DOCSLIB.ORG

(12) Patent Application Publication (10) Pub. No.: US 2015/0071901 A1 Liu Et Al

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
(12) Patent Application Publication (10) Pub. No.: US 2015/0071901 A1 Liu Et Al US 2015 0071901A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0071901 A1 Liu et al. (43) Pub. Date: Mar. 12, 2015 (54) MRNA-SENSING SWITCHABLE GRNAS (52) U.S. Cl. (71) Applicant: President and Fellows of Harvard CPC .............. CI2N 15/01 (2013.01); C12N 15/I 13 College, Cambridge, MA (US) (2013.01); C12N 9/22 (2013.01); C12N 23 10/10 (2013.01) (72) Inventors: JohnnyDavid R. Hao Liu, Hu, Lexington, Cambridge, MA MA(US); (US) USPC ........ 424/94.3: 536/24. 1; 435/188: 435/91.1; 435/320.1; 435/325; 536/23.1 (73) Assignee: President and Fellows of Harvard College, Cambridge, MA (US) (57) ABSTRACT (21) Appl. No.: 14/326,340 Some aspects of this disclosure provide compositions, meth (22) Filed: Jul. 8, 2014 ods, systems, and kits for controlling the activity and/or Related U.S. Application Data improving the specificity of RNA-programmable endonu (60) Provisional application No. 61/874,682, filed on Sep. cleases, such as Cas9. For example, provided are guide RNAs 6, 2013. (gRNAs) that are engineered to exist in an “on” or “off” state, Publication Classification which control the binding and hence cleavage activity of RNA-programmable endonucleases. Some aspects of this (51) y;5/0 (2006.01) disclosure provide mRNA-sensing gRNAs that modulate the CI2N 9/22 (2006.01) activity of RNA-programmable endonucleases based on the CI2N IS/II3 (2006.01) presence or absence of a target mRNA. Patent Application Publication Mar. 12, 2015 Sheet 1 of 12 US 2015/0071901 A1 SSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSSS Patent Application Publication Mar. 12, 2015 Sheet 2 of 12 US 2015/0071901 A1 Patent Application Publication Mar. 12, 2015 Sheet 3 of 12 US 2015/0071901 A1 s: s DI‘ROHH 3. Patent Application Publication Mar. 12, 2015 Sheet 4 of 12 US 2015/0071901 A1 (II‘50IH Patent Application Publication Mar. 12, 2015 Sheet 5 of 12 US 2015/0071901 A1 VZ'5018 Patent Application Publication Mar. 12, 2015 Sheet 6 of 12 US 2015/0071901 A1 Patent Application Publication Mar. 12, 2015 Sheet 7 of 12 US 2015/0071901 A1 OZ."?INH Patent Application Publication Mar. 12, 2015 Sheet 8 of 12 US 2015/0071901 A1 WWW ww. yA. Mar. 12, 2015 Sheet 9 of 12 US 2015/0071901 A1 Patent Application Publication Mar. 12, 2015 Sheet 10 of 12 US 2015/0071901 A1 Patent Application Publication Mar. 12, 2015 Sheet 11 of 12 US 2015/0071901 A1 Patent Application Publication Mar. 12, 2015 Sheet 12 of 12 US 2015/0071901 A1 *3.§§§§§§§§ {} US 2015/007 1901 A1 Mar. 12, 2015 MRNA-SENSING SWITCHABLE GRNAS ligand bound to the aptamer; and (ii) a Cas9 protein. In some embodiments, the aptamer is bound by a ligand. In some RELATED APPLICATIONS aspects, the ligand is any molecule. In some aspects, the 0001. This application claims priority under 35 U.S.C. ligand is a small molecule, a metabolite, a carbohydrate, a S119(e) to U.S. provisional application, U.S. Ser. No. 61/874, peptide, a protein, or a nucleic acid. In some embodiments, 682, filed Sep. 6, 2013, which is incorporated herein by ref the gRNA:ligand:Cas9 complex binds to and mediates cleav CCC. age of a target nucleic acid. See, e.g., FIG. 1. 