphorylation (OXPHOS) complex, NADH–ubiquinone oxi- 5 September 2010; doreductase (complex I), and the interactions among its 45 subunits are accepted 13 September 2010 not fully understood. Since complex I harbors subunits encoded by Available online mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) genomes, with 22 September 2010 the former evolving ∼10 times faster than the latter, tight cytonuclear coevolution is expected and observed. Recently, we identified three Edited by M. Sternberg nDNA-encoded complex I subunits that underwent accelerated amino acid replacement, suggesting their adjustment to the elevated mtDNA rate Keywords: of change. Hence, they constitute excellent candidates for binding coevolution; mtDNA-encoded subunits. complex I; Here, we further disentangle the network of physical cytonuclear correlated mutation analysis; interactions within complex I by analyzing subunits coevolution. Firstly, mitochondrial DNA; relying on the bioinformatic analysis of 10 protein complexes possessing mitochondria solved structures, we show that signals of coevolution identified physically interacting subunits with nearly 90% accuracy, thus lending support to our approach. When applying this approach to cytonuclear interaction within complex I, we predict that the ‘rate-accelerated’ nDNA-encoded subunits of complex I, NDUFC2 and NDUFA1, likely interact with the mtDNA-encoded subunits ND5/ND4 and ND5/ND4/ND1, respectively. Furthermore, we predicted interactions among mtDNA-encoded complex I subunits. Using the yeast two-hybrid system, we experimentally confirmed the predicted interactions of human NDUFC2 with ND4, the interactions of human NDUFA1 with ND1 and ND4, and the lack of interaction of NDUFC2 with ND3 and NDUFA1, thus providing a proof of concept for our approach. *Corresponding authors. E-mail addresses: [email protected]; [email protected]. † M.G. and A.F. contributed equally to this study. Abbreviations used: OXPHOS, oxidative phosphorylation; complex I, NADH–ubiquinone oxidoreductase; mtDNA, mitochondrial DNA; nDNA, nuclear DNA; McBASC, McLachlan-based substitution correlation; OMES, observed minus expected squared; ELSC, explicit likelihood of subset covariation; ROC, receiver operator characteristic; AUC, area under the curve. 0022-2836/$ - see front matter © 2010 Elsevier Ltd. All rights reserved. Coevolution in Oxidative Phosphorylation Complex I 159 Our study shows, for the first time, evidence for direct interactions between nDNA-encoded and mtDNA-encoded subunits of human OXPHOS complex I and paves the path towards deciphering subunit interactions within complexes lacking three-dimensional structures. Our subunit-interactions-predicting method, ComplexCorr, is available at http://webclu.bio.wzw.tum.de/complexcorr. © 2010 Elsevier Ltd. All rights reserved. Introduction encoded subunits that underwent accelerated amino acid replacement during the course of Subunit interactions within large protein com- primate evolution and are thus likely candidates to plexes, such as the nuclear pore and the proteasome, interact with the fast-evolving mtDNA-encoded are readily apparent from their crystal structures. subunits.13 Since cytonuclear subunit interactions However, the three-dimensional structures of many play important roles in disease and evolution,14,15 biologically important protein complexes have yet we sought to decipher such direct interactions to be resolved, thus limiting our understanding of within complex I. Here, we applied combined their subunit interactions and functionality. One evolutionary and experimental approaches to ana- such protein complex is the membrane-bound lyze the interaction of the fast-evolving nDNA- oxidative phosphorylation (OXPHOS) complex encoded subunits NDUFC2 and NDUFA1 with the NADH–ubiquinone oxidoreductase (complex I).1 mtDNA-encoded subunits of complex I. Complex I, the first and largest of the OXPHOS While coevolving amino acid residues were initially complexes (45 subunits in mammals), is the most used to predict intramolecular contacts,16 several common mutational target for mitochondrial groups have recently attempted to employ this dysfunction.2 This protein complex increased almost approach to predict residue contacts at the interface threefold in size from the so-called 