1
|
Site-Selective Artificial Ribonucleases: Renaissance of Oligonucleotide Conjugates for Irreversible Cleavage of RNA Sequences. Molecules 2021; 26:molecules26061732. [PMID: 33808835 PMCID: PMC8003597 DOI: 10.3390/molecules26061732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/17/2022] Open
Abstract
RNA-targeting therapeutics require highly efficient sequence-specific devices capable of RNA irreversible degradation in vivo. The most developed methods of sequence-specific RNA cleavage, such as siRNA or antisense oligonucleotides (ASO), are currently based on recruitment of either intracellular multi-protein complexes or enzymes, leaving alternative approaches (e.g., ribozymes and DNAzymes) far behind. Recently, site-selective artificial ribonucleases combining the oligonucleotide recognition motifs (or their structural analogues) and catalytically active groups in a single molecular scaffold have been proven to be a great competitor to siRNA and ASO. Using the most efficient catalytic groups, utilising both metal ion-dependent (Cu(II)-2,9-dimethylphenanthroline) and metal ion-free (Tris(2-aminobenzimidazole)) on the one hand and PNA as an RNA recognising oligonucleotide on the other, allowed site-selective artificial RNases to be created with half-lives of 0.5-1 h. Artificial RNases based on the catalytic peptide [(ArgLeu)2Gly]2 were able to take progress a step further by demonstrating an ability to cleave miRNA-21 in tumour cells and provide a significant reduction of tumour growth in mice.
Collapse
|
2
|
Mikutis S, Gu M, Sendinc E, Hazemi ME, Kiely-Collins H, Aspris D, Vassiliou GS, Shi Y, Tzelepis K, Bernardes GJL. meCLICK-Seq, a Substrate-Hijacking and RNA Degradation Strategy for the Study of RNA Methylation. ACS CENTRAL SCIENCE 2020; 6:2196-2208. [PMID: 33376781 PMCID: PMC7760485 DOI: 10.1021/acscentsci.0c01094] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Indexed: 06/01/2023]
Abstract
The fates of RNA species in a cell are controlled by ribonucleases, which degrade them by exploiting the universal structural 2'-OH group. This phenomenon plays a key role in numerous transformative technologies, for example, RNA interference and CRISPR/Cas13-based RNA editing systems. These approaches, however, are genetic or oligomer-based and so have inherent limitations. This has led to interest in the development of small molecules capable of degrading nucleic acids in a targeted manner. Here we describe click-degraders, small molecules that can be covalently attached to RNA species through click-chemistry and can degrade them, that are akin to ribonucleases. By using these molecules, we have developed the meCLICK-Seq (methylation CLICK-degradation Sequencing) a method to identify RNA modification substrates with high resolution at intronic and intergenic regions. The method hijacks RNA methyltransferase activity to introduce an alkyne, instead of a methyl, moiety on RNA. Subsequent copper(I)-catalyzed azide-alkyne cycloaddition reaction with the click-degrader leads to RNA cleavage and degradation exploiting a mechanism used by endogenous ribonucleases. Focusing on N6-methyladenosine (m6A), meCLICK-Seq identifies methylated transcripts, determines RNA methylase specificity, and reliably maps modification sites in intronic and intergenic regions. Importantly, we show that METTL16 deposits m6A to intronic polyadenylation (IPA) sites, which suggests a potential role for METTL16 in IPA and, in turn, splicing. Unlike other methods, the readout of meCLICK-Seq is depletion, not enrichment, of modified RNA species, which allows a comprehensive and dynamic study of RNA modifications throughout the transcriptome, including regions of low abundance. The click-degraders are highly modular and so may be exploited to study any RNA modification and design new technologies that rely on RNA degradation.
Collapse
Affiliation(s)
- Sigitas Mikutis
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Muxin Gu
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
| | - Erdem Sendinc
- Boston
Childrens’ Hospital, Harvard Medical
School, 300 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Madoka E. Hazemi
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Hannah Kiely-Collins
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Demetrios Aspris
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
- The
Center for the Study of Haematological Malignancies, Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus
| | - George S. Vassiliou
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
- The
Center for the Study of Haematological Malignancies, Karaiskakio Foundation, Nicandrou Papamina Avenue, 2032 Nicosia, Cyprus
- Wellcome-MRC
Cambridge Stem Cell Institute, University
of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Yang Shi
- Boston
Childrens’ Hospital, Harvard Medical
School, 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- Ludwig
Institute for Cancer Research, Oxford University, Old Road Campus Research Build,
Roosevelt Dr., Oxford OX3
7DQ, U.K.
| | - Konstantinos Tzelepis
- Haematological
Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10
1SA, U.K.
