1
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Kalra S, Donnelly A, Singh N, Matthews D, Del Villar-Guerra R, Bemmer V, Dominguez C, Allcock N, Cherny D, Revyakin A, Rusling DA. Functionalizing DNA Origami by Triplex-Directed Site-Specific Photo-Cross-Linking. J Am Chem Soc 2024; 146:13617-13628. [PMID: 38695163 PMCID: PMC11100008 DOI: 10.1021/jacs.4c03413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
Here, we present a cross-linking approach to covalently functionalize and stabilize DNA origami structures in a one-pot reaction. Our strategy involves adding nucleotide sequences to adjacent staple strands, so that, upon assembly of the origami structure, the extensions form short hairpin duplexes targetable by psoralen-labeled triplex-forming oligonucleotides bearing other functional groups (pso-TFOs). Subsequent irradiation with UVA light generates psoralen adducts with one or both hairpin staples leading to site-specific attachment of the pso-TFO (and attached group) to the origami with ca. 80% efficiency. Bis-adduct formation between strands in proximal hairpins further tethers the TFO to the structure and generates "superstaples" that improve the structural integrity of the functionalized complex. We show that directing cross-linking to regions outside of the origami core dramatically reduces sensitivity of the structures to thermal denaturation and disassembly by T7 RNA polymerase. We also show that the underlying duplex regions of the origami core are digested by DNase I and thus remain accessible to read-out by DNA-binding proteins. Our strategy is scalable and cost-effective, as it works with existing DNA origami structures, does not require scaffold redesign, and can be achieved with just one psoralen-modified oligonucleotide.
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Affiliation(s)
- Shantam Kalra
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Amber Donnelly
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Nishtha Singh
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Daniel Matthews
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Rafael Del Villar-Guerra
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Victoria Bemmer
- Centre
for Enzyme Innovation, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2DY, U.K.
| | - Cyril Dominguez
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Natalie Allcock
- Core
Biotechnology Services Electron Microscopy Facility, University of Leicester, Leicester LE1 7RH, U.K.
| | - Dmitry Cherny
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - Andrey Revyakin
- Department
of Molecular and Cell Biology, and Leicester Institute of Chemical
Biology, University of Leicester, Leicester LE1 7RH, U.K.
| | - David A. Rusling
- School
of Medicine, Pharmacy and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DT, U.K.
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2
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Michelini F, Jalihal AP, Francia S, Meers C, Neeb ZT, Rossiello F, Gioia U, Aguado J, Jones-Weinert C, Luke B, Biamonti G, Nowacki M, Storici F, Carninci P, Walter NG, d'Adda di Fagagna F. From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chem Rev 2018; 118:4365-4403. [PMID: 29600857 DOI: 10.1021/acs.chemrev.7b00487] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.
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Affiliation(s)
- Flavia Michelini
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Ameya P Jalihal
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Sofia Francia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Chance Meers
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Zachary T Neeb
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | | | - Ubaldo Gioia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Julio Aguado
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | | | - Brian Luke
- Institute of Developmental Biology and Neurobiology , Johannes Gutenberg University , 55099 Mainz , Germany.,Institute of Molecular Biology (IMB) , 55128 Mainz , Germany
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Mariusz Nowacki
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | - Francesca Storici
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Piero Carninci
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku , Yokohama City , Kanagawa 230-0045 , Japan
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Fabrizio d'Adda di Fagagna
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
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3
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D'Alessandro G, d'Adda di Fagagna F. Transcription and DNA Damage: Holding Hands or Crossing Swords? J Mol Biol 2017; 429:3215-3229. [DOI: 10.1016/j.jmb.2016.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 01/12/2023]
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4
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Reines D, Dvir A, Conaway JW, Conaway RC. Assays for investigating transcription by RNA polymerase II in vitro. Methods 1997; 12:192-202. [PMID: 9237163 DOI: 10.1006/meth.1997.0471] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
With the availability of the general initiation factors (TFIIB, TFIID, TFIIE, TFIIF, and TFIIH), it is now possible to investigate aspects of the mechanism of eukaryotic messenger RNA synthesis in purified, reconstituted RNA polymerase II transcription systems. Rapid progress in these investigations has been spurred by use of a growing number of assays that are proving valuable not only for dissecting the molecular mechanisms of transcription initiation and elongation by RNA polymerase II, but also for identifying and purifying novel transcription factors that regulate polymerase activity. Here we describe a variety of these assays and discuss their utility in the analysis of transcription by RNA polymerase II.
