1
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Wu LF, Liu Z, Roberts SJ, Su M, Szostak JW, Sutherland JD. Template-Free Assembly of Functional RNAs by Loop-Closing Ligation. J Am Chem Soc 2022; 144:13920-13927. [PMID: 35880790 PMCID: PMC9354263 DOI: 10.1021/jacs.2c05601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first ribozymes are thought to have emerged at a time when RNA replication proceeded via nonenzymatic template copying processes. However, functional RNAs have stable folded structures, and such structures are much more difficult to copy than short unstructured RNAs. How can these conflicting requirements be reconciled? Also, how can the inhibition of ribozyme function by complementary template strands be avoided or minimized? Here, we show that short RNA duplexes with single-stranded overhangs can be converted into RNA stem loops by nonenzymatic cross-strand ligation. We then show that loop-closing ligation reactions enable the assembly of full-length functional ribozymes without any external template. Thus, one can envisage a potential pathway whereby structurally complex functional RNAs could have formed at an early stage of evolution when protocell genomes might have consisted only of collections of short replicating oligonucleotides.
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Affiliation(s)
- Long-Fei Wu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Samuel J Roberts
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Meng Su
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Jack W Szostak
- Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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2
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Kühnlein A, Lanzmich SA, Braun D. tRNA sequences can assemble into a replicator. eLife 2021; 10:e63431. [PMID: 33648631 PMCID: PMC7924937 DOI: 10.7554/elife.63431] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/28/2021] [Indexed: 11/29/2022] Open
Abstract
Can replication and translation emerge in a single mechanism via self-assembly? The key molecule, transfer RNA (tRNA), is one of the most ancient molecules and contains the genetic code. Our experiments show how a pool of oligonucleotides, adapted with minor mutations from tRNA, spontaneously formed molecular assemblies and replicated information autonomously using only reversible hybridization under thermal oscillations. The pool of cross-complementary hairpins self-selected by agglomeration and sedimentation. The metastable DNA hairpins bound to a template and then interconnected by hybridization. Thermal oscillations separated replicates from their templates and drove an exponential, cross-catalytic replication. The molecular assembly could encode and replicate binary sequences with a replication fidelity corresponding to 85-90 % per nucleotide. The replication by a self-assembly of tRNA-like sequences suggests that early forms of tRNA could have been involved in molecular replication. This would link the evolution of translation to a mechanism of molecular replication.
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Affiliation(s)
- Alexandra Kühnlein
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Simon A Lanzmich
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Dieter Braun
- Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität MünchenMunichGermany
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3
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Liang X, Chen H, Li L, An R, Komiyama M. Ring-Structured DNA and RNA as Key Players In Vivoand In Vitro. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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4
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Obianyor C, Newnam G, Clifton BE, Grover MA, Hud NV. Towards Efficient Nonenzymatic DNA Ligation: Comparing Key Parameters for Maximizing Ligation Rates and Yields with Carbodiimide Activation**. Chembiochem 2020; 21:3359-3370. [DOI: 10.1002/cbic.202000335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/21/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Chiamaka Obianyor
- Georgia Institute of Technology School of Chemical and Biomolecular Engineering Atlanta Georgia 30332-0400 USA
| | - Gary Newnam
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
| | - Bryce E. Clifton
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
| | - Martha A. Grover
- Georgia Institute of Technology School of Chemical and Biomolecular Engineering Atlanta Georgia 30332-0400 USA
| | - Nicholas V. Hud
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
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5
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Chen J, Baker YR, Brown A, El-Sagheer AH, Brown T. Enzyme-free synthesis of cyclic single-stranded DNA constructs containing a single triazole, amide or phosphoramidate backbone linkage and their use as templates for rolling circle amplification and nanoflower formation. Chem Sci 2018; 9:8110-8120. [PMID: 30542561 PMCID: PMC6238721 DOI: 10.1039/c8sc02952k] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 08/23/2018] [Indexed: 12/31/2022] Open
Abstract
Cyclic oligonucleotides are valuable targets with a broad range of potential applications spanning molecular biology and nanotechnology. Of particular importance is their role as templates in the rolling circle amplification (RCA) reaction. We describe three different chemical cyclisation methods for the preparation of single-stranded cyclic DNA constructs. These chemical cyclisation reactions are cheaper to carry out than the enzymatic reaction, and more amenable to preparative scale purification and characterisation of the cyclic product. They can also be performed under denaturing conditions and are therefore particularly valuable for cyclic DNA templates that contain secondary structures. The resulting single-stranded cyclic DNA constructs contain a single non-canonical backbone linkage at the ligation point (triazole, amide or phosphoramidate). They were compared to unmodified cyclic DNA in rolling circle amplification reactions using φ-29 and Bst 2.0 DNA polymerase enzymes. The cyclic templates containing a phosphoramidate linkage were particularly well tolerated by φ-29 polymerase, consistently performing as well in RCA as the unmodified DNA controls. Moreover, these phosphoramidate-modified cyclic constructs can be readily produced in oligonucleotide synthesis facilities from commercially available precursors. Phosphoramidate ligation therefore holds promise as a practical, scalable method for the synthesis of fully biocompatible cyclic RCA templates. The triazole-modified cyclic templates generally gave lower and more variable yields of RCA products, a significant proportion of which were double-stranded, while the performances of the templates containing an amide linkage lie in between those of the phosphoramidate- and triazole-containing templates.
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Affiliation(s)
- Jinfeng Chen
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Ysobel R Baker
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
| | - Asha Brown
- ATDBio , Magdalen Centre , Oxford Science Park , Oxford , OX4 4GA , UK
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
- Chemistry Branch , Department of Science and Mathematics , Suez University , Suez 43721 , Egypt
| | - Tom Brown
- Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK .
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6
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Kramer M, Richert C. Enzyme-Free Ligation of 5'-Phosphorylated Oligodeoxynucleotides in a DNA Nanostructure. Chem Biodivers 2017; 14. [PMID: 28710838 DOI: 10.1002/cbdv.201700315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 07/12/2017] [Indexed: 01/05/2023]
Abstract
Multicomponent reactions are difficult synthetic transformations. For DNA, there is a special opportunity to align multiple strands in a folded nanostructure, so that they are preorganized to give a specific sequence. Multistrand reactions in DNA origami structures have previously been performed using photochemical crosslinking, 1,3-diploar cycloadditions or phosphoramidate-forming reactions. Here we report carbodiimide-driven phosphodiester formation in a small origami sheet that produces DNA strands up to 600 nucleotides in length in a single step. The method uses otherwise unmodified oligodeoxynucleotides with a 5'-terminal phosphate as starting materials. Compared to an enzymatic multistrand ligation involving linear duplexes, the carbodiimide-driven ligation gave fewer side products, as detected by gel electrophoresis. The full-length 600mer product was successfully amplified by polymerase chain reaction.
