1
|
Abstract
RNA 5'-modifications are known to extend the functional spectrum of ribonucleotides. In recent years, numerous non-canonical 5'-modifications, including adenosine-containing cofactors from the group of B vitamins, have been confirmed in all kingdoms of life. The structural component of thiamine adenosine triphosphate (thiamine-ATP), a vitamin B1 derivative found to accumulate in Escherichia coli and other organisms in response to metabolic stress conditions, suggests an analogous function as a 5'-modification of RNA. Here, we report the synthesis of thiamine adenosine dinucleotides and the preparation of pure 5'-thiamine-capped RNAs based on phosphorimidazolide chemistry. Furthermore, we present the incorporation of thiamine-ATP and thiamine adenosine diphosphate (thiamine-ADP) as 5'-caps of RNA by T7 RNA polymerase. Transcripts containing the thiamine modification were modified specifically with biotin via a combination of thiazole ring opening, nucleophilic substitution and copper-catalyzed azide-alkyne cycloaddition. The highlighted methods provide easy access to 5'-thiamine RNA, which may be applied in the development of thiamine-specific RNA capture protocols as well as the discovery and confirmation of 5'-thiamine-capped RNAs in various organisms.
Collapse
Affiliation(s)
| | | | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany; (M.M.); (K.H.)
| |
Collapse
|
2
|
Jiménez-Serra I, Martín-Pintado J, Rivilla VM, Rodríguez-Almeida L, Alonso Alonso ER, Zeng S, Cocinero EJ, Martín S, Requena-Torres M, Martín-Domenech R, Testi L. Toward the RNA-World in the Interstellar Medium-Detection of Urea and Search of 2-Amino-oxazole and Simple Sugars. Astrobiology 2020; 20:1048-1066. [PMID: 32283036 DOI: 10.1089/ast.2019.2125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the past decade, astrochemistry has witnessed an impressive increase in the number of detections of complex organic molecules. Some of these species are of prebiotic interest such as glycolaldehyde, the simplest sugar, or aminoacetonitrile, a possible precursor of glycine. Recently, we have reported the detection of two new nitrogen-bearing complex organics, glycolonitrile and Z-cyanomethanimine, known to be intermediate species in the formation process of ribonucleotides within theories of a primordial RNA-world for the origin of life. In this study, we present deep and high-sensitivity observations toward two of the most chemically rich sources in the galaxy: a giant molecular cloud in the center of the Milky Way (G + 0.693-0.027) and a proto-Sun (IRAS16293-2422 B). Our aim is to explore whether the key precursors considered to drive the primordial RNA-world chemistry are also found in space. Our high-sensitivity observations reveal that urea is present in G + 0.693-0.027 with an abundance of ∼5 × 10-11. This is the first detection of this prebiotic species outside a star-forming region. Urea remains undetected toward the proto-Sun IRAS16293-2422 B (upper limit to its abundance of ≤2 × 10-11). Other precursors of the RNA-world chemical scheme such as glycolaldehyde or cyanamide are abundant in space, but key prebiotic species such as 2-amino-oxazole, glyceraldehyde, or dihydroxyacetone are not detected in either source. Future more sensitive observations targeting the brightest transitions of these species will be needed to disentangle whether these large prebiotic organics are certainly present in space.
Collapse
Affiliation(s)
| | | | | | | | - Elena R Alonso Alonso
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, (UPV-EHU), Bilbao, Spain
- Biofisika Institute (CSIC, UPV/EHU), Leioa, Spain
| | - Shaoshan Zeng
- School of Physics and Astronomy, Queen Mary University of London, London, United Kingdom
| | - Emilio J Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, (UPV-EHU), Bilbao, Spain
- Biofisika Institute (CSIC, UPV/EHU), Leioa, Spain
| | - Sergio Martín
- European Southern Observatory, Vitacura, Chile
- Joint ALMA Observatory, Vitacura, Chile
| | | | | | - Leonardo Testi
- INAF-Osservatorio Astrofisico di Arcetri, Florence, Italy
- European Southern Observatory, Garching bei München, Germany
| |
Collapse
|
3
|
Krasheninina OA, Fishman VS, Lomzov AA, Ustinov AV, Venyaminova AG. Postsynthetic On-Column 2' Functionalization of RNA by Convenient Versatile Method. Int J Mol Sci 2020; 21:E5127. [PMID: 32698484 PMCID: PMC7404181 DOI: 10.3390/ijms21145127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/08/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
We report a universal straightforward strategy for the chemical synthesis of modified oligoribonucleotides containing functional groups of different structures at the 2' position of ribose. The on-column synthetic concept is based on the incorporation of two types of commercial nucleotide phosphoramidites containing orthogonal 2'-O-protecting groups, namely 2'-O-thiomorpholine-carbothioate (TC, as "permanent") and 2'-O-tert-butyl(dimethyl)silyl (tBDMS, as "temporary"), to RNA during solid-phase synthesis. Subsequently, the support-bound RNA undergoes selective deprotection and follows postsynthetic 2' functionalization of the naked hydroxyl group. This convenient method to tailor RNA, utilizing the advantages of solid phase approaches, gives an opportunity to introduce site-specifically a wide range of linkers and functional groups. By this strategy, a series of RNAs containing diverse 2' functionalities were synthesized and studied with respect to their physicochemical properties.
Collapse
Affiliation(s)
- Olga A. Krasheninina
- Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 80-82, Innsbruck 6020, Austria
| | - Veniamin S. Fishman
- Institute of Cytology and Genetics SB RAS Lavrentiev Ave. 10, 630090 Novosibirsk, Russia;
| | - Alexander A. Lomzov
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
| | - Alexey V. Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia;
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS Lavrentiev Ave. 8, 630090 Novosibirsk, Russia; (A.A.L.); (A.G.V.)
| |
Collapse
|
4
|
Abstract
Continuous reaction networks, which do not rely on purification or timely additions of reagents, serve as models for chemical evolution and have been demonstrated for compounds thought to have played important roles for the origins of life such as amino acids, hydroxy acids, and sugars. Step-by-step chemical protocols for ribonucleotide synthesis are known, but demonstrating their synthesis in the context of continuous reaction networks remains a major challenge. Herein, compounds proposed to be important for prebiotic RNA synthesis, including glycolaldehyde, cyanamide, 2-aminooxazole, and 2-aminoimidazole, are generated from a continuous reaction network, starting from an aqueous mixture of NaCl, NH4Cl, phosphate, and HCN as the only carbon source. No well-timed addition of any other reagents is required. The reaction network is driven by a combination of γ radiolysis and dry-down. γ Radiolysis results in a complex mixture of organics, including the glycolaldehyde-derived glyceronitrile and cyanamide. This mixture is then dried down, generating free glycolaldehyde that then reacts with cyanamide/NH3 to furnish a combination of 2-aminooxazole and 2-aminoimidazole. This continuous reaction network models how precursors for generating RNA and other classes of compounds may arise spontaneously from a complex mixture that originates from simple reagents.
Collapse
Affiliation(s)
- Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Quoc Phuong Tran
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Sarfaraz Ali
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Isao Yoda
- Co-60 Radiation Facility, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Zachary R Adam
- Department of Planetary Sciences, University of Arizona, Tucson, AZ 85721
- Blue Marble Space Institute of Science, Seattle, WA 98154
| | - H James Cleaves
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
- Blue Marble Space Institute of Science, Seattle, WA 98154
- Program in Interdisciplinary Studies, Institute for Advanced Study, Princeton, NJ 08540
| | - Albert C Fahrenbach
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia;
| |
Collapse
|
5
|
Motsch S, Tremmel P, Richert C. Regioselective formation of RNA strands in the absence of magnesium ions. Nucleic Acids Res 2020; 48:1097-1107. [PMID: 31819977 PMCID: PMC7026634 DOI: 10.1093/nar/gkz1125] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/08/2019] [Accepted: 11/18/2019] [Indexed: 11/28/2022] Open
Abstract
The oligomerization of ribonucleotides can produce short RNA strands in the absence of enzymes. This reaction gives one of two regioisomeric phosphodiester linkages, a 2',5'- or a 3',5'-diester. The former, non-natural linkage is detrimental for duplex stability, and is known to form preferentially in oligomerizations occurring in homogeneous solution with preactivated nucleotides in the presence of magnesium cations. We have studied ribonucleotide oligomerization with in situ activation, using NMR as monitoring technique. Unexpectedly, the known preference for 2',5'-linkages in the oligomerization of AMP was reversed in the absence of magnesium ions at slightly basic pH. Further, oligomerization was surprisingly efficient in the absence of Mg2+ salts, producing oligomers long enough for duplex formation. A quantitative systems chemistry analysis then revealed that the absence of magnesium ions favors the activation of nucleotides, and that the high concentration of active species can compensate for slower coupling. Further, organocatalytic intermediates can help to overcome the unfavorable regioselectivity of the magnesium-catalyzed reactions. Our findings allay concerns that RNA may have been difficult to form in the absence of enzymes. They also show that there is an efficient path to genetic material that does not require mineral surfaces or cations known to catalyze RNA hydrolysis.