- Boston
Childrens’ Hospital, Harvard Medical
School, 300 Longwood Avenue, Boston, Massachusetts 02115, United States
- Milner Therapeutics
Institute, University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, U.K.
| | - Gonçalo J. L. Bernardes
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
- Instituto
de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
| |
Collapse
|
3
|
Gebrezgiabher M, Zalloum WA, Clarke DJ, Miles SM, Fedorova AA, Zenkova MA, Bichenkova EV. RNA knockdown by synthetic peptidyl-oligonucleotide ribonucleases: behavior of recognition and cleavage elements under physiological conditions. J Biomol Struct Dyn 2020; 39:2555-2574. [PMID: 32248755 DOI: 10.1080/07391102.2020.1751711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Sequence-specific protein-based ribonucleases are not found in nature. Absolute sequence selectivity in RNA cleavage in vivo normally requires multi-component complexes that recruit a guide RNA or DNA for target recognition and a protein-RNA assembly for catalytic functioning (e.g. RNAi molecular machinery, RNase H). Recently discovered peptidyl-oligonucleotide synthetic ribonucleases selectively knock down pathogenic RNAs by irreversible cleavage to offer unprecedented opportunities for control of disease-relevant RNA. Understanding how to increase their potency, selectivity and catalytic turnover will open the translational pathway to successful therapeutics. Yet, very little is known about how these chemical ribonucleases bind, cleave and leave their target. Rational design awaits this understanding in order to control therapy, particularly how to overcome the trade-off between sequence specificity and potency through catalytic turnover. We illuminate this here by characterizing the interactions of these chemical RNases with both complementary and non-complementary RNAs using Tm profiles, fluorescence, UV-visible and NMR spectroscopies. Crucially, the level of counter cations, which are tightly-controlled within cellular compartments, also controlled these interactions. The oligonucleotide component dominated interaction between conjugates and complementary targets in the presence of physiological levels of counter cations (K+), sufficient to prevent repulsion between the complementary nucleic acid strands to allow Watson-Crick hydrogen bonding. In contrast, the positively-charged catalytic peptide interacted poorly with target RNA, when counter cations similarly screened the negatively-charged sugar-phosphate RNA backbones. The peptide only became the key player, when counter cations were insufficient for charge screening; moreover, only under such non-physiological conditions did conjugates form strong complexes with non-complementary RNAs.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Mengisteab Gebrezgiabher
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Waleed A Zalloum
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - David J Clarke
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Steven M Miles
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Antonina A Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena V Bichenkova
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| |
Collapse
|
4
|
Patutina OA, Bichenkova EV, Miroshnichenko SK, Mironova NL, Trivoluzzi LT, Burusco KK, Bryce RA, Vlassov VV, Zenkova MA. miRNases: Novel peptide-oligonucleotide bioconjugates that silence miR-21 in lymphosarcoma cells. Biomaterials 2017; 122:163-178. [PMID: 28126663 DOI: 10.1016/j.biomaterials.2017.01.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/09/2017] [Accepted: 01/12/2017] [Indexed: 12/24/2022]
Abstract
MicroRNAs (miRNAs) are active regulators in malignant growth and constitute potential targets for anticancer therapy. Consequently, considerable effort has focused on identifying effective ways to modulate aberrant miRNA expression. Here we introduce and assess a novel type of chemically engineered biomaterial capable of cleaving specific miRNA sequences, i.e. miRNA-specific artificial ribonucleases (hereafter 'miRNase'). The miRNase template presented here consists of the catalytic peptide Acetyl-[(LeuArg)2Gly]2 covalently attached to a miRNA-targeting oligonucleotide, which can be linear or hairpin. The peptide C-terminus is conjugated to an aminohexyl linker located at either the 3'- or 5'-end of the oligonucleotide. The cleavage efficacy, structural aspects of cleavage and biological relevance of a set of these designed miRNases was assayed with respect to highly oncogenic miR-21. Several miRNases demonstrated effective site-selective cleavage of miR-21 exclusively at G-X bonds. One of the most efficient miRNase was shown to specifically inhibit miR-21 in lymphosarcoma cells and lead to a reduction in their proliferative activity. This report provides the first experimental evidence that metallo-independent peptide-oligonucleotide chemical ribonucleases are able to effectively and selectively down-regulate oncogenic miRNA in tumour cells, thus suggesting their potential in development of novel therapeutics aimed at overcoming overexpression of disease-related miRNAs.