14 ‘core’ subunits of interacting proteins. It has been suggested that the in Escherichia coli to 45 subunits in Homo sapiens by spatial distances between coevolving residue pairs gradual recruitment of subunits throughout harbored by interacting proteins are significantly evolution.3 Unlike other OXPHOS complexes, clues smaller than the distances between random residue for subunit interactions within the L-shaped mam- pairs.17,18 Analysis of correlated mutations assisted in malian complex I exist for the mitochondrial matrix the successful identification of interdomain or inter- arm, but not for the membrane arm of the complex.4 protein docking configurations.19,20 Moreover, coe- Hence, much of the knowledge on subunit interac- volving amino acids were found to be prevalent tions and composition within the membrane arm of among interacting residue pairs within and between the complex originates from the investigation of its proteins (‘in silico two-hybrid system’).21 Taken bacterial ortholog, NDH1.5,6 Furthermore, studies of together, these findings indicate that although the complex I assembly have revealed subunit compo- coevolution signal may not be sufficient to discern sition within subcomplexes. Still, such findings only actual contacting residue pairs, it may be informative offer general clues for specific interactions (Vogel for identifying physically interacting protein pairs. et al.7 and references within). Since understanding Hence, residue coevolution constitutes a promising subunit interactions within complex I is important approach to assessing protein–protein interactions for deciphering its function and since disruption within large complexes such as OXPHOS complex I. of complex I assembly causes diseases,7 alterna- Here, using a data set of 10 multisubunit protein tive approaches are needed. complexes with resolved crystal structures, we have Four of the five OXPHOS complexes (i.e., com- detected a clear correlation between the presence of plexes I, III, IV, and V) are composed of subunits highly coevolving residues and physical interactions encoded by nuclear and mitochondrial genomes between subunits. This enabled us to extract optimal [nuclear DNA (nDNA) and mitochondrial DNA parameters and to define the criteria for predicting (mtDNA), respectively] that differ 10 times in terms candidate interactions among mtDNA-encoded and of mutational rates.8 Accordingly, elevated amino nDNA-encoded subunits of complex I. We applied acid replacement rates indicating positive selection these criteria to all of the mtDNA-encoded subunits have been identified in nDNA-encoded subunits of complex I and two candidate nDNA-encoded that closely interact with fast-evolving mtDNA- subunits (NDUFC2 and NDUFA1) thought to encoded subunits within OXPHOS complexes with interact with them.13 This approach predicted experimentally determined three-dimensional struc- interactions between NDUFC2 and two OXPHOS ture, namely complex III, complex IV, and part of complex I mtDNA-encoded subunits (ND4 and – complex V.9 12 In a recent rigorous sequence ND5), interactions between NDUFA1 and three analysis, we identified three complex I nDNA- mtDNA-encoded subunits (ND1, ND4, and ND5), 160 Coevolution in Oxidative Phosphorylation Complex I Table 1. Complexes with known crystal structures used for an analysis of coevolving residues Protein Data Possible Bank ID Description Chains pairsa Alignmentsb Interactionsc 1GW5 AP2 clathrin adaptor core A|B|M|S 6 6 6 1W63 AP1 clathrin adaptor core A|B|M|S 6 6 6 2BCJ Gq-GRK2-G complex A|B|G|Q 6 6 3 2J0S Exon junction complex A|C|D|T 6 3 3 1LDK Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase A|B|C|D|E 10 10 5 complex 2CV5 Nucleosome core particle A|B|G|H 6 6 5 2CK3 F1-ATPase A|D|G|H|I 10 6 4 1SFC Synaptic fusion complex A|B|C|D 6 6 6 1BGY Cytochrome bc1 complex A|B|C|D|E|F|G|H|I|J 45 34 18 1V54 Cytochrome c oxidase A|B|C|D|E|F|G|H|I|J| 66 15 10 K|L a Number of possible protein pairs consisting of two different subunits for the given complex. b Subset of protein pairs in a concatenated alignment with at least 10 sequences. Only these protein pairs could be used for correlated mutation analysis. c Number of protein pairs in a concatenated alignment with at least 10 sequences and at least one residue contact.