Collapse
Affiliation(s)
- Sebastian Motsch
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Peter Tremmel
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
| |
Collapse
|
6
|
Valsangkar VA, Chandrasekaran AR, Zhuo L, Mao S, Lee GW, Kizer M, Wang X, Halvorsen K, Sheng J. Click and photo-release dual-functional nucleic acid nanostructures. Chem Commun (Camb) 2019; 55:9709-9712. [PMID: 31353371 PMCID: PMC6687541 DOI: 10.1039/c9cc03806j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We functionalize nucleic acid nanostructures with click chemistry (for attachment of cargos) and a photocleavable linker (for release). We demonstrate cargo attachment using a fluorescein dye and release using UV trigger from an RNA three-way junction, a DNA star motif and a DNA tetrahedron. Such multifunctional nucleic acid nanostructures have potential in targeted drug delivery.
Collapse
Affiliation(s)
- Vibhav A Valsangkar
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | | | - Lifeng Zhuo
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Song Mao
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Goh Woon Lee
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Megan Kizer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Xing Wang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Ken Halvorsen
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA.
| | - Jia Sheng
- The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA. and Department of Chemistry, University at Albany, State University of New York, Albany, NY 12222, USA.
| |
Collapse
|
7
|
Abstract
The hydrogen peroxide (HP) crucible hypothesis proposed here holds that life began in a localized environment on Earth that was perfused with a flow of hydrogen peroxide from a sustained external source, which powered and mediated molecular evolution and the protocellular RNA world. In this article, we consolidate and review recent evidence, both circumstantial and tested in simulation in our work and in the laboratory in others' work, for its multiple roles in the evolution of the first living systems: (1) it provides a periodic power source as the thiosulfate-hydrogen peroxide (THP) redox oscillator, (2) it may act as an agent of molecular change and evolution and mediator of homochirality, and (3) the THP oscillator, subject to Brownian input perturbations, produces a weighted distribution of output thermal fluctuations that favor polymerization and chemical diversification over chemical degradation and simplification. The hypothesis can help to clarify the hero and villain roles of hydrogen peroxide in cell function, and on the singularity of life: of necessity, life evolved early an armory of catalases, the continuing, and all-pervasive presence of which prevents hydrogen peroxide from accumulating anywhere in sufficient quantities to host a second origin. The HP crucible hypothesis is radical, but based on well-known chemistry and physics, it is eminently testable in the laboratory, and many of our simulations provide recipes for such experiments.
Collapse
Affiliation(s)
- Rowena Ball
- 1 Mathematical Sciences Institute and Research School of Chemistry, Australian National University, Canberra, Australia
| | - John Brindley
- 2 School of Mathematics, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
8
|
Smail BA, Clifton BE, Mizuuchi R, Lehman N. Spontaneous advent of genetic diversity in RNA populations through multiple recombination mechanisms. RNA 2019; 25:453-464. [PMID: 30670484 PMCID: PMC6426292 DOI: 10.1261/rna.068908.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/14/2019] [Indexed: 06/09/2023]
Abstract
There are several plausible abiotic synthetic routes from prebiotic chemical materials to ribonucleotides and even short RNA oligomers. However, for refinement of the RNA World hypothesis to help explain the origins of life on the Earth, there needs to be a manner by which such oligomers can increase their length and expand their sequence diversity. Oligomers longer than at least 10-20 nucleotides would be needed for raw material for subsequent natural selection. Here, we explore spontaneous RNA-RNA recombination as a facile means by which such length and diversity enhancement could have been realized. Motivated by the discovery that RNA oligomers stored for long periods of time in the freezer expand their lengths, we systematically investigated RNA-RNA recombination processes. In addition to one known mechanism, we discovered at least three new mechanisms. In these, one RNA oligomer acts as a splint to catalyze the hybridization of two other oligomers and facilitates the attack of a 5'-OH, a 3'-OH, or a 2'-OH nucleophile of one oligomer onto a target atom of another. This leads to the displacement of one RNA fragment and the production of new recombinant oligomers. We show that this process can explain the spontaneous emergence of sequence complexity, both in vitro and in silico.
Collapse
Affiliation(s)
- Benedict A Smail
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
| | - Bryce E Clifton
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
| | - Ryo Mizuuchi
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
| | - Niles Lehman
- Department of Chemistry, Portland State University, Portland, Oregon 97207, USA
| |
Collapse
|
9
|
Miyagi-Shiohira C, Nakashima Y, Kobayashi N, Kitamura S, Saitoh I, Watanabe M, Noguchi H. Induction of Expandable Adipose-Derived Mesenchymal Stem Cells from Aged Mesenchymal Stem Cells by a Synthetic Self-Replicating RNA. Int J Mol Sci 2018; 19:E3489. [PMID: 30404192 PMCID: PMC6274871 DOI: 10.3390/ijms19113489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/30/2018] [Accepted: 11/01/2018] [Indexed: 12/22/2022] Open
Abstract
Adipose-derived mesenchymal stem cells (ADSCs) have attracted attention due to their potential for use in the treatment of various diseases. However, the self-renewal capacity of ADSCs is restricted and their function diminishes during passage. We previously generated induced tissue-specific stem cells from mouse pancreatic cells using a single synthetic self-replicating Venezuelan Equine Encephalitis (VEE)-reprogramming factor (RF) RNA replicon (SR-RNA) expressing the reprogramming factors POU class 5 homeobox 1 (OCT4), Krueppel-like factor 4 (KLF4), Sex determining region Y-box 2 (SOX2), and Glis Family Zinc Finger 1 (GLIS1). This vector was used to generate induced pluripotent stem (iPS) cells. Here, we applied this SR-RNA vector to generate human iTS cells from aged mesenchymal stem cells (hiTS-M cells) deficient in self-renewal that were derived from adipose tissue. These hiTS-M cells transfected with the SR-RNA vector survived for 15 passages. The hiTS-M cells expressed cell surface markers similar to those of human adipose-derived mesenchymal stem cells (hADSCs) and differentiated into fat cells and osteoblasts. Global gene expression profiling showed that hiTS-M cells were transcriptionally similar to hADSCs. These data suggest that the generation of iTS cells has important implications for the clinical application of autologous stem cell transplantation.
Collapse
Affiliation(s)
- Chika Miyagi-Shiohira
- Department of Regenerative Medicine, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan.
| | - Yoshiki Nakashima
- Department of Regenerative Medicine, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan.
| | - Naoya Kobayashi
- Department of Surgery, Okayama Saidaiji Hospital, Okayama 704-8192, Japan.
| | - Shinji Kitamura
- Department of Nephrology, Rheumatology, Endocrinology and Metabolism, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan.
| | - Issei Saitoh
- Division of Pediatric Dentistry, Graduate School of Medical and Dental Science, Niigata University, Niigata 951-8514, Japan.
| | - Masami Watanabe
- Department of Urology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan.
| | - Hirofumi Noguchi
- Department of Regenerative Medicine, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa 903-0215, Japan.
| |
Collapse
|
10
|
Todisco M, Fraccia TP, Smith GP, Corno A, Bethge L, Klussmann S, Paraboschi EM, Asselta R, Colombo D, Zanchetta G, Clark NA, Bellini T. Nonenzymatic Polymerization into Long Linear RNA Templated by Liquid Crystal Self-Assembly. ACS Nano 2018; 12:9750-9762. [PMID: 30280566 DOI: 10.1021/acsnano.8b05821] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Self-synthesizing materials, in which supramolecular structuring enhances the formation of new molecules that participate to the process, represent an intriguing notion to account for the first appearance of biomolecules in an abiotic Earth. We present here a study of the abiotic formation of interchain phosphodiester bonds in solutions of short RNA oligomers in various states of supramolecular arrangement and their reaction kinetics. We found a spectrum of conditions in which RNA oligomers self-assemble and phase separate into highly concentrated ordered fluid liquid crystal (LC) microdomains. We show that such supramolecular state provides a template guiding their ligation into hundred-bases long chains. The quantitative analysis presented here demonstrates that nucleic acid LC boosts the rate of end-to-end ligation and suppresses the formation of the otherwise dominant cyclic oligomers. These results strengthen the concept of supramolecular ordering as an efficient pathway toward the emergence of the RNA World in the primordial Earth.
Collapse
Affiliation(s)
- Marco Todisco
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | - Tommaso P Fraccia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
- Dipartimento di Scienze Umane e Promozione della Qualità della Vita , Università San Raffaele di Roma , via di Val Cannuta, 247 , I-00166 Roma , Italy
| | - Greg P Smith
- Department of Physics and Soft Materials Research Center , University of Colorado , Boulder , Colorado 80309-0390 , United States
| | - Andrea Corno
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | | | | | - Elvezia M Paraboschi
- Department of Biomedical Sciences , Humanitas University , via Rita Levi Montalcini 4 , Pieve Emanuele, Milano I-20090 , Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences , Humanitas University , via Rita Levi Montalcini 4 , Pieve Emanuele, Milano I-20090 , Italy
- Humanitas Clinical and Research Center , via Alessandro Manzoni 56 , Rozzano, Milano I-20089 , Italy
| | - Diego Colombo
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| | - Noel A Clark
- Department of Physics and Soft Materials Research Center , University of Colorado , Boulder , Colorado 80309-0390 , United States
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale , Università di Milano , via Vanvitelli 32 , 20129 Milano , Italy
| |
Collapse
|
11
|
Abstract
Prebiotic evolution is the stage that is assumed to have taken place prior to the emergence of the first living entities, during which time the abiotic synthesis of monomers, oligomers, and supramolecular systems that led to the hypothesized RNA world occurred. In this Perspective, the success of one-pot Miller-Urey type synthesis of organic compounds is compared with the multipot syntheses developed within the framework of systems chemistry, which attempts to demonstrate that RNA could have been formed directly in the primitive environment. The prebiotic significance of liquid-crystal ordering of nucleic acid oligomers and self-organizing assemblages of RNA and DNA that are formed in the absence of membranes or mineral matrices is also addressed.