Collapse
Affiliation(s)
- Olga A Patutina
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Svetlana K Miroshnichenko
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia
| | - Nadezhda L Mironova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia
| | - Linda T Trivoluzzi
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Kepa K Burusco
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Richard A Bryce
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Valentin V Vlassov
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia
| | - Marina A Zenkova
- Laboratory of Nucleic Acids Biochemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev ave., 8, Novosibirsk, 630090, Russia.
| |
Collapse
|
5
|
Staroseletz Y, Williams A, Burusco KK, Alibay I, Vlassov VV, Zenkova MA, Bichenkova EV. 'Dual' peptidyl-oligonucleotide conjugates: Role of conformational flexibility in catalytic cleavage of RNA. Biomaterials 2016; 112:44-61. [PMID: 27744220 DOI: 10.1016/j.biomaterials.2016.09.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/23/2016] [Accepted: 09/26/2016] [Indexed: 02/06/2023]
Abstract
Traditional therapeutic interventions against abnormal gene expression in disease states at the level of expressed proteins are becoming increasingly difficult due to poor selectivity, off-target effects and associated toxicity. Upstream catalytic targeting of specific RNA sequences offers an alternative platform for drug discovery to achieve more potent and selective treatment through antisense interference with disease-relevant RNAs. We report a novel class of catalytic biomaterials, comprising amphipathic RNA-cleaving peptides placed between two RNA recognition motifs, here demonstrated to target the TΨC loop and 3'- acceptor stem of tRNAPhe. These unique peptidyl-oligonucleotide 'dual' conjugates (DCs) were created by phosphoramidate or thiol-maleimide conjugation chemistry of a TΨC-targeting oligonucleotide to the N-terminus of the amphipathic peptide sequence, followed by amide coupling of a 3'-acceptor stem-targeting oligonucleotide to the free C-terminal carboxylic acid functionality of the same peptide. Hybridization of the DCs bearing two spatially-separated recognition motifs with the target tRNAPhe placed the peptide adjacent to a single-stranded RNA region and promoted cleavage within the 'action radius' of the catalytic peptide. Up to 100% cleavage of the target tRNAPhe was achieved by the best candidate (i.e. DC6) within 4 h, when conformational flexibility was introduced into the linker regions between the peptide and oligonucleotide components. This study provides the strong position for future development of highly selective RNA-targeting agents that can potentially be used for disease-selective treatment at the level of messenger, micro, and genomic viral RNA.
Collapse
Affiliation(s)
- Yaroslav Staroseletz
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Aled Williams
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Kepa K Burusco
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Irfan Alibay
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK
| | - Valentin V Vlassov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Marina A Zenkova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Elena V Bichenkova
- School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| |
Collapse
|
6
|
Tamkovich N, Koroleva L, Kovpak M, Goncharova E, Silnikov V, Vlassov V, Zenkova M. Design, RNA cleavage and antiviral activity of new artificial ribonucleases derived from mono-, di- and tripeptides connected by linkers of different hydrophobicity. Bioorg Med Chem 2016; 24:1346-55. [PMID: 26899594 DOI: 10.1016/j.bmc.2016.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Revised: 01/29/2016] [Accepted: 02/05/2016] [Indexed: 11/15/2022]
Abstract
A novel series of metal-free artificial ribonucleases (aRNases) was designed, synthesized and assessed in terms of ribonuclease activity and ability to inactivate influenza virus WSN/A33/H1N1 in vitro. The compounds were built of two short peptide fragments, which include Lys, Ser, Arg, Glu and imidazole residues in various combinations, connected by linkers of different hydrophobicity (1,12-diaminododecane or 4,9-dioxa-1,12-diaminododecane). These compounds efficiently cleaved different RNA substrates under physiological conditions at rates three to five times higher than that of artificial ribonucleases described earlier and displayed RNase A-like cleavage specificity. aRNases with the hydrophobic 1,12-diaminododecane linker displayed ribonuclease activity 3-40 times higher than aRNases with the 4,9-dioxa-1,12-diaminododecane linker. The assumed mechanism of RNA cleavage was typical for natural ribonucleases, that is, general acid-base catalysis via the formation of acid/base pairs by functional groups of amino acids present in the aRNases; the pH profile of cleavage confirmed this mechanism. The most active aRNases under study exhibited high antiviral activity and entirely inactivated influenza virus A/WSN/33/(H1N1) after a short incubation period of viral suspension under physiological conditions.