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Affiliation(s)
- Markus Kramer
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
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7
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Liu Y, Sousa R, Wang YX. Specific labeling: An effective tool to explore the RNA world. Bioessays 2015; 38:192-200. [DOI: 10.1002/bies.201500119] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yu Liu
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
| | - Rui Sousa
- Department of Biochemistry; University of Texas Health Science Center; San Antonio TX USA
| | - Yun-Xing Wang
- Protein-Nucleic Acid Interaction Section; Structural Biophysics Laboratory; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Frederick MD USA
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8
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Altstein AD. The progene hypothesis: the nucleoprotein world and how life began. Biol Direct 2015; 10:67. [PMID: 26612610 PMCID: PMC4662029 DOI: 10.1186/s13062-015-0096-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 11/13/2015] [Indexed: 12/16/2022] Open
Abstract
In this article, I review the results of studies on the origin of life distinct from the popular RNA world hypothesis. The alternate scenario postulates the origin of the first bimolecular genetic system (a polynucleotide gene and a polypeptide processive polymerase) with simultaneous replication and translation and includes the following key features: 1. The bimolecular genetic system emerges not from mononucleotides and monoamino acids, but from progenes, namely, trinucleotides aminoacylated on 3'-end by a non-random amino acid (NpNpNp ~ pX ~ Aa, where N--deoxyribo- or ribonucleoside, p--phosphate, X--a bifunctional agent, for example ribose, Aa--amino acid, ~ macroerge bond). Progenes are used as substrates for simultaneous synthesis of a polynucleotide and a polypeptide. Growth of the system is controlled by the growing polypeptide, and the bimolecular genetic system emerges as an extremely rare event. The first living being (virus-like organism protoviroid, Protoviroidum primum) arises and reproduces in prebiotic liposome-like structures using progenes. A population of protoviroids possessing the genetic system evolves in accordance with the Darwinian principle. Early evolution from protoviroid world to protocell world is shortly described. 2. The progene forming mechanism (NpNp + Np ~ pX ~ Aa) makes it possible to explain the emergence of the prebiotic physicochemical group genetic code, as well as the selection of organic compounds for the future genetic system from the racemic environment. 3. The protoviroid is reproduced on a progene basis via replicative transcription-translation (RTT, the first molecular genetic process) that is similar to its modern counterparts. Nothing is required for the emergence and reproduction of the protoviroid except for progenes and conditions for their formation. 4. The general scheme of early evolution is as follows: prebiotic world → protoviroid (nucleoprotein) world → protocell (DNA-RNA-protein) world → LUCA (Last Universal Common Ancestor) → modern cell world. This scheme exclude the existence of an independent RNA world as predecessor of the cellular world.
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Affiliation(s)
- Anatoly D Altstein
- Institute of Gene Biology RAS, NF Gamaleya Federal Center of Epidemiology and Microbiology, IM Sechenov First Moscow State Medical University, Moscow, Russia.
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9
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Frommer J, Hieronymus R, Selvi Arunachalam T, Heeren S, Jenckel M, Strahl A, Appel B, Müller S. Preparation of modified long-mer RNAs and analysis of FMN binding to the ypaA aptamer from B. subtilis. RNA Biol 2014; 11:609-23. [PMID: 24755604 DOI: 10.4161/rna.28526] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In recent years, RNA has been shown to fulfil a number of cellular functions. This has led to much interest in elucidation of the structure of functional RNA molecules, and thus, in the preparation of suitably functionalized RNAs. The chemical synthesis of RNAs allows for the site-specific modification; however, is limited to sequences of about 60-70 nucleotides in length. At the example of the flavine mononucleotide (FMN) responsive aptamer of the ypaA riboswitch from B. subtilis, we demonstrate the highly efficient preparation of site-specifically modified long-mer RNAs. Our strategy consists of the chemical synthesis of fragments followed by enzymatic or chemical ligation. Splint ligation with T4 RNA ligase turned out to be most successful among the enyzymatic protocols. Highly efficient chemical ligation was performed by azide-alkyne cycloaddition of suitably modified RNA fragments. Wild-type and 2-aminopurine (2-AP)-modified variants of the ypaA aptamer were prepared. FMN binding to all synthesized ypaA aptamer variants is demonstrated. However, dissociation of FMN from its binding site by reduction of the isoalloxazin unit as demonstrated before for a small-hairpin-derived aptazyme could not be shown. This implies that either FMN is less accessible to reduction when it is bound to its natural aptamer; that reduced FMN remains bound to the aptamer; or that FMN upon reduction indeed is released from its binding site, without the aptamer folding back in the natural ligand-free state. The results of this study are of general interest to the preparation of site-specifically modified RNAs for investigation into structure and function.