Collapse
Affiliation(s)
- Antonio Lazcano
- El Colegio Nacional and Facultad de Ciencias , Universidad Nacional Autónoma de México , Mexico City 04510 , Mexico
| |
Collapse
|
12
|
Palmer CR, Jacobson ME, Fedorova O, Pyle AM, Wilson JT. Environmentally Triggerable Retinoic Acid-Inducible Gene I Agonists Using Synthetic Polymer Overhangs. Bioconjug Chem 2018; 29:742-747. [PMID: 29350913 PMCID: PMC6407425 DOI: 10.1021/acs.bioconjchem.7b00697] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Retinoic acid-inducible gene I (RIG-I) is a cytosolic pattern recognition receptor (PRR) that potently activates antiviral innate immunity upon recognition of 5' triphosphorylated double-stranded RNA (pppRNA). Accordingly, RNA ligands of the RIG-I pathway have recently emerged as promising antiviral agents, vaccine adjuvants, and cancer immunotherapeutics. However, RIG-I is expressed constitutively in virtually all cell types, and therefore administration of RIG-I agonists causes risk for systemic inflammation and possible dose-limiting toxicities. Here, we establish proof-of-concept and initial design criteria for pppRNA prodrugs capable of activating the RIG-I pathway in response to specific environmental stimuli. We show that covalent conjugation of poly(ethylene glycol) (PEG) to the 3' end of the complementary strand, i.e., on the same side but opposite strand as the 5' triphosphate group, can generate a synthetic overhang that prevents RIG-I activation. Additionally, conjugation of PEG through a cleavable linker-here, a reducible disulfide bond-allows for removal of the synthetic overhang and restoration of immunostimulatory activity. Furthermore, we demonstrate that blockade of RIG-I activation via synthetic overhangs is dependent on PEG molecular weight, with a critical molecular weight between 550 and 1000 Da required to inhibit activity. Additionally, we demonstrate that blockade of RIG-I activity is conjugation site-dependent, as ligation of PEG to the opposite end of the RNA did not influence ligand activity. Collectively, this work demonstrates that conjugation of synthetic polymer overhangs to pppRNA through cleavable linkers is a viable strategy for the development of environmentally triggerable RIG-I-targeting prodrugs.
Collapse
Affiliation(s)
- Christian R. Palmer
- Department of Chemical and Biomolecular Engineering; Vanderbilt University Nashville, TN 37235, USA
| | - Max E. Jacobson
- Department of Chemical and Biomolecular Engineering; Vanderbilt University Nashville, TN 37235, USA
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology; Yale University New Haven, CT 06511
| | - Anna M. Pyle
- Department of Molecular, Cellular and Developmental Biology; Yale University New Haven, CT 06511
- Department of Chemistry, Howard Hughes Medical Institute, Yale University
| | - John T. Wilson
- Department of Chemical and Biomolecular Engineering; Vanderbilt University Nashville, TN 37235, USA
- Department of Biomedical Engineering; Vanderbilt University
- Vanderbilt Center for Immunobiology; Vanderbilt University
- Vanderbilt Institute for Infection, Immunology and Inflammation; Vanderbilt University
| |
Collapse
|
13
|
Wu K, Ma C, Deng Z, Fang N, Tang Z, Zhu X, Wang K. Label-free and nicking enzyme-assisted fluorescence signal amplification for RNase H determination based on a G-quadruplexe/thioflavin T complex. Talanta 2018; 182:142-147. [PMID: 29501133 DOI: 10.1016/j.talanta.2018.01.075] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/13/2018] [Accepted: 01/29/2018] [Indexed: 12/21/2022]
Abstract
In this paper, we describe a novel, label-free and nicking enzyme-assisted fluorescence signal amplification strategy that demonstrates to be cost efficient, sensitive, and unique for assaying the RNase H activity and inhibition based on G-quadruplex formation using a thioflavin T (ThT) dye. This novel assay method is able to detect RNase H with a detection limit of 0.03 U /mL and further exhibits a good linearity R2 = 0.9923 at a concentration range of 0.03-1 U/mL under optimized conditions. Moreover, the inhibition effect of gentamycin on the RNase H activity is also studied. This strategy provides a potential tool for the biochemical enzyme analysis and inhibitor screening.
Collapse
Affiliation(s)
- Kefeng Wu
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Changbei Ma
- School of Life Sciences, Central South University, Changsha 410013, China.
| | - Zhiyi Deng
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Ning Fang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Zhenwei Tang
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Xingxing Zhu
- School of Life Sciences, Central South University, Changsha 410013, China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan University, Changsha 410081, China
| |
Collapse
|
14
|
Abstract
A templated RNA synthesis is characterized in which G5'pp5'G accelerates synthesis of A5'pp5'A from pA and chemically activated ImpA precursors. Similar acceleration is not observable in the presence of UppU, CppC, AppG, AppA, or pG alone. Thus, it seems likely that AppA is templated by GppG via a form or forms of G:A base-pairing. AppA also appears, more slowly, via a previously known untemplated second-order chemical route. Such AppA synthesis requires only ordinary near-neutral solutions containing monovalent and divalent salts, and rates are only slightly sensitive to variation in pH. Templated synthesis rates are first order in pA, ImpA, and template GppG; thus third order overall. Therefore, this reaction resembles cross-templating of AppA on poly(U), but is notably slower and less sensitive to temperature. Viewing AppA as a coenzyme analog, GppG templating provides a simpler molecular route, termed para-templating, to encoded chemical functions. Para-templating can also arise from a single, localized nucleobase geosynthetic event which yields purines. It requires only a single backbone-forming chemistry. Thus it may have appeared earlier and served as evolutionary precursor for more complex forms of encoded genetic expression.
Collapse
Affiliation(s)
- Deepa Puthenvedu
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, Colorado 80309-0347, USA
| | - Irene Majerfeld
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, Colorado 80309-0347, USA
| | - Michael Yarus
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Boulder, Colorado 80309-0347, USA
| |
Collapse
|
15
|
Tanpure AA, Balasubramanian S. Synthesis and Multiple Incorporations of 2'-O-Methyl-5-hydroxymethylcytidine, 5-Hydroxymethylcytidine and 5-Formylcytidine Monomers into RNA Oligonucleotides. Chembiochem 2017; 18:2236-2241. [PMID: 28901692 PMCID: PMC5779611 DOI: 10.1002/cbic.201700492] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Indexed: 01/09/2023]
Abstract
The synthesis of 2'-O-methyl-5-hydroxymethylcytidine (hm5 Cm), 5-hydroxymethylcytidine (hm5 C) and 5-formylcytidine (f5 C) phosphoramidite monomers has been developed. Optimisation of mild post-synthetic deprotection conditions enabled the synthesis of RNA containing all four naturally occurring cytosine modifications (hm5 Cm, hm5 C, f5 C plus 5-methylcytosine). Given the considerable interest in RNA modifications and epitranscriptomics, the availability of synthetic monomers and RNAs containing these modifications will be valuable for elucidating their biological function(s).
Collapse
Affiliation(s)
- Arun A. Tanpure
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Shankar Balasubramanian
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research (UK)Cambridge InstituteLi Ka Shing Centre University of CambridgeRobinson WayCambridgeCB2 0REUK
- School of Clinical MedicineUniversity of CambridgeCambridgeCB2 0SPUK
| |
Collapse
|
16
|
Alibakhshi MA, Halman JR, Wilson J, Aksimentiev A, Afonin KA, Wanunu M. Picomolar Fingerprinting of Nucleic Acid Nanoparticles Using Solid-State Nanopores. ACS Nano 2017; 11:9701-9710. [PMID: 28841287 PMCID: PMC5959297 DOI: 10.1021/acsnano.7b04923] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nucleic acid nanoparticles (NANPs) are an emerging class of programmable structures with tunable shape and function. Their promise as tools for fundamental biophysics studies, molecular sensing, and therapeutic applications necessitates methods for their detection and characterization at the single-particle level. In this work, we study electrophoretic transport of individual ring-shaped and cube-shaped NANPs through solid-state nanopores. In the optimal nanopore size range, the particles must deform to pass through, which considerably increases their residence time within the pore. Such anomalously long residence times permit detection of picomolar amounts of NANPs when nanopore measurements are carried out at a high transmembrane bias. In the case of a NANP mixture, the type of individual particle passing through nanopores can be efficiently determined from analysis of a single electrical pulse. Molecular dynamics simulations provide insight into the mechanical barrier to transport of the NANPs and corroborate the difference in the signal amplitudes observed for the two types of particles. Our study serves as a basis for label-free analysis of soft programmable-shape nanoparticles.
Collapse
Affiliation(s)
| | - Justin R. Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - James Wilson
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana—Champaign, Urbana, Illinois 61801, United States
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Meni Wanunu
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| |
Collapse
|
17
|
Aldersley MF, Joshi PC, Huang Y. The Comparison of Hydrochloric Acid and Phosphoric Acid Treatments in the Preparation of Montmorillonite Catalysts for RNA Synthesis. ORIGINS LIFE EVOL B 2017; 47:297-304. [PMID: 28210992 DOI: 10.1007/s11084-017-9533-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/26/2017] [Indexed: 11/27/2022]
Abstract
The treatment of clay minerals with a preliminary acid wash and titration to pH 7 has proven to generate catalysts for the most interesting of oligomerization reactions in which activated RNA-nucleotides generate oligomers up to 40-mers. Significantly, not all clay minerals become catalytic following this treatment and none are catalytic in the absence of such treatment. The washing procedure has been modified and explored further using phosphoric acid and the outcomes are compared to those obtained when clay samples are prepared following a hydrochloric acid wash.