0006. According to another embodiment, gRNAs com BACKGROUND OF THE INVENTION prising an aptamer are provided. In some embodiments, the gRNA does not hybridize to a target nucleic acid in the 0002 Site-specific endonucleases theoretically allow for absence of a ligand bound to the aptamer. Such gRNAS may the targeted manipulation of a single site within a genome and be referred to as “switchable gRNAs. For example, in some are useful in the context of gene targeting as well as for aspects, the gRNA does not bind Cas9 in the absence of a therapeutic applications. In a variety of organisms, including ligand bound to the aptamer. See, e.g., FIGS. 1A-B. In some mammals, site-specific endonucleases have been used for embodiments, the gRNA binds Cas9 when the aptamer is genome engineering by stimulating either non-homologous bound by a ligand specific to the aptamer. In some embodi end joining or homologous recombination. In addition to ments, the gRNA binds Cas9 in the absence or presence of a providing powerful research tools, site-specific nucleases ligand bound to the aptamer but binds to a target nucleic acid also have potential as gene therapy agents, and two site only in the presence of a ligand bound to the aptamer. In some specific endonucleases have recently entered clinical trials: aspects, the ligand is any molecule. In some aspects, the one, CCR5-2246, targeting a human CCR-5 allele as part of ligand is a small molecule, a metabolite, a carbohydrate, a an anti-HIV therapeutic approach (NCT00842634, peptide, a protein, or a nucleic acid. In some embodiments, NCT01044654, NCT01252641), and the other one, the aptamer is an RNA aptamer, for example, an RNA VF24684, targeting the human VEGF-A promoter as part of aptamer derived from a riboswitch. In some embodiments, an anti-cancer therapeutic approach (NCT01082926). the riboswitch from which the aptamer is derived is selected 0003 Specific cleavage of the intended nuclease target site from a theophylline riboswitch, a thiamine pyrophosphate without or with only minimal off-target activity is a prereq (TPP) riboswitch, an adenosine cobalamin (AdoCbl) uisite for clinical applications of site-specific endonuclease, riboswitch, an S-adenosyl methionine (SAM) riboswitch, an and also for high-efficiency genomic manipulations in basic SAH riboswitch, a flavin mononucleotide(FMN) riboswitch, research applications. For example, imperfect specificity of a tetrahydrofolate riboswitch, a lysine riboswitch, a glycine engineered site-specific binding domains has been linked to riboswitch, a purine riboswitch, a GlmS riboswitch, or a cellular toxicity and undesired alterations of genomic loci pre-queosine (PreCR1) riboswitch. In some embodiments, the other than the intended target. Most nucleases available aptamer is derived from a theophylline riboswitch and com today, however, exhibit significant off-target activity, and thus prises SEQ ID NO:3. In other embodiments, the aptamer is may not be suitable for clinical applications. An emerging non-naturally occurring, and in some aspects, is engineered to nuclease platform for use in clinical and research settings are bind a specific ligand using a systematic evolution of ligands the RNA-guided nucleases, such as Cas9. While these by exponential enrichment (SELEX) platform. In some nucleases are able to bind guide RNAs (gRNAs) that direct embodiments, the non-aptamer portion of the gRNA com cleavage of specific target sites, off-target activity is still prises at least 50, at least 60, at least 70, at least 80, at least 90, observed for certain Cas9:gRNA complexes (Pattanayak et at least 100, at least 110, at least 120, at least 130, at least 140, al., “High-throughput profiling of off-target DNA cleavage or at least 150 nucleotides, and the aptamer comprises at least reveals RNA-programmed Cas9 nuclease specificity.” Nat 20, at least 30, at least 40, at least 50, at least 60, at least 70, Biotechnol. 2013; doi:10.1038/nbt.2673). Technology for at least 80, at least 90, at least 100, at least 110, at least 120, engineering nucleases with improved specificity is therefore at least 130, at least 140, at least 150, at least 175, at least 200, needed. at least 250, or at least 300 nucleotides. 