Load more

Recommended publications
  • Sequence-Selective Recognition of Double-Stranded RNA And
    Downloaded from rnajournal.cshlp.org on October 8, 2021 - Published by Cold Spring Harbor Laboratory Press Hnedzko et al. Sequence-Selective Recognition of Double-Stranded RNA and Enhanced Cellular Uptake of Cationic Nucleobase and Backbone- Modified Peptide Nucleic Acids Dziyana Hnedzko1,*, Dennis W. McGee,2 Yannis A. Karamitas1 and Eriks Rozners1,* Departments of 1 Chemistry and 2 Biological Sciences, Binghamton University, The State University of New York, Binghamton, New York 13902, United States. * To whom correspondence should be addressed. Tel: +1-607-777-2441; Fax: +1-607-777- 4478; Email: [email protected] and [email protected] Running Tittle: RNA recognition and cellular uptake of PNA 1 Downloaded from rnajournal.cshlp.org on October 8, 2021 - Published by Cold Spring Harbor Laboratory Press Hnedzko et al. ABSTRACT Sequence-selective recognition of complex RNAs in live cells could find broad applications in biology, biomedical research and biotechnology. However, specific recognition of structured RNA is challenging and generally applicable and effective methods are lacking. Recently, we found that peptide nucleic acids (PNAs) were unusually well suited ligands for recognition of double-stranded RNAs. Herein, we report that 2-aminopyridine (M) modified PNAs and their conjugates with lysine and arginine tripeptides form strong (Ka = 9.4 to 17 × 107 M-1) and sequence-selective triple helices with RNA hairpins at physiological pH and salt concentration. The affinity of PNA-peptide conjugates for the matched RNA hairpins was unusually high compared to the much lower affinity for DNA hairpins of the same 7 -1 sequence (Ka = 0.05 to 0.11 × 10 M ). The binding of double-stranded RNA by M-modified 4 -1 -1 PNA-peptide conjugates was a relatively fast process (kon = 2.9 × 10 M s ) compared to 3 -1 -1 the notoriously slow triple helix formation by oligodeoxynucleotides (kon ~ 10 M s ).
    [Show full text]
  • Nuclear and Mitochondrial DNA Sequences from Two Denisovan Individuals
    Nuclear and mitochondrial DNA sequences from two Denisovan individuals Susanna Sawyera,1, Gabriel Renauda,1, Bence Violab,c,d, Jean-Jacques Hublinc, Marie-Theres Gansaugea, Michael V. Shunkovd,e, Anatoly P. Dereviankod,f, Kay Prüfera, Janet Kelsoa, and Svante Pääboa,2 aDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany; bDepartment of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada; cDepartment of Human Evolution, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany; dInstitute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, RU-630090, Russia; eNovosibirsk National Research State University, Novosibirsk, RU-630090, Russia; and fAltai State University, Barnaul, RU-656049, Russia Contributed by Svante Pääbo, October 13, 2015 (sent for review April 16, 2015; reviewed by Hendrik N. Poinar, Fred H. Smith, and Chris B. Stringer) Denisovans, a sister group of Neandertals, have been described on DNA to the ancestors of present-day populations across Asia the basis of a nuclear genome sequence from a finger phalanx and Oceania suggests that in addition to the Altai Mountains, (Denisova 3) found in Denisova Cave in the Altai Mountains. The they may have lived in other parts of Asia. In addition to the only other Denisovan specimen described to date is a molar (Deni- finger phalanx, a molar (Denisova 4) was found in the cave in sova 4) found at the same site. This tooth carries a mtDNA se- 2000. Although less than 0.2% of the DNA in the tooth derives quence similar to that of Denisova 3. Here we present nuclear from a hominin source, the mtDNA was sequenced and differed DNA sequences from Denisova 4 and a morphological description, from the finger phalanx mtDNA at only two positions, suggesting as well as mitochondrial and nuclear DNA sequence data, from it too may be from a Denisovan (2, 3).