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Affiliation(s)
- Jennifer Frommer
- Ernst Moritz Arndt University Greifswald; Institute for Biochemistry; Greifswald, Germany
| | - Robert Hieronymus
- Ernst Moritz Arndt University Greifswald; Institute for Biochemistry; Greifswald, Germany
| | - Tamil Selvi Arunachalam
- Ernst Moritz Arndt University Greifswald; Institute for Biochemistry; Greifswald, Germany; PG and Research Department of Chemistry; Thiagarajar College (Autonomous); Madurai, India
| | - Sabine Heeren
- Ernst Moritz Arndt University Greifswald; Institute for Biochemistry; Greifswald, Germany; Hochschule Neubrandenburg; Fachbereich Agrarwirtschaft und Lebensmittelwissenschaften; AG Landwirtschaftliche Chemie; Neubrandenburg, Germany
| | - Maria Jenckel
- Ernst Moritz Arndt University Greifswald; Institute for Biochemistry; Greifswald, Germany; Friedrich-Loeffler-Institut; Institut für Virusdiagnostik; Südufer 10; Riems, Germany
| | - Anne Strahl
- Ernst Moritz Arndt University Greifswald; Institute for Biochemistry; Greifswald, Germany
| | - Bettina Appel
- Ernst Moritz Arndt University Greifswald; Institute for Biochemistry; Greifswald, Germany
| | - Sabine Müller
- Ernst Moritz Arndt University Greifswald; Institute for Biochemistry; Greifswald, Germany
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10
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Patzke V, McCaskill JS, von Kiedrowski G. DNA mit 3′-5′-Disulfid-Verknüpfung - schnelle chemische Ligation durch isosteren Ersatz. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310644] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Patzke V, McCaskill JS, von Kiedrowski G. DNA with 3'-5'-disulfide links--rapid chemical ligation through isosteric replacement. Angew Chem Int Ed Engl 2014; 53:4222-6. [PMID: 24623660 DOI: 10.1002/anie.201310644] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/28/2014] [Indexed: 11/11/2022]
Abstract
Efforts to chemically ligate oligonucleotides, without resorting to biochemical enzymes, have led to a multitude of synthetic analogues, and have extended oligomer ligation to reactions of novel oligonucleotides, peptides, and hybrids such as PNA.1 Key requirements for potential diagnostic tools not based on PCR include a fast templated chemical DNA ligation method that exhibits high pairing selectivity, and a sensitive detection method. Here we report on a solid-phase synthesis of oligonucleotides containing 5'- or 3'-mercapto-dideoxynucleotides and their chemical ligations, yielding 3'-5'-disulfide bonds as a replacement for 3'-5'-phosphodiester units. Employing a system designed for fluorescence monitoring, we demonstrate one of the fastest ligation reactions with half-lives on the order of seconds. The nontemplated ligation reaction is efficiently suppressed by the choice of DNA modification and the 3'-5' orientation of the activation site. The influence of temperature on the templated reaction is shown.
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Affiliation(s)
- Volker Patzke
- Lehrstuhl für Bioorganische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany).
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12
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Solomatin S, Herschlag D. Methods of site-specific labeling of RNA with fluorescent dyes. Methods Enzymol 2009; 469:47-68. [PMID: 20946784 DOI: 10.1016/s0076-6879(09)69003-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single molecule fluorescence techniques offer unique insights into mechanisms of conformational changes of RNA. Knowing how to make fluorescently labeled RNA molecules and understanding potential limitations of different labeling strategies is essential for successful implementation of single molecule fluorescence techniques. This chapter offers a step by step overview of the process of obtaining RNA constructs ready for single molecule measurements. Several alternative methods are described for each step, and ways of troubleshooting the most common problems, in particular, splinted RNA ligation, are suggested.
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Affiliation(s)
- Sergey Solomatin
- Department of Biochemistry, Stanford University, Stanford, California, USA
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13
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Human uridine-cytidine kinase phosphorylation of ribavirin: a convenient method for activation of ribavirin for conjugation to proteins. J Biomed Sci 2007; 15:205-13. [PMID: 18080217 DOI: 10.1007/s11373-007-9224-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2007] [Accepted: 11/19/2007] [Indexed: 11/27/2022] Open
Abstract
Ribavirin is a synthetic nucleoside analog that is used for the treatment of hepatitis C virus (HCV) infection. Its primary toxicity is hemolytic anemia, which sometimes necessitates dose reduction or discontinuation of therapy. Selective delivery of ribavirin into liver cells would be desirable to enhance its antiviral activity and avoid systemic side effects. One approach to liver-specific targeting is conjugation of the ribavirin with asialoglycoprotein that is taken up specifically by liver cells. Human uridine-cytidine kinase-1 (UCK-1) was used for ribavirin phosphorylation to its monophosphate form. 1-Ethyl-3-diisopropylaminocarbodiimide (EDC) was used as a coupling agent. The best results were obtained using direct conjugation protocol with a molar ratio of 6.5 ribavirin monophosphate (RMP) molecules per one asialoorosomucoid (AsOR) molecule. Our findings show that ribavirin is a potential substrate of UCK-1, and RMP formed could be chemically coupled to AsOR to form a conjugate for liver specific targeting.
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14
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Miller GP, Silverman AP, Kool ET. New, stronger nucleophiles for nucleic acid-templated chemistry: Synthesis and application in fluorescence detection of cellular RNA. Bioorg Med Chem 2007; 16:56-64. [PMID: 17502150 PMCID: PMC2265789 DOI: 10.1016/j.bmc.2007.04.051] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 09/15/2006] [Accepted: 04/27/2007] [Indexed: 01/14/2023]
Abstract
Nucleic acid-templated chemistry is a promising strategy for imaging genetic sequences in living cells. Here we describe the synthesis of two new nucleophiles for use in templated nucleophilic displacements with DNA probes. The nucleophilic groups are phosphorodithioate and phosphorotrithioate; we report on synthetic methods for introducing these groups at the 3'-terminus of oligonucleotides. Both new nucleophiles are found to be more highly reactive than earlier phosphoromonothioates. This increased nucleophilicity is shown to result in more rapid templated reactions with electrophilic DNA probes. The new probes were demonstrated in detection of specific genetic sequences in solution, with clear signal over background being generated in as little as 20 min. The probes were also tested for imaging ribosomal RNA sequences in live Escherichia coli; useful signal was generated in 20 min to 1h, approximately one quarter to one-half the time of earlier monothioate probes, and the signal-to-noise ratio was increased as well.
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15
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Ficht S, Mattes A, Seitz O. Single-nucleotide-specific PNA-peptide ligation on synthetic and PCR DNA templates. J Am Chem Soc 2004; 126:9970-81. [PMID: 15303871 DOI: 10.1021/ja048845o] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA-directed chemical synthesis has matured into a useful tool with applications such as fabrication of defined (nano)molecular architectures, evolution of amplifiable small-molecule libraries, and nucleic acid detection. Most commonly, chemical methods were used to join oligonucleotides under the control of a DNA or RNA template. The full potential of chemical ligation reactions can be uncovered when nonnatural oligonucleotide analogues that can provide new opportunities such as increased stability, DNA affinity, hybridization selectivity, and/or ease and accuracy of detection are employed. It is shown that peptide nucleic acid (PNA) conjugates, nonionic biostable DNA analogues, allowed the fashioning of highly chemoselective and sequence-selective peptide ligation methods. In particular, PNA-mediated native chemical ligations proceed with sequence selectivities and ligation rates that reach those of ligase-catalyzed oligodeoxynucleotide reactions. Usually, sequence-specific ligations can only be achieved by employing short-length probes, which show DNA affinities that are too low to allow stable binding to target segments in large, double-stranded DNA. It is demonstrated that the PNA-based ligation chemistry allowed the development of a homogeneous system in which rapid single-base mutation analyses can be performed even on double-stranded PCR DNA templates.