Collapse
Affiliation(s)
- Nikolay Tamkovich
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Lyudmila Koroleva
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Mikhail Kovpak
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Elena Goncharova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Vladimir Silnikov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Valentin Vlassov
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia
| | - Marina Zenkova
- Institute of Chemical Biology and Fundamental Medicine, Lavrentiev Ave, 8, Novosibirsk 630090, Russia.
| |
Collapse
|
7
|
Dogandzhiyski P, Ghidini A, Danneberg F, Strömberg R, Göbel MW. Studies on Tris(2-aminobenzimidazole)-PNA Based Artificial Nucleases: A Comparison of Two Analytical Techniques. Bioconjug Chem 2015; 26:2514-9. [PMID: 26544527 DOI: 10.1021/acs.bioconjchem.5b00534] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A new peptide nucleic acid (PNA) construct carrying a tris(2-aminobenzimidazole) phosphodiester cleaver is presented. This non-metal-based artificial nuclease hydrolyzes RNA substrates that form a bulge upon binding to the PNA. Reaction rates depend on the bulge sequence. For conjugates of tris(2-aminobenzimidazole), substrate turnover is shown for the first time. Two methods of analysis for the kinetics are compared: IE-HPLC separation of oligonucleotide fragments and analysis of Cy5-labeled oligonucleotide fragments by denaturating PAGE on a DNA sequencer, respectively. The different methods give rates that are in the same range where, in general, the substrates for the sequencer method give slightly lower rates.
Collapse
Affiliation(s)
- Plamena Dogandzhiyski
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
| | - Alice Ghidini
- Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden
| | - Friederike Danneberg
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
| | - Roger Strömberg
- Department of Biosciences and Nutrition, Karolinska Institutet , Novum, S-14157, Huddinge, Sweden
| | - Michael W Göbel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt , Max-von-Laue-Str. 7, D-60439 Frankfurt am Main, Germany
| |
Collapse
|
8
|
Dhawan G, Chandra R, Gupta KC, Kumar P. Facile and rapid deprotection conditions for the cleavage of synthetic oligonucleotides from 1,4-anhydroerythritol-based universal polymer support. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:149-62. [PMID: 25710353 DOI: 10.1080/15257770.2014.975244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In our previous report [Kumar, P.; Dhawan, G.; Chandra, R.; Gupta, K.C. Polyamine-assisted rapid and clean cleavage of oligonucleotides from cis-diol bearing universal support. Nucl. Acids Res. 2002, 30, e130 (1-8)], we demonstrated polyamine-mediated deprotection of oligonucleotides from cis-diol group bearing universal polymer support (I). However, vulnerability of the conventional dC(bz) to modifications under these conditions compelled us to employ dC(ac) during synthesis of oligonucleotide using conventional synthons. Here, a new set of simple and rapid deprotection conditions has been developed for the complete cleavage of oligonucleotides from the 1,4-anhydroerythritol-based universal polymer support employing conventional dC(bz) synthon. Using manganese-imidazole complex in aqueous ammonium hydroxide (∼ 30%), fully deprotected oligonucleotide sequences were obtained in 40 min, which were analyzed on reverse phase-HPLC and compared with the standard oligomers in terms of their retention time. Finally, their biological compatibility was established by analyzing PCR amplified products of npsA gene of N. meningitidis.
Collapse
Affiliation(s)
- Gagan Dhawan
- a Nucleic Acids Research Laboratory, CSIR-Institute of Genomics and Integrative Biology , Delhi , India
| | | | | | | |
Collapse
|
9
|
Williams A, Staroseletz Y, Zenkova MA, Jeannin L, Aojula H, Bichenkova EV. Peptidyl-oligonucleotide conjugates demonstrate efficient cleavage of RNA in a sequence-specific manner. Bioconjug Chem 2015; 26:1129-43. [PMID: 25955796 DOI: 10.1021/acs.bioconjchem.5b00193] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Described here is a new class of peptidyl-oligonucleotide conjugates (POCs) which show efficient cleavage of a target RNA in a sequence-specific manner. Through phosphoramidate attachment of a 17-mer TΨC-targeting oligonucleotide to amphiphilic peptide sequences containing leucine, arginine, and glycine, zero-linker conjugates are created which exhibit targeted phosphodiester cleavage under physiological conditions. tRNA(Phe) from brewer's yeast was used as a model target sequence in order to probe different structural variants of POCs in terms of selective TΨC-arm directed cleavage. Almost quantitative (97-100%) sequence-specific tRNA cleavage is observed for several POCs over a 24 h period with a reaction half-life of less than 1 h. Nontargeted cleavage of tRNA(Phe) or HIV-1 RNA is absent. Structure-activity relationships reveal that removal of the peptide's central glycine residue significantly decreases tRNA cleavage activity; however, this can be entirely restored through replacement of the peptide's C-terminal carboxylic acid group with the carboxamide functionality. Truncation of the catalytic peptide also has a detrimental effect on POC activity. Based on the encouraging results presented, POCs could be further developed with the aim of creating useful tools for molecular biology or novel therapeutics targeting specific messenger, miRNA, and genomic viral RNA sequences.