    [Show full text]
  • Hammerhead Ribozymes Against Virus and Viroid Rnas
    Hammerhead Ribozymes Against Virus and Viroid RNAs Alberto Carbonell, Ricardo Flores, and Selma Gago Contents 1 A Historical Overview: Hammerhead Ribozymes in Their Natural Context ................................................................... 412 2 Manipulating Cis-Acting Hammerheads to Act in Trans ................................. 414 3 A Critical Issue: Colocalization of Ribozyme and Substrate . .. .. ... .. .. .. .. .. ... .. .. .. .. 416 4 An Unanticipated Participant: Interactions Between Peripheral Loops of Natural Hammerheads Greatly Increase Their Self-Cleavage Activity ........................... 417 5 A New Generation of Trans-Acting Hammerheads Operating In Vitro and In Vivo at Physiological Concentrations of Magnesium . ...... 419 6 Trans-Cleavage In Vitro of Short RNA Substrates by Discontinuous and Extended Hammerheads ........................................... 420 7 Trans-Cleavage In Vitro of a Highly Structured RNA by Discontinuous and Extended Hammerheads ........................................... 421 8 Trans-Cleavage In Vivo of a Viroid RNA by an Extended PLMVd-Derived Hammerhead ........................................... 422 9 Concluding Remarks and Outlooks ........................................................ 424 References ....................................................................................... 425 Abstract The hammerhead ribozyme, a small catalytic motif that promotes self- cleavage of the RNAs in which it is found naturally embedded, can be manipulated to recognize and cleave specifically
    [Show full text]
  • Ribozymes Targeted to the Mitochondria Using the 5S Ribosomal Rna
    RIBOZYMES TARGETED TO THE MITOCHONDRIA USING THE 5S RIBOSOMAL RNA By JENNIFER ANN BONGORNO A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2005 Copyright 2005 by Jennifer Bongorno To my grandmother, Hazel Traster Miller, whose interest in genealogy sparked my interest in genetics, and without whose mitochondria I would not be here ACKNOWLEDGMENTS I would like to thank all the members of the Lewin lab; especially my mentor, Al Lewin. Al was always there for me with suggestions and keeping me motivated. He and the other members of the lab were like my second family; I would not have had an enjoyable experience without them. Diana Levinson and Elizabeth Bongorno worked with me on the fourth and third mouse transfections respectively. Joe Hartwich and Al Lewin tested some of the ribozymes in vitro and cloned some of the constructs I used. James Thomas also helped with cloning and was an invaluable lab manager. Verline Justilien worked on a related project and was a productive person with whom to bounce ideas back and forth. Lourdes Andino taught me how to use the new phosphorimager for my SYBR Green-stained gels. Alan White was there through it all, like the older brother I never had. Mary Ann Checkley was with me even longer than Alan, since we both came to Florida from Ohio Wesleyan, although she did manage to graduate before me. Jia Liu and Frederic Manfredsson were there when I needed a beer.
    [Show full text]
  • Into the Mitochondrial and Nuclear DNA and RNA of Two Transplantable Hepatomas (3924A and H-35Tc2) and Host Livers'
    [CANCERRESEARCH28.2164-2167,October1968] Brief Communication Comparative Incorporation of Tritiated Thymidine and Cytidine into the Mitochondrial and Nuclear DNA and RNA of Two Transplantable Hepatomas (3924A and H-35tc2) and Host Livers' Lillie 0. Chang, Harold P.Morris,2and William B. Looney Radiobiology and Biophysics Laboratory, Department of Radiology, University of Virginia School of Medicine, Charlottesville, Vir ginia f@29O1(L. 0. C. and W. B. L.), and Laboratory of Biochemistry, National Cancer institute, NIH, Bethesda, Maryland ?LXJ114 (H. P. M.) Summary interesting questions as to the different precursor pools and It has been found that the specific activity of thymidine-5- the biosynthetic pathways of nucleic acid synthesis in the methyl-3H incorporation into the mitochondrial DNA of two mitochondria and nuclei of the hepatomas as well as of their transplantable hepatomas (3924A and H-35tc2) and host livers host livers. The purpose of this communication is to report the is less than the specific activity of the nuclear DNA. However, relative rates of uptake of the labeled thymidine and cytidine the ratio of mitochondrial DNA to nuclear DNA specific ac into DNA, and the incorporation of cytidine into RNA of the tivity in both hepatomas and host livers is 10—100times greater mitochondrial and nuclear fractions of Hepatomas 3924A and H-35tc2 and their host livers. following cytidine-5-3H administration than the ratio following thymidine-5-methyl-3H administration. This marked difference in the ratios of the specific activities of thymidine and cytidine Materials and Methods in mitochondrial and nuclear DNA of hepatomas and host livers The growth patterns of transplantable rat hepatoma lines appears to be the result of both an increase in cytidine incor have been described by Morris (8, 9) .