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Affiliation(s)
- Simon Ficht
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
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16
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Abstract
Double-helical DNA accelerates the rate of ligation of two six-ring hairpin polyamides which bind adjacent sites in the minor groove via a 1,3-dipolar cycloaddition to form a tandem dimer. The rate of the templated reaction is dependent on DNA sequence as well as on the distance between the hairpin-binding sites. The tandem dimer product of the DNA-templated reaction has improved binding properties with respect to the smaller hairpin fragments. Since cell and nuclear uptake of DNA-binding polyamides will likely be dependent on size, this is a minimum first step toward the design of self-assembling small gene-regulating fragments to produce molecules of increasing complexity with more specific genomic targeting capabilities.
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Affiliation(s)
- Adam T Poulin-Kerstien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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17
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Alexander RC, Johnson AK, Thorpe JA, Gevedon T, Testa SM. Canonical nucleosides can be utilized by T4 DNA ligase as universal template bases at ligation junctions. Nucleic Acids Res 2003; 31:3208-16. [PMID: 12799448 PMCID: PMC162249 DOI: 10.1093/nar/gkg415] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
T4 DNA ligase catalyzes the template-dependent ligation of DNA. Using T4 DNA ligase under specific experimental conditions, we demonstrate that each of the four canonical nucleosides, centrally located on a template molecule such that they flank the site of ligation, can direct the ligation of nucleic acids regardless of the identity of the terminal nucleosides being covalently joined. This universal templating capability extends to those positions adjacent to the ligation junction. This is the first report, irrespective of the ligation method used or the identity of the template nucleosides (including analogs), which shows that nucleosides can act essentially as universal templates at ligation junctions in vitro. The canonical nucleosides do, however, differ in their ability to template sequence- independent ligations, with thymidine and guanosine being equally effective, yet more effective than adenosine and cytidine. Results indicate that hybridization strength surrounding the ligation junction is an important factor. The implications of this previously undiscovered property of T4 DNA ligase with canonical nucleosides are discussed.
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18
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19
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Wu X, Delgado G, Krishnamurthy R, Eschenmoser A. 2,6-diaminopurine in TNA: effect on duplex stabilities and on the efficiency of template-controlled ligations. Org Lett 2002; 4:1283-6. [PMID: 11950343 DOI: 10.1021/ol020016p] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Replacement of adenine by 2,6-diaminopurine-two nucleobases to be considered equivalent from an etiological point of view-strongly enhances the stability of TNA/TNA, TNA/RNA, or TNA/DNA duplexes and efficiently accelerates template-directed ligation of TNA ligands. [reaction: see text]
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Affiliation(s)
- Xiaolin Wu
- The Skaggs Institute for Chemical Biology at the Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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20
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Schöneborn H, Bülle J, von Kiedrowski G. Kinetic monitoring of self-replicating systems through measurement of fluorescence resonance energy transfer. Chembiochem 2001; 2:922-7. [PMID: 11948882 DOI: 10.1002/1439-7633(20011203)2:12<922::aid-cbic922>3.0.co;2-u] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- H Schöneborn
- Lehrstuhl für Bioorganische Chemie, Universitätsstrasse 150, NC2/173 44780 Bochum, Germany
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21
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Chemical ligation and recombination of DNA fragments through formation (exchange) of disulfide bonds located in the sugar-phosphate backbone. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2000. [DOI: 10.1007/bf02759167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Liu J, Taylor JS. Template-directed photoligation of oligodeoxyribonucleotides via 4-thiothymidine. Nucleic Acids Res 1998; 26:3300-4. [PMID: 9628933 PMCID: PMC147698 DOI: 10.1093/nar/26.13.3300] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Non-enzymatic, template-directed ligation of oligonucleotides in aqueous solution has been of great interest because of its potential synthetic and biomedical utility and implications for the origin of life. Though there are many methods for template-directed chemical ligation of oligonucleotides, there are only three reported photochemical methods. In the first report, template-directed photoligation was effected by cyclobutane dimer formation between the 5'- and 3'-terminal thymidines of two oligonucleotides with >290 nm light, which also damages DNA itself. To make the photochemistry of native DNA more selective, we have replaced the thymidine at the 5'-end of one oligonucleotide with 4-thiothymidine (s4T) and show that it photoreacts at 366 nm with a T at the 3'-endof another oligonucleotide in the presence of a complementary template. When a single mismatch is introduced opposite either the s4T or its adjoining T, the ligation efficiency drops by a factor of five or more. We also show that by linking the two ends of the oligonucleotides together, photoligation can be used to form circular DNA molecules and to 'photopadlock' circular DNA templates. Thus, s4T-mediated photo-ligation may have applications to phototriggered antisense-based or antigene-based genetic tools, diagnostic agents and drugs, especially for those situations in which chemical or enzyme-mediated ligation isundesirable or impossible, for example inside a cell.
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Affiliation(s)
- J Liu
- Department of Chemistry, Washington University in St Louis, St Louis, MO 63130, USA
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23
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Petrauskene OV, Babkina OV, Tashlitsky VN, Kazankov GM, Gromova ES. EcoRII endonuclease has two identical DNA-binding sites and cleaves one of two co-ordinated recognition sites in one catalytic event. FEBS Lett 1998; 425:29-34. [PMID: 9541001 DOI: 10.1016/s0014-5793(98)00184-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
EcoRII is a typical restriction enzyme that cleaves DNA using a two-site mechanism. EcoRII endonuclease is unable to cleave DNA which contains a small number of EcoRII recognition sites but the enzyme activity can be stimulated in the presence of DNA with a high frequency of EcoRII sites. To investigate the mechanism of activation, the kinetics of stimulated EcoRII cleavage has been studied. A 14 bp substrate activated the cleavage of the 71 bp substrate, containing one EcoRII recognition site (trans-activation) by a competitive mechanism: the activator increased substrate binding but not catalysis. The activation increased if the substrate concentration decreased and if the activator had a lower affinity for the enzyme than the substrate. The introduction of the second recognition site into the 71 bp duplex also enabled cleavage of this substrate (cis-activation). Pyrophosphate bonds were incorporated into one of two recognition sites to switch off the cleavage of the phosphodiester bonds. Analysis of cleavage products of these modified substrates showed that EcoRII cuts one of two coordinated recognition sites in one catalytic event.