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Affiliation(s)
- D Reines
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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5
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Takagi Y, Conaway JW, Conaway RC. A novel activity associated with RNA polymerase II elongation factor SIII. SIII directs promoter-independent transcription initiation by RNA polymerase II in the absence of initiation factors. J Biol Chem 1995; 270:24300-5. [PMID: 7592640 DOI: 10.1074/jbc.270.41.24300] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
General transcription factor SIII, a heterotrimer of 110-, 18-, and 15-kDa subunits, was shown previously to stimulate the overall rate of RNA chain elongation by RNA polymerase II by suppressing transient pausing by polymerase at many sites along DNA templates (Bradsher, J. N., Jackson, K. W., Conaway, R. C., and Conaway, J. W. (1993) J. Biol. Chem. 268, 25587-25593). In this report, SIII is shown to possesses the novel ability to direct robust but promiscuous transcription by RNA polymerase II on duplex DNA templates in the absence of initiation factors. Mechanistic studies reveal that SIII promotes RNA synthesis by substantially increasing the efficiency with which RNA polymerase II initiates promoter-independent transcription from the ends of duplex DNA. Remarkably, SIII appears to have a negligible effect on de novo synthesis of end-to-end transcripts. Instead, analysis of reaction products indicates that SIII is capable of promoting a dramatic increase in the ability of RNA polymerase II to extend the 3'-hydroxyl termini of duplex DNA fragments, in a template-directed reaction exhibiting no strong preference for 3'-protruding, 3'-recessed, or blunt DNA ends. Although RNA polymerase II has been shown previously to catalyze primer-dependent transcription, SIII is the first eukaryotic transcription factor found to promote this reaction. Based on these findings, we propose that SIII may suppress transient pausing by RNA polymerase II by helping to maintain the 3'-hydroxyl terminus of the nascent RNA chain in its proper position in the polymerase active site.
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Affiliation(s)
- Y Takagi
- Program in Molecular and Cell Biology, Oklahoma Medical Research Foundation, Oklahoma City 73104, USA
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6
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Rodi CP, Sauerbier W. Structure of transcriptionally active chromatin: radiological evidence for requirement of torsionally constrained DNA. J Cell Physiol 1989; 141:346-52. [PMID: 2478570 DOI: 10.1002/jcp.1041410216] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Synthesis of alpha- and beta-globin RNA in DMSO-induced Friend's erythroleukemia cells and synthesis of immunoglobulin gamma- and kappa-chain RNA, total RNA, 5S RNA, and tRNA in mouse myeloma cells (MPC-11) was inhibited by gamma-irradiation. For all RNA species, synthesis decreased nearly exponentially as a function of radiation dose, whereas RNA size distributions, turnover rates, and specific activities of radioactively labeled RNA were affected only insignificantly. D37 values for the loss of synthesis of various RNA species correspond to target sizes ranging from 21,000 to 53,000 kd, or 30-80 kbp of DNA. These target sizes are several-fold larger than the structural genes in question; however, they correspond well with the size of DNA loops, or "domains" constrained by the nuclear matrix. The data suggest that the eukaryotic transcription unit is the torsionally constrained chromatin loop, transcription of which may be inactivated, or significantly reduced by a DNA single-strand break.
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MESH Headings
- Animals
- Cell Line
- Chromatin/physiology
- Chromatin/radiation effects
- Chromatin/ultrastructure
- DNA/physiology
- DNA/ultrastructure
- DNA, Single-Stranded/drug effects
- DNA, Single-Stranded/ultrastructure
- DNA-Directed RNA Polymerases/pharmacology
- Dimethyl Sulfoxide
- Gamma Rays
- Leukemia, Erythroblastic, Acute/chemically induced
- Leukemia, Erythroblastic, Acute/pathology
- Mice
- Multiple Myeloma/pathology
- RNA/biosynthesis
- RNA/radiation effects
- RNA, Nuclear/metabolism
- RNA, Nuclear/radiation effects
- Transcription, Genetic/physiology
- Tumor Cells, Cultured/pathology
- Tumor Cells, Cultured/radiation effects
- Tumor Cells, Cultured/ultrastructure
- Uridine/metabolism
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Affiliation(s)
- C P Rodi
- Institute of Human Genetics, University of Minnesota Medical School, Minneapolis 55455
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7
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Rose KM, Szopa J, Han FS, Cheng YC, Richter A, Scheer U. Association of DNA topoisomerase I and RNA polymerase I: a possible role for topoisomerase I in ribosomal gene transcription. Chromosoma 1988; 96:411-6. [PMID: 2851418 DOI: 10.1007/bf00303034] [Citation(s) in RCA: 82] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
RNA polymerase I preparations purified from a rat hepatoma contained DNA topoisomerase activity. The DNA topoisomerase associated with the polymerase had an Mr of 110,000, required Mg2+ but not ATP, and was recognized by anti-topoisomerase I antibodies. When added to RNA polymerase I preparations containing topoisomerase activity, anti-topoisomerase I antibodies were able to inhibit the DNA relaxing activity of the preparation as well as RNA synthesis in vitro. RNA polymerase II prepared by analogous procedures did not contain topoisomerase activity and was not recognized by the antibodies. The topoisomerase I: polymerase I complex was reversibly dissociated by column chromatography on Sephacryl S200 in the presence of 0.25 M (NH4)2SO4. Topoisomerase I was immunolocalized in the transcriptionally active ribosomal gene complex containing RNA polymerase I in situ. These data indicate that topoisomerase I and RNA polymerase I are tightly complexed both in vivo and in vitro, and suggest a role for DNA topoisomerase I in the transcription of ribosomal genes.