    [Show full text]
  • Isolation of Active Genes Containing CAG Repeats by DNA Strand Invasion by a Peptide Nucleic Acid (Chromatin/Transcription Factors/Microsatellite DNA) LIDIA C
    Proc. Natl. Acad. Sci. USA Vol. 92, pp. 1901-1905, March 1995 Biochemistry Isolation of active genes containing CAG repeats by DNA strand invasion by a peptide nucleic acid (chromatin/transcription factors/microsatellite DNA) LIDIA C. BOFFA*, ELISABETrA M. CARPANETO*, AND VINCENT G. ALLFREYtt *Istituto Nazionale per la Ricerca sul Cancro IST, Genoa 16132, Italy; and tThe Rockefeller University, New York, NY 10021 Communicated by Bruce Merrifield, The Rockefeller University, New York, NY December 7, 1994 ABSTRACT An amplification of tandem CAG trinucle- can be captured quantitatively on streptavidin-coated mag- otide sequences in DNA due to errors in DNA replication is netic beads. involved in at least four hereditary neurodegenerative dis- An amplification of CAG triplet repeats occurs in at least eases. The CAG triplet repeats when translated into protein four inherited neurodegenerative diseases. In all cases, the give rise to tracts of glutamine residues, which are a promi- severity of the disease increases with the expansion of the CAG nent feature of many transcription factors, including the repeat region that occurs as a consequence of errors in DNA TATA-binding protein of transcription factor TFIID. We have replication. In Huntington disease, expansion of the CAG used a biotin-labeled, complementary peptide nucleic acid repeats in the gene results in an elongation of a glutamine-rich (PNA) to invade the CAG repeats in intact chromatin and then domain in the encoded protein from 35 to over 100 residues employed a method for the selective isolation of transcrip- (11). The functional consequence of similar glutamine expan- tionally active chromatin restriction fragments containing the sions for transcriptional control is indicated by the finding that PNA-DNA hybrids.
    [Show full text]
  • Non-Coding RNA: Microrna Stimulates Mitochondrial Translation
    RESEARCH HIGHLIGHTS Nature Reviews Genetics | AOP, published online 12 August 2014 IN BRIEF THERAPEUTICS Targeting huntingtin through morpholino oligomers Huntington’s disease is caused by a mutant huntingtin (HTT) gene that contains an expanded tract of poly(CAG) repeats. Sun et al. designed phosphorodiamidate morpholino oligomers (PMOs, which are stable nucleic acid mimics) as antisense reagents to target the CAG tract in HTT mRNA. Applying the PMOs to HTT-mutant human neurons in vitro decreased HTT protein levels and reduced toxicity caused by mutant HTT. Furthermore, in two mouse models of Huntington’s disease, intracranial injection of PMOs resulted in downregulation of mutant HTT levels and partially reduced disease symptoms. ORIGINAL RESEARCH PAPER Sun, X. et al. Phosphorodiamidate morpholino oligomers suppress mutant huntingtin expression and attenuate neurotoxicity. Hum. Mol. Genet. http://dx.doi.org/10.1093/hmg/ddu349 (2014) TECHNOLOGY Using DNA repair to detect modified bases There is great interest in characterizing the locations and functions of chemically modified bases in genomes. Bryan et al. report their Excision-seq method, in which DNA repair enzymes are used to cut genomic DNA at sites of the particular damaged bases they recognize, followed by high-throughput sequencing to characterize these cleavage sites. The researchers characterized the locations and sequence contexts of uracils (that is, demethylated thymines) in Escherichia coli and Saccharomyces cerevisiae genomes, and of ultraviolet-light-induced pyrimidine dimers in S. cerevisiae. ORIGINAL RESEARCH PAPER Bryan, D. S. et al. High resolution mapping of modified DNA nucleobases using excision repair enzymes. Genome Res. http://dx.doi.org/10.1101/ gr.174052.114 (2014) NON-CODING RNA MicroRNA stimulates mitochondrial translation The muscle-specific microRNA miR‑1 stimulates translation of various transcripts encoded by mitochondrial DNA, while repressing its nuclear DNA-encoded targets in the cytoplasm, report Zhang and colleagues.