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Affiliation(s)
- O V Petrauskene
- Belozersky Institute of Physico-Chemical Biology and Chemistry Department, Moscow State University, Russia
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24
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Ordoukhanian P, Taylor JS. Solid phase-supported thymine dimers for the construction of dimer-containing DNA by combined chemical and enzymatic synthesis: a potentially general method for the efficient incorporation of modified nucleotides into DNA. Nucleic Acids Res 1997; 25:3783-6. [PMID: 9380498 PMCID: PMC146970 DOI: 10.1093/nar/25.19.3783] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The ability to study the structure-activity relationships of the cis-syn thymine dimer, the major photoproduct of DNA, has been greatly aided by the availability of a building block suitable for its sequence-specific incorporation into oligonucleotides by standard automated DNA synthesis. Unfortunately, its usefulness is compromised by the fact that it takes six steps to synthesize in low overall yield and, as with all phosphoramidite building blocks, has to be used in great excess over the support in standard automated synthesis. To extend the usefulness of this building block, we have directly coupled it to standard A, C, G and T long chain alkylamine-linked controlled pore glass supports to yield a solid phase-supported dimer. We then demonstrate that 13mers containing a 3'-terminal d(T[cis-syn]TN) group synthesized with this support at 0.2 micromol scale can be efficiently incorporated into longer oligonucleotides by both primer extension with 3'-->5'exonuclease-deficient Klenow fragment or T4 polymerase and dNTPs or by enzymatic ligation with T4 DNA ligase to another oligonucleotide opposite a complementary template. The site specificity and integrity of the cis-syn thymine dimer after both primer extension and ligation was confirmed by cis-syn dimer-specific cleavage with T4 denV endonuclease V. This general approach should be applicable to the synthesis of many types of site-specific nucleic acid modifications and would be of particular use for those for which the required building blocks are expensive or difficult to make.
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Affiliation(s)
- P Ordoukhanian
- Department of Chemistry, Washington University, St Louis, MO 63130, USA
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25
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Dolinnaya NG, Shabarova ZA. Chemical ligation as a method for the assembly of double-stranded nucleic acids: Modifications and local structure studies. Russ Chem Bull 1996. [DOI: 10.1007/bf01457755] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Bruick RK, Dawson PE, Kent SB, Usman N, Joyce GF. Template-directed ligation of peptides to oligonucleotides. CHEMISTRY & BIOLOGY 1996; 3:49-56. [PMID: 8807828 DOI: 10.1016/s1074-5521(96)90084-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Oligonucleotide-peptide conjugates have several applications, including their potential use as therapeutic agents. We developed a strategy for the chemical ligation of unprotected peptides to oligonucleotides in aqueous solution. The two compounds are joined via a stable amide bond in a template-directed reaction. RESULTS Peptides, ending in a carboxy-terminal thioester, were converted to thioester-linked oligonucleotide-peptide intermediates. The oligonucleotide portion of the intermediate binds to a complementary oligonucleotide template, placing the peptide in close proximity to an adjacent template-bound oligonucleotide that terminates in a 3' amine. The ensuing reaction results in the efficient formation of an amide-linked oligonucleotide-peptide conjugate. CONCLUSIONS An oligonucleotide template can be used to direct the ligation of peptides to oligonucleotides via a highly stable amide linkage. The ligation reaction is sequence-specific, allowing the simultaneous ligation of multiple oligonucleotide-peptide pairs.
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Affiliation(s)
- R K Bruick
- The Scripps Research Institute, 10666 North Torrey Pines Road, La Jolla, CA 92037, USA
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27
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Kool ET. Topologically Modified Biopolymers: Properties of Synthetic Circular DNAs and RNAs. TRENDS IN POLYMER SCIENCE 1995; 3:396-402. [PMID: 28042207 PMCID: PMC5199043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Circular nucleic acid molecules can have chemical and biological properties very different from those of the corresponding linear nucleic acid polymers. Described here are methods used recently for construction of such circular molecules, and some of the properties that can arise from making this topological change. Among the unusual properties found for circular nucleic acids are: strong resistance to degradation in biological media; high affinity of binding to other nucleic acids; high sequence selectivity in nucleic acid binding; topological linkage to biomolecules; and the ability to template the synthesis of specific repeating nucleic acid and protein polymers. These properties may be useful in biochemical, medical diagnostic and therapeutic applications.
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Affiliation(s)
- Eric T Kool
- Dept of Chemistry, University of Rochester, Rochester, NY 14627, USA (
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28
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Petrauskene OV, Schmidt S, Karyagina AS, Nikolskaya II, Gromova ES, Cech D. The interaction of DNA duplexes containing 2-aminopurine with restriction endonucleases EcoRII and SsoII. Nucleic Acids Res 1995; 23:2192-7. [PMID: 7610047 PMCID: PMC307007 DOI: 10.1093/nar/23.12.2192] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Oligonucleotides containing 2-aminopurine (2-AP) in place of G or A in the recognition site of EcoRII (CCT/AGG) or SsoII (CCNGG) restriction endonucleases have been synthesized in order to investigate the specific interaction of DNA with these enzymes. Physicochemical properties (CD spectra and melting behaviour) have shown that DNA duplexes containing 2-aminopurine exist largely in a stable B-like form. 2-Aminopurine base paired with cytidine, however, essentially influences the helix structure. The presence of a 2-AP-C mismatch strongly reduces the stability of the duplexes in comparison with the natural double strand, indicated by a biphasic melting behaviour. SsoII restriction endonuclease recognizes and cleaves the modified substrate with a 2-AP-T mismatch in the centre of the recognition site, but it does not cleave the duplexes containing 2-aminopurine in place of inner and outer G, or both. EcoRII restriction endonuclease does not cleave duplexes containing 2-aminopurine at all. The two-substrate mechanism of EcoRII-DNA interaction, however, allows hydrolysis of the duplex containing 2-aminopurine in place of adenine in the presence of the canonical substrate.