Collapse
Affiliation(s)
- Aled Williams
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
| | - Yaroslav Staroseletz
- ‡Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Marina A Zenkova
- ‡Institute of Chemical Biology and Fundamental Medicine SB RAS, 8 Laurentiev Avenue, 630090, Novosibirsk, Russia
| | - Laurent Jeannin
- §Peptisyntha S.A., 310 Rue de Ransbeek, 1120 Brussels, Belgium
| | - Harmesh Aojula
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
| | - Elena V Bichenkova
- †Manchester Pharmacy School, University of Manchester, Oxford Road, Manchester, United Kingdom, M13 9PT
| |
Collapse
|
10
|
Burakova E, Kovalev N, Zenkova M, Vlassov V, Silnikov V. Structure–activity relationships in new polycationic molecules based on two 1,4-diazabicyclo[2.2.2]octanes as artificial ribonucleases. Bioorg Chem 2014; 57:127-131. [DOI: 10.1016/j.bioorg.2014.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 10/10/2014] [Accepted: 10/12/2014] [Indexed: 11/30/2022]
|
11
|
Patel S, Rana J, Roy J, Huang H. Cleavage of pyrene-stabilized RNA bulge loops by trans-(±)-cyclohexane-1,2-diamine. Chem Cent J 2012; 6:3. [PMID: 22244351 PMCID: PMC3319420 DOI: 10.1186/1752-153x-6-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 01/13/2012] [Indexed: 11/10/2022] Open
Abstract
Chemical agents that cleave HIV genome can be potentially used for anti-HIV therapy. In this report, the cleavage of the upper stem-loop region of HIV-1 TAR RNA was studied in a variety of buffers containing organic catalysts. trans-(±)-Cyclohexane-1,2-diamine was found to cleave the RNA with the highest activity (31%, 37°C, 18 h). Cleavage of the RNA in trans-(±)-cyclohexane-1,2-diamine buffer was also studied when the RNA was hybridized with complementary DNAs. A pyrene-modified C3 spacer was incorporated to the DNA strand to facilitate the formation of a RNA bulge loop in the RNA/DNA duplex. In contrast, unmodified DNAs cannot efficiently generate RNA bulge loops, regardless of the DNA sequences. The results showed that the pyrene-stablized RNA bulge loops were efficiently and site-specifically cleaved by trans-(±)-cyclohexane-1,2-diamine.
Collapse
Affiliation(s)
- Sejal Patel
- Department of Chemistry and Environmental Science, New Jersey Institute of Technology, 323 Martin L, King Blvd, Newark, NJ, 07102, USA.
| | | | | | | |
Collapse
|
12
|
Beloglazova NG, Fabani MM, Polushin NN, Sil'nikov VV, Vlassov VV, Bichenkova EV, Zenkova MA. Site-selective artificial ribonucleases: oligonucleotide conjugates containing multiple imidazole residues in the catalytic domain. J Nucleic Acids 2011; 2011:748632. [PMID: 21961054 PMCID: PMC3180074 DOI: 10.4061/2011/748632] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 07/05/2011] [Indexed: 12/05/2022] Open
Abstract
Design of site-selective artificial ribonucleases (aRNases) is one of the most challenging tasks in RNA targeting. Here, we designed and studied oligonucleotide-based aRNases containing multiple imidazole residues in the catalytic part and systematically varied structure of cleaving constructs. We demonstrated that the ribonuclease activity of the conjugates is strongly affected by the number of imidazole residues in the catalytic part, the length of a linker between the catalytic imidazole groups of the construct and the oligonucleotide, and the type of anchor group, connecting linker structure and the oligonucleotide. Molecular modeling of the most active aRNases showed that preferable orientation(s) of cleaving constructs strongly depend on the structure of the anchor group and length of the linker. The inclusion of deoxyribothymidine anchor group significantly reduced the probability of cleaving groups to locate near the cleavage site, presumably due to a stacking interaction with the neighbouring nucleotide residue. Altogether the obtained results show that dynamics factors play an important role in site-specific RNA cleavage. Remarkably high cleavage activity was displayed by the conjugates with the most flexible and extended cleaving construct, which presumably provides a better opportunity for imidazole residues to be correctly positioned in the vicinity of scissile phosphodiester bond.