Collapse
Affiliation(s)
- Michael Frank Aldersley
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
| | - Prakash C Joshi
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Yixing Huang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| |
Collapse
|
18
|
Abstract
Long structured RNAs are useful biochemical and biological tools. They are usually prepared enzymatically, but this precludes their site-specific modification with functional groups for chemical biology studies. One solution is to perform solid-phase synthesis of multiple RNAs loaded with 5'-terminal phosphate groups, so that RNAs can be concatenated using template ligation reactions. However, there are currently no readily available reagents suitable for the incorporation of the phosphate group into long RNAs by solid-phase synthesis. Here we describe an easy-to-prepare phosphoramidite reagent suitable for the chemical introduction of 5'-terminal phosphate groups into long RNAs. The phosphate is protected by a dinitrobenzhydryl group that serves as an essential lipophilic group for the separation of oligonucleotide by-products. The phosphate is unmasked quantitatively by brief UV irradiation. We demonstrate the value of this reagent in the preparation of a library of long structured RNAs that are site-specifically modified with functional groups.
Collapse
Affiliation(s)
- Ugo Pradère
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH Zürich8093ZürichSwitzerland
| | - François Halloy
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH Zürich8093ZürichSwitzerland
| | - Jonathan Hall
- Institute of Pharmaceutical SciencesDepartment of Chemistry and Applied BiosciencesETH Zürich8093ZürichSwitzerland
| |
Collapse
|
19
|
Abstract
5-Hydroxymethylcytosine is an epigenetic base modification that is part of the demethylation pathway of 5-methylcytosine in DNA. 5-Methylcytosine is iteratively oxidized to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxycytosine by enzymes of the TET protein family. Since the discovery of 5-hydroxymethylcytosine also in RNA its role in regulatory processes and metabolism remains elusive. To gain more insight into the function of RNA containing 5-hydroxymethylcytidine, innovative and interdisciplinary approaches are required. In this context, synthetic oligoribonucleotides containing 5-hyroxymethylcytidine are an inevitable tool. Therefore, in this chapter, we present the efficient synthesis of RNA oligonucleotides containing 5-hydroxymethylcytosine by solid-phase synthesis. The incorporation of the modified cytosine derivative into RNA is compatible with standard phosphoramidite-based synthesis procedures of oligoribonucleotides.
Collapse
Affiliation(s)
- Christian Riml
- Institute of Organic Chemistry and Center for Molecular Biosciences, CMBI, Leopold-Franzens University, Innrain 80-82, 6020, Innbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences, CMBI, Leopold-Franzens University, Innrain 80-82, 6020, Innbruck, Austria.
| |
Collapse
|
20
|
Kim H, Lee JB. Formation of RNA Beads from Various DNA Nanoring Structures. J Nanosci Nanotechnol 2016; 16:4464-4468. [PMID: 27483774 DOI: 10.1166/jnn.2016.10988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
By taking advantages of rolling circle transcription, one of the powerful methods to overcome the instability of RNA, we successfully synthesized RNA particles having high copy numbers of RNA strands. To examine dependence of RNA particle formation to template circular DNA strands, we synthesized RNA beads with 65-nt, 92-nt and 200-nt DNA nanoring structures as template circular DNA. Our conclusion is that characteristics of RNA beads could be controlled with various template circular DNA for RCT. It is feasible that our RNA beads could be used for RNAzyme-based metal sensors such as aqueous lead ion sensing. In this case, we expect that multi-metal ion detection would be possible by using 200-nt circular DNA bearing multiple desired functions as a template for RNA bead formation. Furthermore, certain features of RNA beads such as sensitivity to nuclease digestion and maximum loading amount of drugs when used as a carrier are expected to be further adjusted by choosing appropriate porosity and size.
Collapse
|
21
|
Zhao C, Rajashankar KR, Marcia M, Pyle AM. Crystal structure of group II intron domain 1 reveals a template for RNA assembly. Nat Chem Biol 2015; 11:967-72. [PMID: 26502156 PMCID: PMC4651773 DOI: 10.1038/nchembio.1949] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 09/18/2015] [Indexed: 12/17/2022]
Abstract
Although the importance of large noncoding RNAs is increasingly appreciated, our understanding of their structures and architectural dynamics remains limited. In particular, we know little about RNA folding intermediates and how they facilitate the productive assembly of RNA tertiary structures. Here, we report the crystal structure of an obligate intermediate that is required during the earliest stages of group II intron folding. Composed of domain 1 from the Oceanobacillus iheyensis group II intron (266 nucleotides), this intermediate retains native-like features but adopts a compact conformation in which the active site cleft is closed. Transition between this closed and the open (native) conformation is achieved through discrete rotations of hinge motifs in two regions of the molecule. The open state is then stabilized by sequential docking of downstream intron domains, suggesting a 'first come, first folded' strategy that may represent a generalizable pathway for assembly of large RNA and ribonucleoprotein structures.
Collapse
Affiliation(s)
- Chen Zhao
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Kanagalaghatta R. Rajashankar
- NE-CAT and Dept. of Chemistry and Chemical Biology, Cornell University Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439
| | - Marco Marcia
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Anna Marie Pyle
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| |
Collapse
|
22
|
Tago N, Katolik A, Clark NE, Montemayor EJ, Seio K, Sekine M, Hart PJ, Damha MJ. Design, Synthesis, and Properties of Phosphoramidate 2',5'-Linked Branched RNA: Toward the Rational Design of Inhibitors of the RNA Lariat Debranching Enzyme. J Org Chem 2015; 80:10108-18. [PMID: 26378468 PMCID: PMC4749351 DOI: 10.1021/acs.joc.5b01719] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Two RNA fragments linked by means of a 2',5' phosphodiester bridge (2' hydroxyl of one fragment connected to the 5' hydroxyl of the other) constitute a class of nucleic acids known as 2'-5' branched RNAs (bRNAs). In this report we show that bRNA analogues containing 2'-5' phosphoramidate linkages (bN-RNAs) inhibit the lariat debranching enzyme, a 2',5'-phosphodiesterase that has recently been implicated in neurodegenerative diseases associated with aging. bN-RNAs were efficiently generated using automated solid-phase synthesis and suitably protected branchpoint building blocks. Two orthogonally removable groups, namely the 4-monomethoxytrityl (MMTr) group and the fluorenylmethyl-oxycarbonyl (Fmoc) groups, were evaluated as protecting groups of the 2' amino functionality. The 2'-N-Fmoc methodology was found to successfully produce bN-RNAs on solid-phase oligonucleotide synthesis. The synthesized bN-RNAs resisted hydrolysis by the lariat debranching enzyme (Dbr1) and, in addition, were shown to attenuate the Dbr1-mediated hydrolysis of native bRNA.
Collapse
Affiliation(s)
- Nobuhiro Tago
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama, Kanagawa, 226-8501, Japan
| | - Adam Katolik
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| | - Nathaniel E. Clark
- Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX 78229, United States
| | - Eric J. Montemayor
- Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX 78229, United States
- Departments of Biochemistry and Biomolecular Chemistry, University of Wisconsin-Madison, 433 Babcock Dr., Madison, WI 53706, United States
| | - Kohji Seio
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama, Kanagawa, 226-8501, Japan
| | - Mitsuo Sekine
- Department of Life Science, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama, Kanagawa, 226-8501, Japan
| | - P. John Hart
- Department of Veterans Affairs, South Texas Veterans Health Care System, San Antonio, TX 78229, United States
- Department of Biochemistry, University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229, United States
| | - Masad J. Damha
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montréal, Québec H3A 0B8, Canada
| |
Collapse
|
23
|
Abstract
Microbial nucleic acids have been described as important activators of human innate immune responses by triggering so-called pattern recognition receptors (PRRs) that are expressed on innate immune cells, including plasmacytoid dendritic cells and monocytes. Although host and microbial nucleic acids share pronounced chemical and structural similarities, they significantly differ in their posttranscriptional modification profile, allowing the host to discriminate between self and nonself. In this regard, ribose 2'-O-methylation has been discovered as suppressor of RNA-induced PRR activation. Although 2'-O-methylation occurs with higher frequencies in eukaryotic than in prokaryotic RNA, the immunosuppressive properties of 2'-O-methylated nucleotides may be misused by certain bacteria as immune evasion mechanism. In the course of identifying inhibitory RNA modifications, our groups have synthesized and comparatively analyzed a series of differentially modified RNAs, so-called modivariants, for their immune stimulatory capacities. In this chapter, we will detail the protocols for the design and synthesis of RNA modivariants by molecular cut-and-paste techniques (referred to as molecular surgery) and describe testing of their immune stimulatory properties upon transfection into peripheral blood mononuclear cells.