0007 According to another embodiment, methods for SUMMARY OF THE INVENTION site-specific DNA cleavage using the inventive Cas9 variants 0004 Some aspects of this disclosure are based on the are provided. For example, in some aspects, the methods recognition that the reported toxicity of some engineered comprise contacting a DNA with a complex comprising (i) a site-specific endonucleases is based on off-target DNA cleav gRNA comprising an aptamer, wherein the gRNA comprises age. Further, the activity of existing RNA-guided nucleases a sequence that binds to a portion of the DNA, (ii) a specific generally cannot be controlled at the molecular level, for ligand bound to the aptamer of the gRNA, and (iii) a Cas9 example, to switch a nuclease from an “off to an “on” state. protein, under conditions in which the Cas9 protein cleaves Controlling the activity of nucleases could decrease the like the DNA. lihood of incurring off-target effects. Some aspects of this 0008 According to another embodiment, methods for disclosure provide strategies, compositions, systems, and inducing site-specific DNA cleavage in a cell are provided. methods to control the binding and/or cleavage activity RNA For example, in Some embodiments, the methods comprise: programmable endonucleases, such as Cas9 endonuclease. (a) contacting a cell or expressing within a cell a gRNA 0005 Accordingly, one embodiment of the disclosure pro comprising an aptamer, wherein the gRNA comprises a vides RNA-guided nuclease complexes comprising a “Swit sequence capable of binding to a DNA target sequence; (b) chable' guide RNA (gRNA). For example, in some embodi contacting a cell or expressing within a cell a Cas9 protein; ments, the invention provides a complex comprising: (i) a and (c) contacting the cell with a ligand that binds the aptamer gRNA comprising an aptamer, wherein the gRNA does not of the gRNA, resulting in the formation of a gRNA:ligand: hybridize to a target nucleic acid in the absence of a specific Cas9 complex that cleaves the DNA target. In some embodi US 2015/007 1901 A1 Mar. 12, 2015 ments, the cell produces the ligand intracellularly, for at least 5, at least 10, at least 15, at least 20, at least 25, at least example as a part of physiological or pathophysiological 30, at least 40, at least 50, at least 75, or at least 100 nucle process.
Load more

Recommended publications
  • Nucleic Acids Research
    Volume 1 1 Number 4 1983 Nucleic Acids Research Isolation and nudeotide sequence of a plant tRNA gene: petunia asparagine tRNA Nurit Bawnik, Jacques S.Beckmann*, Sara Sarid + and Violet Daniel Departments of Biochemistry and + Biophysics, The Weizmann Institute of Science, Rehovot 76100, Israel, and *Institute of Field and Garden Crops, The Volcani Center, Bet Dagan 50200, Israel Received 29 October 1982; Revised and Accepted 18 January 1983 ABSTRACT A 14.3 kb petunia genomic DNA fragment was isolated and found to contain a single tRNA gene coding for asparagine tRNA. The nucleotide sequence of the asparagine tRNA gene and its flanking regions has been determined. This gene does not contain intervening sequences nor the 3'-end CCA sequence of the ma- ture tRNA and presents a similar overall sequence homology (70%) to both E. coli and mammalian asparagine tRNA. As in other eukaryotic tRNA genes the 5'-flanking region does not seem to contain any special sequence that could function as a regulatory element and the 3'-end is followed by a short cluster of T that may function as the transcription termination site. INTRODUCTION In contrast to the large amount of information that has been accumulated on the arrangement and structure of tRNA genes from a variety of eukaryotes such as yeast, Neurospora, Bombyx, Xenopus, Drosophila, rat and man (1-13), nothing is known about plant nuclear tRNA genes. To study genes for tRNA in plant cells, we have constructed a petunia genomic library and screened it with an unfractionated cytoplasmic petunia tRNA probe. Here we describe the detailed analysis of a tRNA gene-containing clone and the nucleotide se- Asn quence of a DNA fragment carrying a tRNAMKC(U) gene.