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Affiliation(s)
- O V Petrauskene
- A. N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Russia
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29
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Gottikh M, Baud-Demattei MV, Lescot E, Giorgi-Renault S, Shabarova Z, Dautry F, Malvy C, Bertrand JR. In vitro inhibition of the pim-1 protooncogene by chimeric oligodeoxyribonucleotides composed of alpha- and beta-anomeric fragments. Gene 1994; 149:5-12. [PMID: 7958988 DOI: 10.1016/0378-1119(94)90405-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We show that oligodeoxyribonucleotides (oligos) composed of alpha- and beta-anomeric sections can be used as antisense compounds. An octamer has been chosen as an effector domain to form a substrate for RNaseH. This octamer is complementary to the translation start site of the pim-1 protooncogene mRNA. Chimeric alpha-beta oligos and their beta-analogs have a similar binding affinity for their target. These oligos also direct efficient RNaseH-mediated cleavage of target mRNA. Among all alpha-beta oligos studied, one with an alpha-fragment bound by its 3'-end to the 3'-end of the beta-octamer is the most resistant to nucleolytic digestion in biological media. The alpha-beta oligos have been found to inhibit in vitro translation of pim-1 RNA with specificity.
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Affiliation(s)
- M Gottikh
- Laboratoire de Biochimie-Enzymologie, CNRS URA 147, Institut Gustave Roussy, Villejuif, France
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30
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Synthesis of dinucleotides containing a bridged non-chiral internucleotide 5′- or 3′-phosphoramidate linkage. Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)81755-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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31
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Zuber G, Behr JP. Nonenzymatic plasmid ligation mediated by minor groove-binding molecules. Biochemistry 1994; 33:8122-7. [PMID: 8025117 DOI: 10.1021/bi00192a017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DNA ligation is the weak link in the chain of gene cloning. We have developed a straightforward nonenzymatic alternative to this reaction that employs easily available commercial reagents. The method uses the affinity of distamycin for the minor groove to join DNA ends together. Phosphodiester bonds are formed after cyanoimidazole-promoted phosphate activation in the presence of manganese(II) cations. When transfected into eukaryotic cells, the chemically ligated plasmid is transcribed even more efficiently than after enzymatic ligation. At present this technique compares favorably with T4 ligation for AT-rich cohesive termini, but in principle it could be extended to any restriction site.
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Affiliation(s)
- G Zuber
- Laboratoire de Chimie Génétique, CNRS URA 1386, Faculté de Pharmacie de Strasbourg, Illkirch, France
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32
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Harada K, Orgel LE. In vitro selection of optimal DNA substrates for ligation by a water-soluble carbodiimide. J Mol Evol 1994; 38:558-60. [PMID: 8083882 DOI: 10.1007/bf00175874] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have used in vitro selection to investigate the sequence requirements for efficient template-directed ligation of oligonucleotides at 0 degrees C using a water-soluble carbodiimide as condensing agent. We find that only 2 bp at each side of the ligation junction are needed. We also studied chemical ligation of substrate ensembles that we have previously selected as optimal for ligation by RNA ligase or by DNA ligase. As anticipated, we find that substrates selected with DNA ligase ligate efficiently with a chemical ligating agent, and vice versa. Substrates selected using RNA ligase are not ligated by the chemical condensing agent and vice versa. The implications of these results for prebiotic chemistry are discussed.
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Affiliation(s)
- K Harada
- Salk Institute for Biological Studies, San Diego, CA 92186-5800
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33
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Dolinnaya N, Gryaznov S, Ahle D, Chang CA, Shabarova ZA, Ureda MS, Horn T. Construction of branched DNA (bDNA) molecules by chemical ligation. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80672-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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34
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Gottikh M, Bertrand JR, Baud-Dematteï MV, Lescot E, Giorgi-Renault S, Shabarova Z, Malvy C. Alpha beta chimeric antisense oligonucleotides: synthesis and nuclease resistance in biological media. ANTISENSE RESEARCH AND DEVELOPMENT 1994; 4:251-8. [PMID: 7734939 DOI: 10.1089/ard.1994.4.251] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A new type of chimeric oligonucleotides composed of alpha- and beta-sections is described. The sequence of eight beta-nucleotides flanked at 3'- or/and 5'-ends by nuclease-resistant alpha-oligonucleotides has been chosen as an effector domain to form a substrate for RNase H. The synthesized oligonucleotides are complementary to the translation initiation site of the pim protooncogene mRNA. We used the chemical ligation method to prepare the chimeric oligonucleotides. The thermal stability of heteroduplexes formed by the alpha beta oligonucleotides with a complementary strand is not significantly altered compared to that of their beta-analogs. These oligonucleotides promote efficient RNase H-mediated cleavage of pim mRNA. Among the alpha beta oligonucleotides studied, one with an alpha-fragment bound by its 3'-end to the 3'-end of the beta-octanucleotide proved to be the most resistant to nucleolytic digestion in human plasma, calf serum, and murine fibroblast lysate. This alpha beta oligonucleotide directs more specific RNA cleavage by RNase H than its beta beta counterpart.
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Affiliation(s)
- M Gottikh
- CNRS URA 147, Institut Gustave Roussy, Villejuif, France
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35
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Dolinnaya NG, Blumenfeld M, Merenkova IN, Oretskaya TS, Krynetskaya NF, Ivanovskaya MG, Vasseur M, Shabarova ZA. Oligonucleotide circularization by template-directed chemical ligation. Nucleic Acids Res 1993; 21:5403-7. [PMID: 8265356 PMCID: PMC310578 DOI: 10.1093/nar/21.23.5403] [Citation(s) in RCA: 59] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
An efficient method for producing the covalent closure of oligonucleotides on complementary templates by the action of BrCN was developed. A rational design of linear precursor oligonucleotides was studied, and the effect of factors such as oligonucleotide concentration and oligomer-template length ratio was evaluated. The efficiency of circularization was shown to correlate well with the secondary structure of the precursor oligomer (as predicted by a simple computer analysis), hairpin-like structures bearing free termini clearly favouring the circularization reaction. A novel idea, consisting of the incorporation of non-nucleotide insertions in the precursor oligomer (namely, 1,2-dideoxy-D-ribofuranose residues), may render this method universal and highly effective. An original set of assays was developed to confirm the circular structure of the covalently closed oligonucleotides.