Collapse
Affiliation(s)
- Tatjana Eigenbrod
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
| | - Patrick Keller
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Steffen Kaiser
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Katharina Rimbach
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
| | - Alexander H Dalpke
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg-University of Mainz, Mainz, Germany.
| |
Collapse
|
24
|
Luo Y, Sintim HO, Dayie TK. Synthesis of a biotinylated photocleavable nucleotide monophosphate for the preparation of natively folded RNAs. Methods Enzymol 2015; 549:115-31. [PMID: 25432747 DOI: 10.1016/b978-0-12-801122-5.00006-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
RNAs are involved in many functional roles in the cell, and this functional diversity is predicated on RNAs adopting requisite three-dimensional architectures. Preparing such "natively folded" RNAs with a homogeneous population is sometimes problematic for structural or enzymatic studies. Yet, standard methods for RNA preparations denature the RNA and create a heterogeneous population of conformers. Therefore, preparation of "natively folded" RNAs without going through the process of denaturing and refolding is important to obtain maximal biological function. Here, we present a simple strategy using "click" chemistry to couple biotin to a "caged" photocleavable (PC) guanosine monophosphate (GMP) in high yield. This biotin-PC-GMP is readily accepted by T7 RNA polymerase to transcribe "natively folded" RNAs ranging in size from 27 to 493 nucleotides. This facile strategy allows efficient biotinylation of RNA and provides a traceless means to remove the biotin after the purification. Such preparation of natively folded RNAs should benefit biophysical and therapeutic applications.
Collapse
Affiliation(s)
- Yiling Luo
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Herman O Sintim
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA.
| | - T Kwaku Dayie
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA; Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland, USA.
| |
Collapse
|
25
|
Abstract
Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid-like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure-property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored.
Collapse
Affiliation(s)
- H. James Cleaves
- Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, Tokyo, Japan
- Institute for Advanced Study, Princeton, New Jersey, USA
- Blue Marble Space Institute of Science, Washington, DC, USA
- Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Markus Meringer
- German Aerospace Center (DLR), Earth Observation Center (EOC), Oberpfaffenhofen-Wessling, Germany
| | - Jay Goodwin
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
| |
Collapse
|
26
|
Burcar BT, Barge LM, Trail D, Watson EB, Russell MJ, McGown LB. RNA Oligomerization in Laboratory Analogues of Alkaline Hydrothermal Vent Systems. Astrobiology 2015; 15:509-522. [PMID: 26154881 DOI: 10.1089/ast.2014.1280] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Discovering pathways leading to long-chain RNA formation under feasible prebiotic conditions is an essential step toward demonstrating the viability of the RNA World hypothesis. Intensive research efforts have provided evidence of RNA oligomerization by using circular ribonucleotides, imidazole-activated ribonucleotides with montmorillonite catalyst, and ribonucleotides in the presence of lipids. Additionally, mineral surfaces such as borates, apatite, and calcite have been shown to catalyze the formation of small organic compounds from inorganic precursors (Cleaves, 2008 ), pointing to possible geological sites for the origins of life. Indeed, the catalytic properties of these particular minerals provide compelling evidence for alkaline hydrothermal vents as a potential site for the origins of life since, at these vents, large metal-rich chimney structures can form that have been shown to be energetically favorable to diverse forms of life. Here, we test the ability of iron- and sulfur-rich chimneys to support RNA oligomerization reactions using imidazole-activated and non-activated ribonucleotides. The chimneys were synthesized in the laboratory in aqueous "ocean" solutions under conditions consistent with current understanding of early Earth. Effects of elemental composition, pH, inclusion of catalytic montmorillonite clay, doping of chimneys with small organic compounds, and in situ ribonucleotide activation on RNA polymerization were investigated. These experiments, under certain conditions, showed successful dimerization by using unmodified ribonucleotides, with the generation of RNA oligomers up to 4 units in length when imidazole-activated ribonucleotides were used instead. Elemental analysis of the chimney precipitates and the reaction solutions showed that most of the metal cations that were determined were preferentially partitioned into the chimneys.
Collapse
Affiliation(s)
- Bradley T Burcar
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 2 Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York
| | - Laura M Barge
- 3 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
- 4 NASA Astrobiology Institute , Icy Worlds
| | - Dustin Trail
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 5 Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute School of Science , Troy, New York
| | - E Bruce Watson
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 5 Department of Earth and Environmental Sciences, Rensselaer Polytechnic Institute School of Science , Troy, New York
| | - Michael J Russell
- 3 NASA Jet Propulsion Laboratory, California Institute of Technology , Pasadena, California
- 4 NASA Astrobiology Institute , Icy Worlds
| | - Linda B McGown
- 1 New York Center for Astrobiology, Rensselaer Polytechnic Institute , Troy, New York
- 2 Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York
| |
Collapse
|
27
|
Gaffney PRJ, Kim JF, Valtcheva IB, Williams GD, Anson MS, Buswell AM, Livingston AG. Liquid-Phase Synthesis of 2'-Methyl-RNA on a Homostar Support through Organic-Solvent Nanofiltration. Chemistry 2015; 21:9535-43. [PMID: 26012874 PMCID: PMC4517100 DOI: 10.1002/chem.201501001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Indexed: 01/04/2023]
Abstract
Due to the discovery of RNAi, oligonucleotides (oligos) have re-emerged as a major pharmaceutical target that may soon be required in ton quantities. However, it is questionable whether solid-phase oligo synthesis (SPOS) methods can provide a scalable synthesis. Liquid-phase oligo synthesis (LPOS) is intrinsically scalable and amenable to standard industrial batch synthesis techniques. However, most reported LPOS strategies rely upon at least one precipitation per chain extension cycle to separate the growing oligonucleotide from reaction debris. Precipitation can be difficult to develop and control on an industrial scale and, because many precipitations would be required to prepare a therapeutic oligonucleotide, we contend that this approach is not viable for large-scale industrial preparation. We are developing an LPOS synthetic strategy for 2'-methyl RNA phosphorothioate that is more amenable to standard batch production techniques, using organic solvent nanofiltration (OSN) as the critical scalable separation technology. We report the first LPOS-OSN preparation of a 2'-Me RNA phosphorothioate 9-mer, using commercial phosphoramidite monomers, and monitoring all reactions by HPLC, (31)P NMR spectroscopy and MS.
Collapse
Affiliation(s)
- Piers R J Gaffney
- Department of Chemical Engineering, Imperial CollegeSouth Kensington Campus, London, SW7 2AZ (UK) E-mail:
| | - Jeong F Kim
- Department of Chemical Engineering, Imperial CollegeSouth Kensington Campus, London, SW7 2AZ (UK) E-mail:
| | - Irina B Valtcheva
- Department of Chemical Engineering, Imperial CollegeSouth Kensington Campus, London, SW7 2AZ (UK) E-mail:
| | - Glynn D Williams
- GSK Medicines Research CentreGunnels Wood Road, Stevenage, Herts, SG1 2NY (UK)
| | - Mike S Anson
- GSK Medicines Research CentreGunnels Wood Road, Stevenage, Herts, SG1 2NY (UK)
| | - Andrew M Buswell
- GSK Medicines Research CentreGunnels Wood Road, Stevenage, Herts, SG1 2NY (UK)
| | - Andrew G Livingston
- Department of Chemical Engineering, Imperial CollegeSouth Kensington Campus, London, SW7 2AZ (UK) E-mail:
| |
Collapse
|
28
|
|
29
|
Martínez-Montero S, Deleavey GF, Dierker-Viik A, Lindovska P, Ilina T, Portella G, Orozco M, Parniak MA, González C, Damha MJ. Synthesis and properties of 2'-deoxy-2',4'-difluoroarabinose-modified nucleic acids. J Org Chem 2015; 80:3083-91. [PMID: 25723361 PMCID: PMC4484724 DOI: 10.1021/jo502948t] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We report the synthesis, thermal stability, and RNase H substrate activity of 2'-deoxy-2',4'-difluoroarabino-modified nucleic acids. 2'-Deoxy-2',4'-difluoroarabinouridine (2,'4'-diF-araU) was prepared in a stereoselective way in six steps from 2'-deoxy-2'-fluoroarabinouridine (2'-F-araU). NMR analysis and quantum mechanical calculations at the nucleoside level reveal that introduction of 4'-fluorine introduces a strong bias toward the North conformation, despite the presence of the 2'-βF, which generally steers the sugar pucker toward the South/East conformation. Incorporation of the novel monomer into DNA results on a neutral to slightly stabilizing thermal effect on DNA-RNA hybrids. Insertion of 2',4'-diF-araU nucleotides in the DNA strand of a DNA-RNA hybrid decreases the rate of both human and HIV reverse transcriptase-associated RNase H-mediated cleavage of the complement RNA strand compared to that for an all-DNA strand or a DNA strand containing the corresponding 2'-F-araU nucleotide units, consistent with the notion that a 4'-fluorine in 2'-F-araU switches the preferred sugar conformation from DNA-like (South/East) to RNA-like (North).