Collapse
Affiliation(s)
- Natalia G Beloglazova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | | | | | | | | | | | | |
Collapse
|
13
|
Saleh AD, Miller PS. Hydrolysis of bulged nucleotides in hybrids formed by RNA and imidazole-derivatized oligo-2'-O-methylribonucleotides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2011; 30:235-55. [PMID: 21491332 DOI: 10.1080/15257770.2011.569810] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In order to enhance the efficacy of small antisense molecules, we examined a series of antisense oligonucleotides derivatized with functional groups designed to enable them to hydrolyze their RNA target. Solid phase synthetic methods were used to prepare imidazole-derivatized antisense oligo-2'-O-methylribonucleotides. Upon binding, these oligonucleotides create internal bulged bases in the target RNA that serve as sites for hydrolysis. We observed that an oligonucleotide derivatized with a side chain containing two imidazole groups was capable of hydrolyzing 58% of its RNA target when incubated with the target for 48 hours at 37°C and physiological pH.
Collapse
Affiliation(s)
- Anthony D Saleh
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | | |
Collapse
|
14
|
Thomas JM, Yoon JK, Perrin DM. Investigation of the catalytic mechanism of a synthetic DNAzyme with protein-like functionality: an RNaseA mimic? J Am Chem Soc 2010; 131:5648-58. [PMID: 20560639 DOI: 10.1021/ja900125n] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The protein enzyme ribonuclease A (RNaseA) cleaves RNA with catalytic perfection, although with little sequence specificity, by a divalent metal ion (M(2+))-independent mechanism in which a pair of imidazoles provides general acid and base catalysis, while a cationic amine provides electrostatic stabilization of the transition state. Synthetic imitation of this remarkable organo-catalyst ("RNaseA mimicry") has been a longstanding goal in biomimetic chemistry. The 9(25)-11 DNAzyme contains synthetically modified nucleotides presenting both imidazole and cationic amine side chains, and catalyzes RNA cleavage with turnover in the absence of M(2+) similarly to RNaseA. Nevertheless, the catalytic roles, if any, of the "protein-like" functional groups have not been defined, and hence the question remains whether 9(25)-11 engages any of these functionalities to mimic aspects of the mechanism of RNaseA. To address this question, we report a mechanistic investigation of 9(25)-11 catalysis wherein we have employed a variety of experiments, such as DNAzyme functional group deletion, mechanism-based affinity labeling, and bridging and nonbridging phosphorothioate substitution of the scissile phosphate. Several striking parallels exist between the results presented here for 9(25)-11 and the results of analogous experiments applied previously to RNaseA. Specifically, our results implicate two particular imidazoles in general acid and base catalysis and suggest that a specific cationic amine stabilizes the transition state via diastereoselective interaction with the scissile phosphate. Overall, 9(25)-11 appears to meet the minimal criteria of an RNaseA mimic; this demonstrates how added synthetic functionality can expand the mechanistic repertoire available to a synthetic DNA-based catalyst.
Collapse
Affiliation(s)
- Jason M Thomas
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | | | | |
Collapse
|
15
|
Metal–bipyridine complexes in DNA backbones and effects on thermal stability. J Biol Inorg Chem 2010; 15:629-39. [DOI: 10.1007/s00775-010-0630-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2009] [Accepted: 01/22/2010] [Indexed: 10/19/2022]
|
16
|
Gamble C, Trotard M, Le Seyec J, Abreu-Guerniou V, Gernigon N, Berrée F, Carboni B, Felden B, Gillet R. Antiviral effect of ribonuclease conjugated oligodeoxynucleotides targeting the IRES RNA of the hepatitis C virus. Bioorg Med Chem Lett 2009; 19:3581-5. [PMID: 19450979 DOI: 10.1016/j.bmcl.2009.04.139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2009] [Revised: 04/27/2009] [Accepted: 04/27/2009] [Indexed: 02/05/2023]
Abstract
Hepatitis C virus (HCV) translation initiation is mediated by a highly structured and conserved RNA, termed the Internal Ribosome Entry Site (IRES), located at the 5'-end of its single stranded RNA genome. It is a key target for the development of new antiviral compounds. Here we made use of the recently developed HCV cell culture system to test the antiviral activity of artificial ribonucleases consisting of imidazole(s) linked to antisense oligodeoxynucleotides targeting the HCV IRES. Results from the cell culture model indicate that the naked antisense oligodeoxynucleotide displayed an efficient antiviral activity. Despite the increased activity observed with the addition of imidazole moieties when tested with the cell-free system, it appears that these improvements were not reproduced in the cellular model.