    [Show full text]
  • Nucleotide Sequence of the Cro-Cii-Oop Region of Bacteriophage
    Volume 6 Number 3 March 1979 Nucleic Acids Research Nucleotide sequence of the cro - cll - oop region of bacteriophage 434 DNA Rudolf Grosschedl and Elisabeth Schwarz* Institut f'ur Biologie III der Universitat Freiburg, Schlanzlestr. 1, D-7800 Freiburg i. Br., GFR Received 2 January 1979 ABSTRACT The nucleotide sequence of a 869 bp segment of phage 434 DNA in- cluding the regulatory genes cro and cII is presented and compared with the corresponding part of the phage A DNA sequence. The 434 cro protein as deduced from the DNA sequence is a highly basic protein of 71 amino acid residues with a calculated molecular weight of 8089. While the cro gene sequences of phage 434 and X DNA are very different, the nuc- leotide sequences to the right of the XAim434 boundary show differences only at 11 out of 512 positions. Nucleotide substitutions in the cII gene occur with one exception in the third positions of the respective codons and only one out of several DNA regulatory signals located in this region of the phage genomes is affected by these nucleotide sub- stitutions. INTRODUCTION Bacteriophage 434 is genetically very similar to phage X and together with several others belongs to the group of lambdoid coliphages. All of them share as common characteristics comparable DNA lengths and a similar structural and functional organization of their genomes. Genes coding for biologically related functions quite often are clustered into contiguous groups such as the imunity and replication regions. Because of their functional equivalence, these groups are exchangeable among the various lambdoid phages, resulting in the formation of hybrid bacteriophages such as X imm434 (1), i21 (2) and others.
    [Show full text]
  • "Unnatural Nucleosides with Unusual Base Pairing Properties"
    Unnatural Nucleosides with Unusual Base UNIT 1.4 Pairing Properties Donald E. Bergstrom1 1Purdue University, West Lafayette, Indiana ABSTRACT Synthetic modified nucleosides designed to pair in unusual ways with natural nucleobases have many potential applications in biology and biotechnology. This overview lays the foundation for future protocol units on synthesis and application of unnatural bases, with particular emphasis on unnatural base analogs that mimic natural bases in size, shape, and biochemical processing. Topics covered include base pairs with alternative H-bonding schemes, dimensionally expanded base pairs, hydrophobic base pairs, metal-ligated bases, degenerate bases, universal nucleosides, and triplex constituents. Curr. Protoc. Nucleic Acid Chem. 37:1.4.1-1.4.32. C 2009 by John Wiley & Sons, Inc. Keywords: nucleoside r mimetic r nonpolar r degenerate r universal INTRODUCTION McCutcheon (2007). Extensive efforts over Synthetic modified nucleosides designed to the past decade on DNA-metal base pairs pair in unusual ways with the natural nucleic has spawned three recent reviews in this area acid bases have many potential applications (Shionoya and Tanaka, 2004; Clever et al., in biology and biotechnology. These range 2007; Muller, 2008). from biochemical tools for probing nucleic To design bases that mimic natural bases acid structure or protein-nucleic acid inter- in function, it is useful to consider the fac- actions to tools for re-engineering DNA and tors that are essential for effective base pair- ultimately proteins. Applications as compo- ing and stable duplex formation. In addition nents of nucleic acid—based diagnostic tools to structures that are configured to hydrogen for clinical analysis have been envisioned.