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36
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Mag M, Schmidt R, Engels JW. Synthesis and selective cleavage of an oligodeoxynucleotide containing a bridged non-chiral internucleotide 3′-phosphoramidate linkage. Tetrahedron Lett 1992. [DOI: 10.1016/s0040-4039(00)60176-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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37
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Gryaznov SM, Letsinger RL. Synthesis and properties of oligonucleotides containing aminodeoxythymidine units. Nucleic Acids Res 1992; 20:3403-9. [PMID: 1630911 PMCID: PMC312496 DOI: 10.1093/nar/20.13.3403] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Procedures are described for synthesis via solid support methodology of oligonucleotide analogues derived in part from 3'-amino-3'-deoxythymidine or 5'-amino-5'-deoxythymidine. Oligothymidylate decamers terminated with a 3'-amino group or containing a 3'-NHP(O)(O-)O-5' internucleoside link are found to form unusually stable complexes with poly(dA), poly(A), and oligo(dA). For related derivatives of 5'-amino-5'-deoxythymidine enhancement is less or absent, and in the case of multiple substitution destabilization of the heteroduplex may be observed. That the effect of the 3'-amino group is general for oligonucleotide derivatives is indicated by enhanced Tm values for heteroduplex complexes of the mixed-base oligomer, d(TATTCAGTCAT(NH2)), and the methyl phosphonate derivatives, TmTmTmTmTmTmTmTmTmT(NH2) and d(TmAmTmTmCmAmGmTmCmAmT(NH2)).
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Affiliation(s)
- S M Gryaznov
- Department of Chemistry, Northwestern University, Evanston, IL 60208
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38
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Abstract
It is proposed that the scaling symmetry of constant charge density with increasing molecular weight, which prevents the separation by electrophoresis of DNA molecules in solution (with respect to molecular weight) be broken by the attachment of a perturbing entity (protein, virus or charged sphere) to one end of the molecule. An application of this idea to a concept for sequencing DNA by capillary electrophoresis is discussed, and the possibility of using the reattachment of the RecA protein to separate large segments of DNA in solution by electrophoresis following sequence-specific cleavage is mentioned.
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Affiliation(s)
- J Noolandi
- Xerox Research Centre of Canada, Mississauga, Ontario
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39
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Shabarova ZA, Merenkova IN, Oretskaya TS, Sokolova NI, Skripkin EA, Alexeyeva EV, Balakin AG, Bogdanov AA. Chemical ligation of DNA: the first non-enzymatic assembly of a biologically active gene. Nucleic Acids Res 1991; 19:4247-51. [PMID: 1870979 PMCID: PMC328569 DOI: 10.1093/nar/19.15.4247] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
An artificial gene comprising 183 base pairs has been assembled by template-directed condensation of 35- to 53-membered oligodeoxyribo nucleotides with cyanogen bromide as a condensing agent. The reaction is complete within several minutes at 0 degrees C in buffer. The resulting mini-gene was cloned and expressed in vivo and in vitro. We have also found that the polymerase inhibition technique (toe-printing) is a good way to ascertain that translation initiation complexes form in the case of single-stranded DNAs as well. Thus, along with the fully chemical assembly of synthetic genes, a rapid and sufficiently reliable method for determining their ribosome-binding properties was developed.
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Affiliation(s)
- Z A Shabarova
- Belozersky Laboratory of Molecular Biology and Bioorganic Chemistry, Moscow State University, USSR
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40
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Gromova ES, Kubareva EA, Vinogradova MN, Oretskaya TS, Shabarova ZA. Peculiarities of recognition of CCA/TGG sequences in DNA by restriction endonucleases MvaI and EcoRII. J Mol Recognit 1991; 4:133-41. [PMID: 1665978 DOI: 10.1002/jmr.300040405] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
To elucidate the mechanism of action of restriction endonucleases MvaI and EcoRII a study was made of their interaction with a set of synthetic substrates in which the heterocyclic bases or the sugar-phosphate backbone had been modified; individual nucleotide residues had been removed or replaced with hydrocarbon bridges, and mismatched base pairs had been introduced. The groups of atoms in the heterocyclic bases and the phosphates in the recognition site that produce the most significant influence on the functioning of endonucleases MvaI and EcoRII were discerned. Profound differences were found in the functioning of the MvaI and EcoRII neoschizomers. The catalytic activity of EcoRII is significantly affected by any alteration in the recognition site structure and conformation, with a modification in one strand of the substrate causing the same decrease in the hydrolysis rate of both strands. Endonuclease MvaI is tolerant to a number of structural abnormalities; the latter sometimes affect only hydrolysis of one strand of the recognition site. The enzyme can preferentially cleave one of the substrate strands. Mismatched base pairs retard and sometimes block the hydrolysis. The effect depends on the particular enzyme, mismatch and its location.
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Affiliation(s)
- E S Gromova
- Department of Chemistry, Lomonosov State University, Moscow, USSR
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41
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Abstract
A series of oligomeric double and triple helical DNAs with irregular sequences of homopurine and homopyrimidine strands were prepared. DNA triplexes were identified by CD spectroscopy and thermal denaturation profiles (biphasic helix-coil transition). Condensation of oligonucleotides on single and double-stranded DNA templates was performed using water-soluble carbodiimide, phosphodiester and pyrophosphate internucleotide bonds being newly formed. Such chemical ligation proved to be a sensitive monitor of changes in the sugar-phosphate backbone resulting from conversion of double to triple helix and of third-strand binding.