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Affiliation(s)
- K M Rose
- Department of Pharmacology, Medical School, University of Texas Health Science Center, Houston 77225
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8
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Albright LM, Kassavetis GA, Geiduschek EP. Bacteriophage T4 late transcription from plasmid templates is enhanced by negative supercoiling. J Bacteriol 1988; 170:1279-89. [PMID: 2830234 PMCID: PMC210904 DOI: 10.1128/jb.170.3.1279-1289.1988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Concurrent viral replication is normally required to activate bacteriophage T4 late promoters; replication is thought to provide a template structure which is competent for late transcription. Transcription from plasmid-borne T4 late promoters, however, is independent of replication in vivo and in vitro. In this work, we have shown that, when the late gene 23 promoter is located on a plasmid, its utilization in vivo depends upon the ability of host DNA gyrase to maintain some degree of negative superhelicity. This suggests that an alternative pathway exists for activation of late promoters: DNA which is under sufficient negative torsional stress is already competent for late transcription. We also describe a method for isolating ternary complexes of plasmid DNA, RNA polymerase, and nascent RNA which have initiated transcription in vivo. The topoisomer distribution of such ternary complexes prepared from T4-infected cells showed that, late in infection, transcriptional activity resides primarily in the subset of the plasmid population with the most negatively supercoiled topoisomers. However, the overall transcriptional pattern in these ternary complexes indicated that both vector and T4 sequences are actively transcribed. Much of this transcriptional activity could be independent of gp55, the T4-specific RNA polymerase-binding protein that confers late promoter recognition.
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Affiliation(s)
- L M Albright
- Department of Biology, University of California, San Diego, La Jolla 92093
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9
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Bateman E, Nicholson BH. Location of DNA and nucleotide binding sites on wheat germ RNA polymerase II. Biochem Biophys Res Commun 1984; 125:569-76. [PMID: 6517913 DOI: 10.1016/0006-291x(84)90577-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We have investigated the roles of the 13 subunits present in wheat germ RNA polymerase II, using the inhibitors; pyridoxal 5'-phosphate and the periodate oxidation product of adenosine (AOP). Pyridoxal 5'-phosphate is shown to interact with at least part of the DNA binding site as well as the nucleotide binding sites, whereas AOP probably binds to the nucleotide binding sites. Reduction of the enzyme:inhibitor complex with sodium [3H] borohydride and identification of labelled subunits shows that in both cases the inhibitors bind primarily to subunits a and b. We conclude that subunits a and b contain at least part of the catalytic site, but do not rule out possible involvement of other subunits in the various steps of transcription.
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10
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Cooke RM, Durand R, Job C, Penon P, Teissere M, Job D. Enzymatic properties of plant RNA polymerases : An approach to the study of transcription in plants. PLANT MOLECULAR BIOLOGY 1984; 3:217-225. [PMID: 24310433 DOI: 10.1007/bf00029657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Results obtained in the past few years in the study of the reaction mechanism of plant RNA polymerases are reviewed and discussed. They suggest that valuable information can be obtained using a highly simplified transcription system composed of purified plant enzymes and cloned genes. This type of approach may provide a starting point for the development of an in vitro transcription system. The detailed study of the fundamental enzymatic properties of the plant RNA polymerases allows a comparison with the well documented corresponding bacterial enzyme.
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Affiliation(s)
- R M Cooke
- Laboratoire de Physiologie, Véǵetale Université de Perpignan, Avenue de Villeneuve, F 66025, Perpignan, Cedex, France
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11
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Studies of in vitro transcription by calf thymus RNA polymerase II using a novel duplex DNA template. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)34669-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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12
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Lewis MK, Burgess RR. 5 Eukaryotic RNA Polymerases. ACTA ACUST UNITED AC 1982. [DOI: 10.1016/s1874-6047(08)60277-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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13
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Purification and characterization of wheat germ DNA topoisomerase I (nicking-closing enzyme). J Biol Chem 1981. [DOI: 10.1016/s0021-9258(19)69287-2] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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