    [Show full text]
  • Download File
    Interaction of DNA Bases with Gold Substrates Marta Rosa, Wenming Sun and Rosa Di Felice∗ Center S3, CNR Institute of Nanoscience, Via Campi 213/A, 41125 Modena, Italy ∗Corresponding author: [email protected] Received 6 December 2012; Accepted 17 December 2012 Abstract The interaction of molecules with inorganic substrates is a crucial issue for applications in molecular electronics. It influences important factors such as the immobilization efficiency and the charge injection through the inter- face. Moreover, mechanical aspects connected to the unfolding of biological molecules are important. We hereby present recent efforts in our group to tackle these problems, based on density functional theory calculations. In particular, we discuss our results on the adsorption of cytosine on Au(111) and on the interaction of guanine, in its natural and size-expanded forms, with small Au clusters. We find that cytosine binds to the Au(111) surface with a mechanism that involves charge sharing, intermediate between chemisorption and physisorp- tion. The investigation of small complexes between guanine and gold clusters reveals the formation of hydrogen bonds: these configurations with unusual bonds are relevant at the corners of nanoparticles, while they can probably be neglected when DNA binds on flat extended metal surfaces. Keywords: DNA/Au interfaces, Density Functional Theory, Van der Waals, DNA modifications, electronic hybridization. Journal of Self-Assembly and Molecular Electronics, Vol. 1, 41–68. doi 10.13052/same2245-4551.112 c 2013 River Publishers. All rights reserved. 42 M. Rosa et al. 1 Introduction The electronic structure of DNA molecules started to attract the attention of scientific research groups because of its implications in DNA damage and repair.
    [Show full text]
  • Modified Nucleic Acids: Replication, Evolution, and Next-Generation Therapeutics Karen Duffy†, Sebastian Arangundy-Franklin† and Philipp Holliger*
    Duffy et al. BMC Biology (2020) 18:112 https://doi.org/10.1186/s12915-020-00803-6 REVIEW Open Access Modified nucleic acids: replication, evolution, and next-generation therapeutics Karen Duffy†, Sebastian Arangundy-Franklin† and Philipp Holliger* Abstract Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs. Nucleic acids: natural and expanded functions afford completely new modalities for therapeutic inter- A heritable genetic system is a defining requirement for vention (e.g., direct protein expression or specific and life. The natural nucleic acids, DNA and RNA, are ex- programmable modulation of gene expression) that can- quisitely suited to store and propagate genetic informa- not be easily accessed by other biologics or small mol- tion with sufficient stability and fidelity to support large ecule drugs. However, several challenges have thus far genomes but also the flexibility to enable evolution. Nu- prevented nucleic acids from reaching their full potential cleic acids are unique among biopolymers in that both as medicines including poor chemical and biological accessible information and functional capacity coexist in stability and narrow chemical diversity. a single molecule.
    [Show full text]
  • Synthetic Biology: Cellular Xdna Readers
    research highlights DRUG DISCOVERY this state, Ooi et al. treated cells with dimethyl Science, published online 17 November 2011, fumarate and found increased expression Malaria under arrest doi:10.1126/science.1211936 of NRF2 and its target genes, suggesting that KEAP1, which is known to control the The malaria parasites from Plasmodium species have both a liver stage (EEF or sporozoite stability of NRF2, is sensitive to fumarate. MS stage) and a blood stage in human hosts. Because EEFs of certain Plasmodium strains can in both studies confirmed the modification of remain dormant for long periods and disease symptoms originate during the blood stage, several residues in KEAP1 to S-(2-succinyl)- therapeutics that can eliminate parasites of both stages are needed, yet most drugs target cysteine (2SC) in fumarate-accumulating only the blood-stage parasites. To find drugs that might inhibit multiple parasite stages, conditions. Ooi et al. further demonstrated Meister et al. screened a library of 5,697 compounds known to be active against P. falciparum that ubiquitinated KEAP1 was elevated in blood stages. In a high-content imaging assay of sporozoite-infected cultured liver cells, the FH-deficient cells compared to controls; authors found 275 compounds that are structurally unrelated to known antimalarial scaffolds additional experiments using proteasomal and decrease parasite size within cells after infection. They then used a hypergeometric inhibitors led to a model where 2SC-modified mean function to determine which of the 2,715 independent chemical-scaffold clusters KEAP1 is ubiquitinated and degraded by a in the original library were fully represented among the hits, identifying quinazoline, the proteasome.