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Affiliation(s)
- N G Dolinnaya
- A.N. Belozersky Laboratory and Chemical Department, Moscow State University, USSR
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42
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Dolinnaya NG, Tsytovich AV, Sergeev VN, Oretskaya TS, Shabarova ZA. Structural and kinetic aspects of chemical reactions in DNA duplexes. Information on DNA local structure obtained from chemical ligation data. Nucleic Acids Res 1991; 19:3073-80. [PMID: 2057363 PMCID: PMC328273 DOI: 10.1093/nar/19.11.3073] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Chemical ligation of oligonucleotides in double-stranded helices has been considered in its structural-kinetic aspect. A study was made of (i) two series of DNA duplexes with various arrangements of reacting groups in the ligation junction induced by mispairing or by alteration of furanose structure (the replacement of dT unit with rU, aU, IU, xU, dxT ones) and of (ii) eight synthetic water-soluble carbodiimides with different substituents at N1 and N3 atoms. We assumed that some information on the local structure of modified sites in the duplex can be obtained from kinetic parameters of oligonucleotide coupling reaction. The ratio of kinetic constants k3/(k2 + k3) for productive and nonproductive decomposition of the activated phosphomonoester derivative apparently reflects the reaction site structure: for a given duplex this parameter is virtually independent of the condensing agent composition. Based on the analysis of the chemical ligation kinetics a suggestion has been made about the conformation of some modified units in the double helix.
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Affiliation(s)
- N G Dolinnaya
- Belozersky Laboratory of Molecular Biology, Moscow State University, USSR
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43
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Dolinnaya NG, Sokolova NI, Ashirbekova DT, Shabarova ZA. The use of BrCN for assembling modified DNA duplexes and DNA-RNA hybrids; comparison with water-soluble carbodiimide. Nucleic Acids Res 1991; 19:3067-72. [PMID: 1711679 PMCID: PMC328272 DOI: 10.1093/nar/19.11.3067] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Both cyanogen bromide (BrCN) and 1-ethyl-3-(3'-dimethylaminopropyl) carbodiimide may be used as coupling reagents for the template-directed assembly of DNA duplexes containing the sugar-phosphate backbone modification. Both reagents show similar ligation site structure-specific trend. Practical recommendations are given for selection of the condensing reagent depending on the properties of the duplex. Based on 31P NMR spectroscopy data, a scheme is suggested for BrCN activation of the nucleotide phosphomonoester group. Using both condensing reagents, we studied the condensation of oligonucleotides containing ribo-segments (from mononucleotide residue to full sequence) on the DNA template. Efficiency of the chemical ligation of RNA oligomers was shown to be much lower than that of DNA analogues. The coupling yield depends on the position of the RNA segment in the hybrid duplexes and on the position of the phosphate group in the nick.
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Affiliation(s)
- N G Dolinnaya
- Belozersky Laboratory of Molecular Biology, Moscow State University, USSR
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44
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Merenkova IN, Romanova EA, Sokolova NI, Dolinnaya NG, Oretskaya TS, Shabarova ZA. Preparation of DNA duplexes containing 2?-fluoro-2?-deoxyuridine and arabinosyluracil. Chem Nat Compd 1991. [DOI: 10.1007/bf00629767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Sokolova NI, Oretskaya TS, Dolinnaya NG, Romanova EA, Shabarova ZA. Phosphorylation Within DNA Duplexes. Synthesis of Modified Oligodeoxyribonucleotide. PHOSPHORUS SULFUR 1990. [DOI: 10.1080/10426509008040904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Gromova ES, Shabarova ZA. DNA-protein interactions: the use of synthetic oligo- and polynucleotides for studying single-stranded-DNA-binding proteins and restriction endonucleases. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1990; 39:1-47. [PMID: 2174177 DOI: 10.1016/s0079-6603(08)60622-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- E S Gromova
- Department of Chemistry, Moscow State University, U.S.S.R
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von Kiedrowski G, Wlotzka B, Helbing J. Sequenzabhängigkeit matrizengesteuerter Synthesen von Hexadesoxynucleotid-Derivaten mit 3′-5′-Pyrophosphatverknüpfung. Angew Chem Int Ed Engl 1989. [DOI: 10.1002/ange.19891010918] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Mag M, Engels JW. Synthesis and selective cleavage of oligodeoxyribonucleotides containing non-chiral internucleotide phosphoramidate linkages. Nucleic Acids Res 1989; 17:5973-88. [PMID: 2771637 PMCID: PMC318254 DOI: 10.1093/nar/17.15.5973] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Oligodeoxynucleotides containing phosphoramidate internucleotide links 3'-OP(O)NH-5' have been prepared using standard solid phase phosphoramidite techniques. For the incorporation of the phosphoramidate linkages we have used monomer as well as dimer building blocks. With the monomer 3'-phosphoramidite building blocks, which are derived from 5'-amino-2',5'-dideoxynucleosides, it is possible to incorporate phosphoramidate links into specific positions within an oligodeoxynucleotide. Furthermore the synthesis of several dinucleoside phosphate derivatives which are linked by phosphoramidate bonds are described. The internucleotide phosphoramidate linkage was performed using the Staudinger reaction followed by a Michaelis-Arbuzov type transformation. After 3'-phosphitylation these dinucleosides are compatible with the current phosphoramidite methodology of oligodeoxynucleotide synthesis.
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Affiliation(s)
- M Mag
- Institut für Organische Chemie, Johann Wolfgang Goethe-Universität Frankfurt, FRG
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Shabarova ZA. Chemical development in the design of oligonucleotide probes for binding to DNA and RNA. Biochimie 1988; 70:1323-34. [PMID: 2466489 DOI: 10.1016/0300-9084(88)90003-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This paper deals with the chemical synthesis of natural and modified oligodeoxyribonucleotides and chimeric oligoribo-oligodeoxyribo-nucleotides. The first part describes the synthesis of oligonucleotide probes bearing different types of spacer groups (aminoalkyl-, hydroxyalkyl-, amino acids), bound to the 5'- or 3'-terminal phosphate group of oligonucleotides. Two types of reagents have been used to convert the oligonucleotide phosphomonoester group into chemically reactive groups in aqueous media: water-soluble carbodiimide and N-hydroxybenzotriazole. The second part involves the description of the chemical ligase method for template-dependent coupling of oligonucleotides. Application of these techniques to replace natural internucleotide bonds in oligonucleotides with modified phosphoramide, pyrophosphate, chimeric ribo-deoxyribo, arabino-deoxyribo, deoxyxylo-deoxyribo, as well as phosphoramidate-alkyl-phosphoramidate internucleotide linkages is described. The final part involves some examples of the interaction of modified oligonucleotide probes with DNA and proteins (restriction enzymes). The use of modified oligonucleotide probes (chimeric oligoribo-oligodeoxyribo-nucleotides linked via the pyrophosphate internucleotide bond) allows the elaboration of a method of regiospecific cleavage of RNA. This method is equivalent to restriction enzyme cleavage of DNA.
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