Collapse
Affiliation(s)
- Saúl Martínez-Montero
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Glen F. Deleavey
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Arden Dierker-Viik
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Petra Lindovska
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| | - Tatiana Ilina
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania 15219-3143, United States
| | - Guillem Portella
- Joint IRB–BSC program on Computational Biology, Institute for Research in Biomedicine, Barcelona Supercomputing Center, and Department of Biochemistry, University of Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Modesto Orozco
- Joint IRB–BSC program on Computational Biology, Institute for Research in Biomedicine, Barcelona Supercomputing Center, and Department of Biochemistry, University of Barcelona, Baldiri Reixac 10-12, 08028 Barcelona, Spain
| | - Michael A. Parniak
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania 15219-3143, United States
| | - Carlos González
- Instituto de Química Física Rocasolano, CSIC, C/Serrano 119, 28006 Madrid, Spain
| | - Masad J. Damha
- Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, QC H3A 0B8, Canada
| |
Collapse
|
30
|
Abstract
RNA can self-assemble into complex structures through base pairing, as well as encode information and bind with proteins to induce enzymatic activity. Furthermore, RNA can possess intrinsic enzymatic-like (ribozymatic) activity, a property that, if necessary, can be activated only upon the binding of a small molecule or another RNA (as is the case in aptazymes). As such, RNA could be of use in nanotechnology as a programmable polymer capable of self-assembling into complex topological structures. In this chapter we describe a method for designing advanced topological structures using self-circulating RNA, exemplified by three tiers of topologically manipulated self-assembling synthetic RNA systems. The first tier of topological manipulation, the RNA knot is a physically locked structure, formed by circularizing one monomer of knotted single-stranded RNA left with loose ends (an "open" knot). The second tier, a two interlocking ring system, is made by interlocking two circular RNA components: a circular RNA target, and an RNA lasso designed to intercalate the target before circularizing. The third tier naturally extends this system into a string of topologically locked circular RNA molecules (an RNA chain). We detail the methodology used for designing such topologically complex RNAs, including computational predictions of secondary structure, and where appropriate, RNA-RNA interactions, illustrated by examples. We then describe the experimental methods used for characterizing such structures, and provide sequences of building blocks that can be used for topological manipulation of RNA.
Collapse
Affiliation(s)
- Jack Hassall
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | | | | | | |
Collapse
|
31
|
Abstract
RNA nanotechnology encompasses the use of RNA as a construction material to build homogeneous nanostructures by bottom-up self-assembly with defined size, structure, and stoichiometry; this pioneering concept demonstrated in 1998 (Guo et al., Molecular Cell 2:149-155, 1998; featured in Cell) has emerged as a new field that also involves materials engineering and synthetic structural biology (Guo, Nature Nanotechnology 5:833-842, 2010). The field of RNA nanotechnology has skyrocketed over the last few years, as evidenced by the burst of publications in prominent journals on RNA nanostructures and their applications in nanomedicine and nanotechnology. Rapid advances in RNA chemistry, RNA biophysics, and RNA biology have created new opportunities for translating basic science into clinical practice. RNA nanotechnology holds considerable promise in this regard. Increased evidence also suggests that substantial part of the 98.5 % of human genome (Lander et al. Nature 409:860-921, 2001) that used to be called "junk DNA" actually codes for noncoding RNA. As we understand more on how RNA structures are related to function, we can fabricate synthetic RNA nanoparticles for the diagnosis and treatment of diseases. This chapter provides a brief overview of the field regarding the design, construction, purification, and characterization of RNA nanoparticles for diverse applications in nanotechnology and nanomedicince.
Collapse
Affiliation(s)
- Farzin Haque
- Nanobiotechnology Center, Markey Cancer Center, Departmentof Pharmaceutical Sciences, University of Kentucky, 789 S Limestone Ave, 576 Biopharm Complex, Lexington, KY, 40536, USA,
| | | |
Collapse
|
32
|
Abstract
Click chemistry has provided us with access to DNA and RNA analogues with non-natural triazole internucleoside linkages. The bond periodicity of the oligonucleotides was designed to enforce duplex formation with natural congeners, and the non-cleavable linkages protect the oligomers against nuclease digestion. This account reviews the progress of the triazole-linked analogues over the past five years. Reinforced by their synthetic robustness, these analogues may find various utilities as tools for exploratory research.
Collapse
|
33
|
Abstract
This unit describes a highly effective method to produce 5'-O-DMT-2'-O-TBS mononucleosides selectively using a small organic catalyst. This methodology avoids the tedious protection/deprotection strategy necessary to differentiate the 2'- and 3'-hydroxyl groups in a ribonucleoside. The catalyst was synthesized in two steps, starting from the condensation of valinol and cyclopentyl aldehyde, followed by anionic addition of N-methylimidazole. Ring closure of the amino alcohol with N,N-dimethylformamide dimethyl acetal in methanol furnishes the catalyst. All four 2'-O-TBS protected mono-nucleosides, U, A(Bz), G(Ib), and C(Ac), were produced in a single step using 10 to 20 mol% of the catalyst at room temperature with excellent yields and selectivity. Further transformation to phosphoramidite demonstrates the utility of this protocol in the preparation of monomers useful for automated synthesis of RNA.
Collapse
Affiliation(s)
- Sunggi Lee
- Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467-3860, United States
| | - Thomas P. Blaisdell
- Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467-3860, United States
| | - Pinar Kasaplar
- Institute of Chemical Research of Catalonia, Av. Paisos Catalans 16, 43007 Tarragona, Spain
| | - Xixi Sun
- Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467-3860, United States
| | - Kian L. Tan
- Boston College, 2609 Beacon Street, Chestnut Hill, Massachusetts 02467-3860, United States
| |
Collapse
|
34
|
Afonin K, Kasprzak WK, Bindewald E, Kireeva M, Viard M, Kashlev M, Shapiro BA. In silico design and enzymatic synthesis of functional RNA nanoparticles. Acc Chem Res 2014; 47:1731-41. [PMID: 24758371 PMCID: PMC4066900 DOI: 10.1021/ar400329z] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Indexed: 12/25/2022]
Abstract
CONSPECTUS: The use of RNAs as scaffolds for biomedical applications has several advantages compared with other existing nanomaterials. These include (i) programmability, (ii) precise control over folding and self-assembly, (iii) natural functionalities as exemplified by ribozymes, riboswitches, RNAi, editing, splicing, and inherent translation and transcription control mechanisms, (iv) biocompatibility, (v) relatively low immune response, and (vi) relatively low cost and ease of production. We have tapped into several of these properties and functionalities to construct RNA-based functional nanoparticles (RNA NPs). In several cases, the structural core and the functional components of the NPs are inherent in the same construct. This permits control over the spatial disposition of the components, intracellular availability, and precise stoichiometry. To enable the generation of RNA NPs, a pipeline is being developed. On one end, it encompasses the rational design and various computational schemes that promote design of the RNA-based nanoconstructs, ultimately producing a set of sequences consisting of RNA or RNA-DNA hybrids, which can assemble into the designed construct. On the other end of the pipeline is an experimental component, which takes the produced sequences and uses them to initialize and characterize their proper assembly and then test the resulting RNA NPs for their function and delivery in cell culture and animal models. An important aspect of this pipeline is the feedback that constantly occurs between the computational and the experimental parts, which synergizes the refinement of both the algorithmic methodologies and the experimental protocols. The utility of this approach is depicted by the several examples described in this Account (nanocubes, nanorings, and RNA-DNA hybrids). Of particular interest, from the computational viewpoint, is that in most cases, first a three-dimensional representation of the assembly is produced, and only then are algorithms applied to generate the sequences that will assemble into the designated three-dimensional construct. This is opposite to the usual practice of predicting RNA structures from a given sequence, that is, the RNA folding problem. To be considered is the generation of sequences that upon assembly have the proper intra- or interstrand interactions (or both). Of particular interest from the experimental point of view is the determination and characterization of the proper thermodynamic, kinetic, functionality, and delivery protocols. Assembly of RNA NPs from individual single-stranded RNAs can be accomplished by one-pot techniques under the proper thermal and buffer conditions or, potentially more interestingly, by the use of various RNA polymerases that can promote the formation of RNA NPs cotransciptionally from specifically designed DNA templates. Also of importance is the delivery of the RNA NPs to the cells of interest in vitro or in vivo. Nonmodified RNAs rapidly degrade in blood serum and have difficulties crossing biological membranes due to their negative charge. These problems can be overcome by using, for example, polycationic lipid-based carriers. Our work involves the use of bolaamphiphiles, which are amphipathic compounds with positively charged hydrophilic head groups at each end connected by a hydrophobic chain. We have correlated results from molecular dynamics computations with various experiments to understand the characteristics of such delivery agents.
Collapse
Affiliation(s)
- Kirill
A. Afonin
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Wojciech K. Kasprzak
- Basic
Science Program, Leidos Biomedical Research,
Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Eckart Bindewald
- Basic
Science Program, Leidos Biomedical Research,
Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Maria Kireeva
- Gene
Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Mathias Viard
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
- Basic
Science Program, Leidos Biomedical Research,
Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
| | - Mikhail Kashlev
- Gene
Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Bruce A. Shapiro
- Basic
Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| |
Collapse
|
35
|
Goldeck M, Tuschl T, Hartmann G, Ludwig J. Efficient solid-phase synthesis of pppRNA by using product-specific labeling. Angew Chem Int Ed Engl 2014; 53:4694-8. [PMID: 24668741 DOI: 10.1002/anie.201400672] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Indexed: 12/14/2022]
Abstract
A novel solid-phase synthesis and purification strategy for 5'-triphosphate oligonucleotides by using lipophilic tagging of the triphosphate moiety is reported. This is based on triphosphate synthesis with 5'-O-cyclotriphosphate intermediates, whereby a lipophilic tag, such as decylamine, is introduced during the ring-opening reaction to give a linear gamma-phosphate-tagged species. This method enables the highly efficient synthesis of 5'-triphosphorylated RNA derivatives and their gamma-phosphate-substituted analogues and will especially facilitate the advancement of therapeutic approaches that make use of 5'-triphosphate oligonucleotides as potent activators of the cytosolic immune sensor RIG-I.