    [Show full text]
  • Template-Independent Enzymatic Oligonucleotide Synthesis (Tieos): Its History, Prospects, and Challenges Michael A
    Perspective Cite This: Biochemistry XXXX, XXX, XXX−XXX pubs.acs.org/biochemistry Template-Independent Enzymatic Oligonucleotide Synthesis (TiEOS): Its History, Prospects, and Challenges Michael A. Jensen*,† and Ronald W. Davis†,‡ † Stanford Genome Technology Center, Department of Biochemistry, Stanford University, Palo Alto, California 94304, United States ‡ Department of Genetics, Stanford University, Palo Alto, California 94304, United States ABSTRACT: There is a growing demand for sustainable methods in research and development, where instead of hazardous chemicals, an aqueous medium is chosen to perform biological reactions. In this Perspective, we examine the history and current methodology of using enzymes to generate artificial single- stranded DNA. By using traditional solid-phase phosphoramidite chemistry as a metric, we also explore criteria for the method of template-independent enzymatic oligonucleotide synthesis (TiEOS). As its key component, we delve into the biology of one of the most enigmatic enzymes, terminal deoxynucleotidyl transferase (TdT). As TdT is found to exponentially increase antigen receptor diversity in the vertebrate immune system by adding nucleotides in a template- free manner, researchers have exploited this function as an alternative to the phosphoramidite synthesis method. Though TdT is currently the preferred enzyme for TiEOS, its random nucleotide incorporation presents a barrier in synthesis automation. Taking a closer look at the TiEOS cycle, particularly the coupling step, we find it is comprised of additions > n+1 and deletions. By tapping into the physical and biochemical properties of TdT, we strive to further elucidate its mercurial behavior and offer ways to better optimize TiEOS for production-grade oligonucleotide synthesis. n the mid-20th century, there were several key break- toward “green” technology development in terms of sustainable I throughs in the fields of genetics and biochemistry that have chemistry.14 Possible advantages of using an enzyme for ssDNA led us to current day medicine.
    [Show full text]
  • Efficient Replication Bypass of Size-Expanded DNA Base Pairs in Bacterial Cells** James C
    Zuschriften DOI: 10.1002/ange.200805683 Unnatural DNA Bases Efficient Replication Bypass of Size-Expanded DNA Base Pairs in Bacterial Cells** James C. Delaney, Jianmin Gao, Haibo Liu, Nidhi Shrivastav, John M. Essigmann,* and Eric T. Kool* One of the long-standing aims of biomimetic chemistry has The four size-expanded DNA base pairs are shown in been to develop molecules that function as much as possible Figure 1. The hydrogen-bonded pairs involve benzo homo- as the natural ones do.[1] Among biopolymers, nucleic acids logues opposite complementary natural partners, yielding have long served as a test bed for bioinspired design. The base pairs 2.4 larger than Watson–Crick pairs.[6] The earliest focus of altered structures for DNA was the redesign of the phosphodiester backbone,[2] and numerous studies found backbone variants that assembled well into helices. Moreover, in recent years, some altered sugars have also been shown to be substrates for certain polymerase enzymes.[3] Such work suggests the possibility of future biological activities associated with altered DNA backbones. More recently, a number of laboratories have focused on design of replacements for the DNA bases themselves, which encode the chemical information of the cell.[4] This is a challenging goal, because biological enzymes have evolved the ability to manipulate these bases and base pairs with extraordinarily high selectivity. The polymerase replication of designed DNA pairs has been studied in a number of laboratories. Significant successes have been reported using varied strategies, including base pairs with altered hydrogen- bonding patterns,[4a] pairs that lack hydrogen bonds altoge- ther,[4b–e,i,j,m–p] and pairs that have larger-than-natural dimen- Figure 1.