Collapse
Affiliation(s)
- Carly Gamble
- Université de Rennes 1, UPRES JE 2311, INSERM U835, Biochimie Pharmaceutique, 2, Avenue du Prof. Léon Bernard, 35043 Rennes, France
| | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Razkin J, Lindgren J, Nilsson H, Baltzer L. Enhanced complexity and catalytic efficiency in the hydrolysis of phosphate diesters by rationally designed helix-loop-helix motifs. Chembiochem 2008; 9:1975-84. [PMID: 18600814 DOI: 10.1002/cbic.200800057] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
HJ1, a 42-residue peptide that folds into a helix-loop-helix motif and dimerizes to form a four-helix bundle, successfully catalyzes the cleavage of "early stage" DNA model substrates in an aqueous solution at pH 7.0, with a rate enhancement in the hydrolysis of heptyl 4-nitrophenyl phosphate of over three orders of magnitude over that of the imidazole-catalyzed reaction, k(2)(HJ1)/k(2)(Im) = 3135. The second-order rate constant, k(2)(HJ1) was determined to be 1.58x10(-4) M(-1) s(-1). The catalyst successfully assembles residues that in a single elementary reaction step are capable of general-acid and general-base catalysis as well as transition state stabilization and proximity effects. The reactivity achieved with the HJ1 polypeptide, rationally designed to catalyze the hydrolysis of phosphodiesters, is based on two histidine residues flanked by four arginines and two adjacent tyrosine residues, all located on the surface of a helix-loop-helix motif. The introduction of Tyr residues close to the catalytic site improves efficiency, in the cleavage of activated aryl alkyl phosphates as well as less activated dialkyl phosphates. HJ1 is also effective in the cleavage of an RNA-mimic substrate, uridine-3'-2,2,2-trichloroethyl phosphate (leaving group pK(a) = 12.3) with a second-order rate constant of 8.23x10(-4) M(-1) s(-1) in aqueous solution at pH 7.0, some 500 times faster than the reaction catalyzed by imidazole, k(2)(HJ1)/k(2)(Im) = 496.
Collapse
Affiliation(s)
- Jesus Razkin
- Department of Applied Chemistry, Public University of Navarra, 31006 Pamplona, Navarra, Spain.
| | | | | | | |
Collapse
|
18
|
Pulido D, López-Alonso JP, Marchán V, González C, Grandas A, Laurents DV. Preparation of ribonuclease S domain-swapped dimers conjugated with DNA and PNA: modulating the activity of ribonucleases. Bioconjug Chem 2007; 19:263-70. [PMID: 18163547 DOI: 10.1021/bc700374q] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Obtaining highly specific and active ribonuclease activities is an important goal with numerous medical and biochemical applications. As a step toward more active and specific ribonucleases, we describe the preparation and the enzymatic and structural properties of RNase S monomers and dimers conjugated to DNA and PNA molecules. Poly(dT)n (2'-oligodeoxyribonucleotides, n = 8, 15) and t8 peptide nucleic acid (PNA) chains have been conjugated to the S-peptide of ribonuclease S. Monomers and dimers of the conjugated enzyme have been obtained and characterized by 1H NMR spectroscopy, showing that DNA or PNA conjugation does not alter the native structure of ribonuclease S. The oligonucleotide-conjugated RNase S monomer and dimer show significant activity against single-stranded RNA and very low/negligible hydrolysis of double-stranded poly(A).poly(U). In contrast, the t8-conjugated RNase S monomer and dimer show substantial activity against both ssRNA and dsRNA. These results highlight the importance of positive charges near but not in the active site in enhancing activity against dsRNA and reveal the promise of PNA-RNase conjugates for modulating RNase activity.