Collapse
Affiliation(s)
- M Goldeck
- Institute for Clinical Chemistry & Clinical Pharmacology, University Hospital Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn (Germany)
| | | | | | | |
Collapse
|
36
|
Xu J, Duffy CD, Chan CKW, Sutherland JD. Solid-phase synthesis and hybrization behavior of partially 2'/3'-O-acetylated RNA oligonucleotides. J Org Chem 2014; 79:3311-26. [PMID: 24666354 PMCID: PMC4323357 DOI: 10.1021/jo5002824] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Indexed: 11/30/2022]
Abstract
Synthesis of partially 2'/3'-O-acetylated oligoribonucleotides has been accomplished by using a 2'/3'-O-acetyl orthogonal protecting group strategy in which non-nucleophilic strong-base (DBU) labile nucleobase protecting groups and a UV-light cleavable linker were used. Strong-base stability of the photolabile linker allowed on-column nucleobase and phosphate deprotection, followed by a mild cleavage of the acetylated oligonucleotides from the solid support with UV light. Two 17nt oligonucleotides, which were synthesized possessing one specific internal 2'- or 3'-acetyl group, were used as synthetic standards in a recent report from this laboratory detailing the prebiotically plausible ligation of RNA oligonucleotides. In order to further investigate the effect of 2'/3'-O-acetyl groups on the stability of RNA duplex structure, two complementary bis-acetylated RNA oligonucleotides were also expediently obtained with the newly developed protocols. UV melting curves of 2'-O-acetylated RNA duplexes showed a consistent ~3.1 °C decrease in Tm per 2'-O-acetyl group.
Collapse
Affiliation(s)
- Jianfeng Xu
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
| | - Colm D. Duffy
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
| | - Christopher K. W. Chan
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
| | - John D. Sutherland
- Medical Research Council
Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.
| |
Collapse
|
37
|
Kasuya T, Hori S, Hiramatsu H, Yanagimoto T. Highly accurate synthesis of the fully 2'-fluoro-modified oligonucleotide by Therminator DNA polymerases. Bioorg Med Chem Lett 2014; 24:2134-6. [PMID: 24703229 DOI: 10.1016/j.bmcl.2014.03.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/07/2014] [Accepted: 03/13/2014] [Indexed: 02/03/2023]
Abstract
Oligonucleotides composed of natural nucleotides are inapplicable for biotechnical and therapeutic use due to its instability under biological conditions. Therminator DNA polymerases, mutant DNA polymerases of thermophilic marine archaea, show that they can efficiently synthesize fully 2'-fluoro-modified (2'F-) oligonucleotides. Furthermore, the sequence analysis reveals that the oligonucleotide sequence is highly accurate, especially the fidelity of a 2'F-oligonucleotide synthesized by Therminator II is more accurate than that of natural RNA synthesized by conventional RNA polymerase. These finding would be helpful for the synthesis of chemically modified oligonucleotides, for the use of biotechnical or medical applications.
Collapse
Affiliation(s)
- Takeshi Kasuya
- Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Shinichiro Hori
- Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Hisanao Hiramatsu
- Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan
| | - Toru Yanagimoto
- Innovative Drug Discovery Research Laboratories, Shionogi & Co., Ltd., 3-1-1, Futaba-cho, Toyonaka, Osaka 561-0825, Japan.
| |
Collapse
|
38
|
Abstract
We describe in this Minireview the synthesis, properties, and applications of artificial genetic sets built from base pairs that are larger than the natural Watson-Crick architecture. Such designed systems are being explored by several research groups to investigate basic chemical questions regarding the functions of the genetic information storage systems and thus of the origin and evolution of life. For example, is the terrestrial DNA structure the only viable one, or can other architectures function as well? Working outside the constraints of purine-pyrimidine geometry provides more chemical flexibility in design, and the added size confers useful properties such as high binding affinity and helix stability as well as fluorescence. These features are useful for the investigation of fundamental biochemical questions as well as in the development of new biotechnological, biomedical, and nanostructural tools and methods.
Collapse
Affiliation(s)
- Malte Winnacker
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
| | - Eric T. Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305 (USA)
| |
Collapse
|
39
|
Graifer D, Karpova G. General approach for introduction of various chemical labels in specific RNA locations based on insertion of amino linkers. Molecules 2013; 18:14455-69. [PMID: 24287984 PMCID: PMC6269657 DOI: 10.3390/molecules181214455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/12/2013] [Accepted: 11/18/2013] [Indexed: 01/06/2023] Open
Abstract
Introduction of reporter groups at designed RNA sites is a widely accepted approach to gain information about the molecular environment of RNAs in their complexes with other biopolymers formed during various cellular processes. A general approach to obtain RNAs bearing diverse reporter groups at designed locations is based on site-specific insertion of groups containing primary aliphatic amine functions (amino linkers) with their subsequent selective derivatization by appropriate chemicals. This article is a brief review on methods for site-specific introduction of amino linkers in different RNAs. These methods comprise: (i) incorporation of a nucleoside carrying an amino-linker or a function that can be substituted with it into oligoribonucleotides in the course of their chemical synthesis; (ii) assembly of amino linker-containing RNAs from short synthetic fragments via their ligation; (iii) synthesis of amino linker-modified RNAs using T7 RNA polymerase; (iv) insertion of amino linkers into unmodified RNAs at functional groups of a certain type such as the 5'-phosphates and N7 of guanosine residues and (v) introduction of an amino linker into long highly structured RNAs exploiting an approach based on sequence-specific modification of nucleic acids. Particular reporter groups used for derivatization of amino linker-containing RNAs together with types of RNA derivatives obtained and fields of their application are presented.
Collapse
Affiliation(s)
- Dmitri Graifer
- Laboratory of Ribosome Structure and Functions, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospect Lavrentieva 8, Novosibirsk 630090, Russia.
| | | |
Collapse
|
40
|
Roy S, Caruthers M. Synthesis of DNA/RNA and their analogs via phosphoramidite and H-phosphonate chemistries. Molecules 2013; 18:14268-84. [PMID: 24252996 PMCID: PMC6270087 DOI: 10.3390/molecules181114268] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/08/2013] [Accepted: 11/08/2013] [Indexed: 11/24/2022] Open
Abstract
The chemical synthesis of DNA and RNA is universally carried out using nucleoside phosphoramidites or H-phosphonates as synthons. This review focuses on the phosphorus chemistry behind these synthons and how it has been developed to generate procedures whereby yields per condensation approach 100% with very few side products. Additionally the synthesis and properties of certain DNA and RNA analogs that are modified at phosphorus will also be discussed. These analogs include boranephosphonates, metallophosphonates, and alkylboranephosphines.
Collapse
Affiliation(s)
- Subhadeep Roy
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
| | | |
Collapse
|
41
|
Cieślak J, Ausín C, Grajkowski A, Beaucage SL. 2'-Hydroxy protection of ribonucleosides as 2-cyano-2,2-dimethylethanimine-N-oxymethyl ethers in solid-phase synthesis of RNA sequences. Curr Protoc Nucleic Acid Chem 2013; 54:3.22.1-3.22.28. [PMID: 24510797 DOI: 10.1002/0471142700.nc0322s54] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The reaction of 2'-O-aminooxymethylribonucleosides with 2-cyano-2-methyl propanal leads to the formation of stable and yet reversible 2'-O-(2-cyano-2,2-dimethylethanimine-N-oxymethyl)ribonucleosides in post-purification yields of 54% to 82%. Phenoxyacetylation of the exocyclic amino functions of these ribonucleosides proceeds in yields of 74% to 89%, and subsequent 5'-O-dimethoxytritylation and 3'-O-phosphitylation of the corresponding N-phenoxyacetylated ribonucleosides provide the fully protected ribonucleoside phosphoramidite monomers in isolated yields of 69% to 88%. These ribonucleoside phosphoramidites are employed in solid-phase synthesis of three chimeric RNA sequences, each differing in purine/pyrimidine content. The stepwise coupling efficiency of the ribonucleoside phosphoramidites (as 0.15 M solutions in acetonitrile) averages 99% over a coupling time of 180 s when 5-benzylthio-1H-tetrazole is used as an activator. Upon completion of RNA chain assembly, removal of the nucleobase- and phosphate-protecting groups and release of sequences from the solid support are carried out under standard basic conditions. Finally, the 2'-O-(2-cyano-2,2-dimethylethanimine-N-oxymethyl) protective groups are cleaved from the RNA sequences by treatment with 0.5 M tetra-n-butylammonium fluoride in dry DMSO for 24 to 48 hr at 55°C without releasing RNA-alkylating side-products. Characterization of the fully deprotected RNA sequences by PAGE, enzymatic hydrolysis, and MALDI-TOF mass spectrometry confirms the identity and high quality of these sequences.
Collapse
|
42
|
Abstract
This unit discusses several methods for generating large amounts of uniformly labeled, end-labeled, and site-specifically labeled RNAs in vitro. The methods involve a number of experimental procedures, including RNA transcription, 5' dephosphorylation and rephosphorylation, 3' terminal nucleotide addition (via ligation), site-specific RNase H cleavage directed by 2'-O-methyl RNA-DNA chimeras, and 2-piece splint ligation. The applications of these RNA radiolabeling approaches are also discussed.
Collapse
Affiliation(s)
- Chao Huang
- Process Science Downstream, Bristol-Myers Squibb Company, East Syracuse, New York, USA
| | | |
Collapse
|
43
|
Abstract
It is a great privilege to contribute to the Reflections essays. In my particular case, this essay has allowed me to weave some of my major scientific contributions into a tapestry held together by what I have learned from three colleagues (Robert Letsinger, Gobind Khorana, and George Rathmann) who molded my career at every important junction. To these individuals, I remain eternally grateful, as they always led by example and showed many of us how to break new ground in both science and biotechnology. Relative to my scientific career, I have focused primarily on two related areas. The first is methodologies we developed for chemically synthesizing DNA and RNA. Synthetic DNA and RNA continue to be an essential research tool for biologists, biochemists, and molecular biologists. The second is developing new approaches for solving important biological problems using synthetic DNA, RNA, and their analogs.