    [Show full text]
  • Expanded DNA Base Pairs in Bacterial Cells
    Efficient replication bypass of size- expanded DNA base pairs in bacterial cells The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Delaney, JamesC. et al. “Efficient Replication Bypass of Size- Expanded DNA Base Pairs in Bacterial Cells.” Angewandte Chemie International Edition 48.25 (2009): 4524–4527. As Published http://dx.doi.org/10.1002/anie.200805683 Publisher Wiley Blackwell Version Author's final manuscript Citable link http://hdl.handle.net/1721.1/75427 Terms of Use Creative Commons Attribution-Noncommercial-Share Alike 3.0 Detailed Terms http://creativecommons.org/licenses/by-nc-sa/3.0/ NIH Public Access Author Manuscript Angew Chem Int Ed Engl. Author manuscript; available in PMC 2012 September 06. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Angew Chem Int Ed Engl. 2009 ; 48(25): 4524–4527. doi:10.1002/anie.200805683. Efficient Replication Bypass of Size-expanded DNA Base Pairs in Bacterial Cells** Dr. James C. Delaney, Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology Cambridge, MA 02139 USA Dr. Jianmin Gao, Department of Chemistry, Stanford University, Stanford, CA 94305 USA Dr. Haibo Liu, Department of Chemistry, Stanford University, Stanford, CA 94305 USA Nidhi Shrivastav, Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology Cambridge, MA 02139 USA Prof. Dr. John M. Essigmann, and Departments of Chemistry and Biological Engineering, Massachusetts Institute of Technology Cambridge, MA 02139 USA Prof. Dr. Eric T. Kool Department of Chemistry, Stanford University, Stanford, CA 94305 USA John M.
    [Show full text]
  • The Enzymatic Repair of Dna, I. Formation of Circular Xdna* by Malcolm L
    THE ENZYMATIC REPAIR OF DNA, I. FORMATION OF CIRCULAR XDNA* BY MALCOLM L. GEFTER, ANDREW BECKER, AND JERARD HURWITZ DEPARTMENT OF DEVELOPMENTAL BIOLOGY AND CANCER, ALBERT EINSTEIN COLLEGE OF MEDICINE, BRONX, NEW YORK Communicated by Alfred Gilman, April 19, 1967 Physical and genetic studies on bacteriophages indicate that genetic recombina- tion involves the breakage and reunion of DNA molecules." 2 It has been postu- lated that the process of reunion occurs first by the formation of a joint structure containing portions of the parental DNA's linked together by noncovalent bonds, and second by the formation of a phosphodiester "seal" between the internal ter- mini of DNA chains held together in this manner.2 In our search for the enzyme(s) responsible for the covalent joining of polynucleotides, we anticipated that phage XDNA, in the hydrogen-bonded circular form ("Hershey circle"),3 might provide a model system for studying the enzymatic fate of DNA termini held in apposition by hydrogen bonds. In agreement with the results reported by Gellert,4 it was found that extracts of Escherichia coli catalyzed the formation of covalently closed circles from hydrogen-bonded circles of XDNA. We have purified this enzyme activity from E. coli K12 approximately 2000-fold. The enzyme also catalyzes the conversion of XDNA containing single-strand breaks to a form which, in al- kaline sucrose gradients, sediments in a manner indistinguishable from intact XDNA. The enzyme requires double-stranded DNA as substrate and is dependent on a heat-stable factor. Similar results have been observed by Olivera and Leh- man.5 Materials and Methods.-Bacterial strains and bacteriophages: E.