    [Show full text]
  • Mechanism of RNA Polymerase II Stalling by DNA Alkylation
    Mechanism of RNA polymerase II stalling by DNA alkylation Stefano Malvezzia,1, Lucas Farnungb,1, Claudia M. N. Aloisia, Todor Angelova, Patrick Cramerb,2, and Shana J. Sturlaa,2 aDepartment of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland; and bMax Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany Edited by Graham C. Walker, Massachusetts Institute of Technology, Cambridge, MA, and approved September 26, 2017 (received for review May 3, 2017) Several anticancer agents that form DNA adducts in the minor Cells have evolved various DNA repair functions, and large groove interfere with DNA replication and transcription to induce helix-distorting adducts are often removed by NER. NER is di- apoptosis. Therapeutic resistance can occur, however, when cells are vided into two subpathways: TC- and global genome- (GG-) NER proficient in the removal of drug-induced damage. Acylfulvenes are (14). TC-NER–deficient human fibroblast cells are more sensitive a class of experimental anticancer agents with a unique repair to illudin S, AF, and HMAF compared with GG-NER–deficient profile suggesting their capacity to stall RNA polymerase (Pol) II and human fibroblast cells, suggesting that TC-NER selectively repairs trigger transcription-coupled nucleotide excision repair. Here we AF adducts (4–6) (Fig. 1A). Moreover, siRNA-mediated down- show how different forms of DNA alkylation impair transcription regulation of TC-NER in a cancer cell line greatly increased their by RNA Pol II in cells and with the isolated enzyme and unravel a sensitivity to AF, whereas down-regulation of GG-NER did not mode of RNA Pol II stalling that is due to alkylation of DNA in the (6) (Fig.
    [Show full text]
  • Localization and Dynamics of Small Circular DNA in Live Mammalian Nuclei
    Published online May 11, 2004 2642±2651 Nucleic Acids Research, 2004, Vol. 32, No. 8 DOI: 10.1093/nar/gkh587 Localization and dynamics of small circular DNA in live mammalian nuclei Giulia Mearini, Peter E. Nielsen1 and Frank O. Fackelmayer* Department of Molecular Cell Biology, Heinrich-Pette-Institute, Martinistraûe 52, 20251 Hamburg, Germany and 1Department of Medical Biochemistry and Genetics, The Panum Institute, University of Copenhagen, Blegdamsvej 3c, DK 2200N, Copenhagen, Denmark Received February 6, 2004; Revised March 23, 2004; Accepted April 15, 2004 Downloaded from https://academic.oup.com/nar/article/32/8/2642/2904593 by guest on 24 September 2021 ABSTRACT interactions of regulatory sequences on the incoming DNA with nuclear components in the host cells can be inferred. While genomic DNA, packaged into chromatin, is However, the mechanism by which this occurs is unclear, as is known to be locally constrained but highly dynamic the question of whether these initial contacts can be modi®ed in the nuclei of living cells, little is known about the or abolished (e.g. for therapeutic use). localization and dynamics of small circular DNA Interestingly, there is often a difference between the molecules that invade cells by virus infection, appli- expression of a gene on a transfected vector in transient cation of gene therapy vectors or experimental assays (comparable to an infecting virus genome) compared transfection. To address this point, we have created with the expression of the same gene after the vector has traceable model substrates by direct labeling of integrated into the genome [reviewed in (2)]. While expres- plasmid DNA with ¯uorescent peptide nucleic acids, sion from episomes only depends on the sequence of the and have investigated their fate after microinjection regulatory sequences on the vector, the expression of a gene after integration is also affected by its relative position to other into living cells.