Collapse
Affiliation(s)
- Marvin H Caruthers
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80303, USA.
| |
Collapse
|
44
|
Abstract
The in vitro synthesis of long RNA can be accomplished using phage RNA polymerase and template DNA. However, the in vitro synthesized RNA, unlike those transcribed in vivo in cells, lacks nucleoside modifications. Introducing modified nucleosides into in vitro transcripts is important because they reduce the potential of RNA to activate RNA sensors and translation of such nucleoside-modified RNA is increased in cell lines, primary cells, and after in vivo delivery. Here, we describe the in vitro synthesis of nucleoside-modified RNA with enhanced translational capacity and reduced ability to activate immune sensors.
Collapse
Affiliation(s)
- Norbert Pardi
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | |
Collapse
|
45
|
Zewge D. Safe deprotection strategy for the tert-butyldimethylsilyl (TBS) group during RNA synthesis. Curr Protoc Nucleic Acid Chem 2012; Chapter 3:Unit3.21. [PMID: 22700337 DOI: 10.1002/0471142700.nc0321s49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This unit describes two protocols for the deprotection of 2'-O-TBS groups in oligoribonucleotides under mild conditions. Desilylation using ammonium fluoride is applicable to fully protected "RNA only" substrates and desilylation using potassium fluoride is applicable to "mixed RNA/non-RNA" substrates. Characterization of products is accomplished using LC/MS, RP HPLC and SAX HPLC.
Collapse
Affiliation(s)
- Daniel Zewge
- Department of Process Research, Merck Research Laboratories, Rahway, New Jersey, USA
| |
Collapse
|
46
|
Morohashi N, Kimoto M, Sato A, Kawai R, Hirao I. Site-specific incorporation of functional components into RNA by an unnatural base pair transcription system. Molecules 2012; 17:2855-76. [PMID: 22399139 PMCID: PMC6268917 DOI: 10.3390/molecules17032855] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/22/2012] [Accepted: 02/24/2012] [Indexed: 01/08/2023] Open
Abstract
Toward the expansion of the genetic alphabet, an unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) functions as a third base pair in replication and transcription, and provides a useful tool for the site-specific, enzymatic incorporation of functional components into nucleic acids. We have synthesized several modified-Pa substrates, such as alkylamino-, biotin-, TAMRA-, FAM-, and digoxigenin-linked PaTPs, and examined their transcription by T7 RNA polymerase using Ds-containing DNA templates with various sequences. The Pa substrates modified with relatively small functional groups, such as alkylamino and biotin, were efficiently incorporated into RNA transcripts at the internal positions, except for those less than 10 bases from the 3′-terminus. We found that the efficient incorporation into a position close to the 3′-terminus of a transcript depended on the natural base contexts neighboring the unnatural base, and that pyrimidine-Ds-pyrimidine sequences in templates were generally favorable, relative to purine-Ds-purine sequences. The unnatural base pair transcription system provides a method for the site-specific functionalization of large RNA molecules.
Collapse
Affiliation(s)
- Nobuyuki Morohashi
- TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mails: (N.M.); (M.K.); (R.K.)
| | - Michiko Kimoto
- TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mails: (N.M.); (M.K.); (R.K.)
- RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mail:
| | - Akira Sato
- RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mail:
| | - Rie Kawai
- TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mails: (N.M.); (M.K.); (R.K.)
- RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mail:
| | - Ichiro Hirao
- TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mails: (N.M.); (M.K.); (R.K.)
- RIKEN Systems and Structural Biology Center (SSBC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +81-45-503-9644; Fax: +81-45-503-9645
| |
Collapse
|
47
|
Cieślak J, Grajkowski A, Ausín C, Gapeev A, Beaucage SL. Permanent or reversible conjugation of 2'-O- or 5'-O-aminooxymethylated nucleosides with functional groups as a convenient and efficient approach to the modification of RNA and DNA sequences. Nucleic Acids Res 2012; 40:2312-29. [PMID: 22067450 PMCID: PMC3300013 DOI: 10.1093/nar/gkr896] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/03/2011] [Accepted: 10/04/2011] [Indexed: 11/14/2022] Open
Abstract
2'-O-Aminooxymethyl ribonucleosides are prepared from their 3',5'-disilylated 2'-O-phthalimidooxymethyl derivatives by treatment with NH(4)F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2'-conjugates in yields of 69-82%. Indeed, exposure of these conjugates to 0.5 M tetra-n-butylammonium fluoride (TBAF) in THF results in the cleavage of their iminoether functions to give the native ribonucleosides along with the innocuous nitrile side product. Conversely, the reaction of 5-cholesten-3-one or dansyl chloride with 2'-O-aminooxymethyl uridine provides permanent uridine 2'-conjugates, which are left essentially intact upon treatment with TBAF. Alternatively, 5'-O-aminooxymethyl thymidine is prepared by hydrazinolysis of its 3'-O-levulinyl-5'-O-phthalimidooxymethyl precursor. Pyrenylation of 5'-O-aminooxymethyl thymidine and the sensitivity of the 5'-conjugate to TBAF further exemplify the usefulness of this nucleoside for modifying DNA sequences either permanently or reversibly. Although the versatility and uniqueness of 2'-O-aminooxymethyl ribonucleosides in the preparation of modified RNA sequences is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2'-conjugate into an RNA sequence, the conjugation of 2'-O-aminooxymethyl ribonucleosides with aldehydes, including those generated from their acetals, provides reversible 2'-O-protected ribonucleosides for potential applications in the solid-phase synthesis of native RNA sequences. The synthesis of a chimeric polyuridylic acid is presented as an exemplary model.
Collapse
Affiliation(s)
- Jacek Cieślak
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892 and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Andrzej Grajkowski
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892 and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Cristina Ausín
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892 and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Alexei Gapeev
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892 and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Serge L. Beaucage
- Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892 and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| |
Collapse
|
48
|
Tulub AA. [Spin polymerization of DNA/RNA nucleotides]. Biofizika 2011; 56:219-225. [PMID: 21542349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The Car-Parrinello molecular dynamics (CPMD) has been used to study the ion-radical (IR) polymerization (triplet (T) and singlet (S/TO) states) of adenine mononucleotides upon interaction with Mg2+(H2O)2-ATP(4-). It has been found that the IR polymerization occurs only upon Mg2+(H2O)2-ATP(4-) excitation into a T state (the Franck-Condon or femtosecond laser excitation); it naturally occurs in the dark with DNA polymerase or another Mg-holoenzyme upon interaction of Mg with two Asp residues. The IR path affects only the HO-C3' group of ribose, leaving the HO-C2' group inactive. The IR polymerization starts with the homolytic removal of the hydrogen atom from the HO-C3' group and its transfer onto the hydroxyl radical *OH, a product of the ATP cleavage, which yields a water molecule. A further progress of the reaction involves interaction between two ion-radicals *AMP. The reaction is sensitive to the recombination of *OH and *AMP. It is mostly suppressed by the appearance of identically directed electron spins on both radicals (the radical pair in the T-state) in the vicinity of the HO-C3' group and not suppressed in the vicinity of the HO-C2' group (the spins in the radical pair are oppositely directed, the radical pair in the To state), making the latter inert on the IR polymerization, but allowing it to be active in the ionic (hydrolytic) polymerization.
Collapse
|
49
|
Illangasekare M, Turk R, Peterson GC, Lladser M, Yarus M. Chiral histidine selection by D-ribose RNA. RNA 2010; 16:2370-2383. [PMID: 20940341 PMCID: PMC2995399 DOI: 10.1261/rna.2385310] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 08/27/2010] [Indexed: 05/30/2023]
Abstract
The invariant choice of L-amino acids and D-ribose RNA for biological translation requires explanation. Here we study this chiral choice using mixed, equimolar D-ribose RNAs having 15, 18, 21, 27, 35, and 45 contiguous randomized nucleotides. These are used for simultaneous affinity selection of the smallest bound and eluted RNAs using equal amounts of L- and D-His immobilized on an achiral glass support, with racemic histidine elution. The experiment as a whole therefore determines whether RNA containing D-ribose binds L-histidine or D-histidine more easily (that is, by using a site that is more abundant/requires fewer nucleotides). The most prevalent/smallest RNA sites are reproducibly and repeatedly selected and there is a four- to sixfold greater abundance of L-histidine sites. RNA's chiral D-ribose therefore yields a more frequent fit to L-histidine. Accordingly, a D-ribose RNA site for L-His is smaller by the equivalent of just over one conserved nucleotide. The most prevalent L-His site also performs better than the most frequent D-His site-but rarer D-ribose RNAs can bind D-His with excellent affinity and discrimination. The prevalent L-His site is one we have selected before under very different conditions. Thus, selection is again reproducible, as is the recurrence of cognate coding triplets in these most probable L-His sites. If our selected RNA population were equilibrated with racemic His, we calculate that L-His would participate in seven of eight His:RNA complexes, or more. Thus, if D-ribose RNA were first chosen biologically, translational L-His usage could have followed.
Collapse
Affiliation(s)
- Mali Illangasekare
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | | | | | | | | |
Collapse
|
50
|
|