    [Show full text]
  • Complete Nucleotide Sequence of Torpedo Marmorata Mrna
    Proc. Natl. Acad. Sci. USA Vol. 81, pp. 7313-7317, December 1984 Biochemistry Complete nucleotide sequence of Torpedo marmorata mRNA coding for the 43,000-dalton v2 protein: Muscle-specific creatine kinase (cDNA cloning/hybrid-selected translation/oligonucleotide-specific primer extension) JRR6ME GIRAUDAT*, ANNE DEVILLERS-THIERY*, JEAN-CLAUDE PERRIARDt, AND JEAN-PIERRE CHANGEUX* *Unitd de Neurobiologie Moldculaire et Laboratoire Associd 270, Centre National de la Recherche Scientifique Interactions Moldculaires et Cellulaires, Institut Pasteur, 25 rue du Docteur Roux, 75 015 Paris, France; and lInstitute for Cell Biology, Swiss Federal Institute for Technology, Honggerberg, CH 8093 Zurich, Switzerland Contributed by Jean-Pierre Changeux, August 1, 1984 ABSTRACT DNA sequences coding for the muscle-specif- charge. We previously reported the construction of cDNA ic subunit of creatine kinase have been isolated from cDNA libraries from Torpedo marmorata electric organ, which en- libraries constructed from Torpedo marmorata electric organ. abled us to isolate cDNA clones coding for the a-subunit of Clones were screened by differential in situ hybridization and the acetylcholine receptor (12, 13). We describe here the iso- hybrid-selected translation. The in vitro translation product of lation of cDNA clones coding for the T. marmorata muscle- the selected mRNA was immunoprecipitated by anti-chicken specific CK and report the complete nucleotide sequence of creatine kinase antibodies and comigrated with Torpedo mus- the corresponding mRNA. cle creatine kinase on two-dimensional gels at the same posi- tion as the cytosolic 43,000-dalton protein referred to as v2. MATERIALS AND METHODS The cDNA inserts hybridized to a mRNA species present in Materials.
    [Show full text]
  • Local Aromaticity in Natural Nucleobases and Their Size-Expanded Benzo-Fused Derivatives
    J. Phys. Chem. A 2006, 110, 12249-12258 12249 Local Aromaticity in Natural Nucleobases and Their Size-Expanded Benzo-Fused Derivatives Oscar Huertas,† Jordi Poater,‡ Miguel Fuentes-Cabrera,§ Modesto Orozco,| Miquel Sola`,*,⊥ and F. Javier Luque*,† Departament de Fisicoquı´mica, Facultat de Farma`cia, UniVersitat de Barcelona, AVenida Diagonal 643, 08028, Barcelona, Spain, Afdeling Theoretische Chemie, Scheikundig Laboratorium der Vrije UniVersiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands, Center for Nanophase Material Sciences and Computer Science and Mathematics DiVision, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831-6494, Departament de Bioquı´mica i Biologia Molecular, Facultat de Quı´mica, UniVersitat de Barcelona, Martı´ i Franque´s 1, 08028 Barcelona, Spain, Unidad de Modelizacio´n Molecular y Bioinforma´tica, Parc Cientı´fic de Barcelona, Josep Samitier 1-6, 08028 Barcelona, Spain, Computacional Biology Program, Barcelona Supercomputing Center. Edificio Nexus II. Barcelona 08028, Spain, and Institut de Quı´mica Computacional and Departament de Quı´mica, UniVersitat de Girona, 17071 Girona, Spain ReceiVed: June 18, 2006; In Final Form: August 29, 2006 The influence of the insertion/addition of a benzene ring to the natural nucleic acid bases on the local aromaticity of the so-called size-expanded (xN, with N being adenine, guanine, cytosine, and thymine) bases is examined. To this end, the local aromaticity of the six- and five-membered rings in both the natural bases and their benzoderivatives is determined using HOMA, NICS, aromatic fluctuation index (FLU), and para-delocalization index (PDI) descriptors. In general, there is a good correspondence between the different indices, so that ring moieties with more negative NICS values also have larger HOMA and PDI measures and lower FLU indices.
    [Show full text]