    [Show full text]
  • Smart DNA Biosensor for in Vitro Detection of Androgen Receptor Mrna
    This open access document is published as a preprint in the Beilstein Archives with doi: 10.3762/bxiv.2020.13.v1 and is considered to be an early communication for feedback before peer review. Before citing this document, please check if a final, peer-reviewed version has been published in the Beilstein Journal of Organic Chemistry. This document is not formatted, has not undergone copyediting or typesetting, and may contain errors, unsubstantiated scientific claims or preliminary data. Preprint Title Smart DNA biosensor for in vitro detection of androgen receptor mRNA Authors Ekaterina A. Bryushkova, Erik R. Gandalipov and Julia V. Nuzhina Publication Date 23 Jan 2020 Article Type Full Research Paper Supporting Information File 1 Bryushkova et al_2020_SI.docx; 206.8 KB ORCID® iDs Ekaterina A. Bryushkova - https://orcid.org/0000-0002-5227-114X; Julia V. Nuzhina - https://orcid.org/0000-0002-4863-9458 License and Terms: This document is copyright 2020 the Author(s); licensee Beilstein-Institut. This is an open access publication under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0). Please note that the reuse, redistribution and reproduction in particular requires that the author(s) and source are credited. The license is subject to the Beilstein Archives terms and conditions: https://www.beilstein-archives.org/xiv/terms. The definitive version of this work can be found at: doi: https://doi.org/10.3762/bxiv.2020.13.v1 Smart DNA biosensor for in vitro detection of androgen receptor mRNA Ekaterina A. Bryushkova1*, Erik R. Gandalipov2, Julia V. Nuzhina2 1Department of Molecular Biology, Lomonosov Moscow State University, Lenin Hills 1/12, Moscow, 119991, Russian Federation 2Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova 9, St.
    [Show full text]
  • Biotechnology Applying the Genetic Revolution
    Biotechnology Applying the Genetic Revolution Chapter 1: Basics of Biotechnology 1. Which statement best describes the central dogma of genetics? a. Genes are made of DNA, expressed as an RNA intermediary that is decoded to make proteins. b. The central dogma only applies to yellow and green peas from Mendel’s experiments. c. Genes are made of RNA, expressed as a DNA intermediary, which is decoded to make proteins. d. Genes made of DNA are directly decoded to make proteins. e. The central dogma only applies to animals. 2. What is the difference between DNA and RNA? a. DNA contains a phosphate group, but RNA does not. b. Both DNA and RNA contain a sugar, but only DNA has a pentose. c. The sugar ring in RNA has an extra hydroxyl group that is missing in the pentose of DNA. d. DNA consists of five different nitrogenous bases, but RNA only contains four different bases. e. RNA only contains pyrimidines and DNA only contains purines. 3. Which of the following statements about eukaryotic DNA packaging is true? a. The process involves DNA gyrase and topoisomerase I. b. All of the DNA in eukaryotes can fit inside of the nucleosome without being packaged. c. Chromatin is only used by prokaryotes and is not necessary for eukaryotic DNA packaging. d. Eukaryotic DNA packaging is a complex of DNA wrapped around proteins called histones, and further coiled into a 30-nanometer fiber. e. Once eukaryotic DNA is packaged, the genes on the DNA can never again be expressed. 4. Which statement about Thermus aquaticus is false? a.
    [Show full text]
  • UNIT-I DNA: Definition, Structure & Discovery DNA
    SRINIVASAN ARTS AND SCIENCE COLLEGE (CO-ED) PERAMBALUlR - 621212 DEPARTMENT OF BIOTECHNOLOGY CLASS : I M.SC., BIOTECHNOLOGY SUBJECT: rDNA TECHNOLOGY SUB CODE : P16BT21 UNIT-I DNA: Definition, Structure & Discovery DNA The structure of the DNA double helix. The atoms in the structure are colour-coded by element and the detailed structures of two base pairs are shown in the bottom right. The structure of part of a DNA double helix Deoxyribonucleic acid is a molecule composed of two polynucleotide chains that coil around each other to form a double helix carrying genetic instructions for the development, functioning, growth and reproduction of all known organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids. Alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life. The two DNA strands are known as polynucleotides as they are composed of simpler monomeric units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases (cytosine [C], guanine [G], adenine [A] or thymine [T]), a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds (known as the phospho-diester linkage) between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two separate polynucleotide strands are bound together, according to base pairing rules (A with T and C with G), with hydrogen bonds to make double- stranded DNA. The complementary nitrogenous bases are divided into two groups, pyrimidines and purines.
    [Show full text]