Collapse
Affiliation(s)
- Daniel Pulido
- Department de Química Orgànica, Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
| | | | | | | | | | | |
Collapse
|
19
|
Kovalev NA, Medvedeva DA, Zenkova MA, Vlassov VV. Cleavage of RNA by an amphiphilic compound lacking traditional catalytic groups. Bioorg Chem 2007; 36:33-45. [PMID: 18061645 DOI: 10.1016/j.bioorg.2007.10.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 10/02/2007] [Accepted: 10/05/2007] [Indexed: 12/23/2022]
Abstract
Recently, in experiments with combinatorial libraries of amphiphilic compounds lacking groups, known as catalysts of transesterification reaction, we discovered novel RNA-cleaving compounds [N. Kovalev, E. Burakova, V. Silnikov, M. Zenkova, V. Vlassov, Bioorg. Chem. 34 (2006) 274-286]. In the present study, we investigate cleavage of RNA by the most active representative of these libraries, compound named Dp12. Sequence-specificity of RNA cleavage and influence of reaction conditions on cleavage rate suggested that Dp12 enormously accelerates spontaneous RNA cleavage. Light scattering experiments revealed that the RNA cleavage proceeds within multiplexes formed by assembles of RNA and Dp12 molecules, at Dp12 concentration far below critical concentration of micelle formation. Under these conditions, Dp12 is presented in the solution as individual molecules, but addition of RNA to this solution triggers formation of the multiplexes. The obtained data suggest a possible mechanism of RNA cleavage, which includes interaction of the compound with RNA sugar-phosphate backbone resulting in changing of ribose conformation. This leads to juxtaposition of the 2'-hydroxyl group and internucleotide phosphorus atom at a distance needed for the transesterification to occur.
Collapse
Affiliation(s)
- N A Kovalev
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, 8 Lavrentiev Avenue, 630090 Novosibirsk, Russian Federation
| | | | | | | |
Collapse
|
20
|
Ma Y, Chen X, Sun M, Wan R, Zhu C, Li Y, Zhao Y. DNA cleavage function of seryl-histidine dipeptide and its application. Amino Acids 2007; 35:251-6. [DOI: 10.1007/s00726-007-0597-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2007] [Accepted: 08/01/2007] [Indexed: 12/01/2022]
|
21
|
Guerniou V, Gillet R, Berrée F, Carboni B, Felden B. Targeted inhibition of the hepatitis C internal ribosomal entry site genomic RNA with oligonucleotide conjugates. Nucleic Acids Res 2007; 35:6778-87. [PMID: 17921501 PMCID: PMC2175329 DOI: 10.1093/nar/gkm770] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Hepatitis C is a major public health concern, with an estimated 170 million people infected worldwide and an urgent need for new drug development. An attractive therapeutic approach is to prevent the ‘cap-independent’ translation initiation of the viral proteins by interfering with both the structure and function of the hepatitis C viral internal ribosomal entry site (HCV IRES). Towards this goal, we report the design, synthesis and purification of novel bi-functional molecules containing DNA or RNA antisenses attached to functional groups performing RNA hydrolysis. These 5′ or 3′-coupled conjugates bind the HCV IRES with affinity and specificity and elicit targeted hydrolysis of the viral genomic RNA after short (1 h) incubation at low (500 nM) concentration at 37°C in vitro. Additional secondary cleavage sites are induced and their mapping within the RNA structure indicates that functional domains IIIb-e are excised from the IRES that, based on cryo-EM studies, becomes incapable of binding the small ribosomal subunit and initiation factor 3 (eIF3). All these molecules inhibit, in a dose-dependent manner, the ‘IRES-dependent’ translation in vitro. The 5′-coupled imidazole conjugate reduces viral protein synthesis by half at a 300 nM concentration (IC50), corresponding to a 4-fold increase of activity when compared to the naked oligonucleotide. These new conjugates are now being tested for activity on infected hepatic cell lines.
Collapse
Affiliation(s)
- Valérie Guerniou
- Biochimie Pharmaceutique, Inserm U835, Upres JE 2311, Université de Rennes 1, France
| | | | | | | | | |
Collapse
|
22
|
Abramova TV, Kassakin MF, Lomzov AA, Pyshnyi DV, Silnikov VN. New oligonucleotide analogues based on morpholine subunits joined by oxalyl diamide tether. Bioorg Chem 2007; 35:258-75. [PMID: 17303213 DOI: 10.1016/j.bioorg.2006.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 12/08/2006] [Accepted: 12/15/2006] [Indexed: 10/23/2022]
Abstract
We report on the design, synthesis and some of the properties of the new oligonucleotide analogues based on morpholine nucleoside (MorB) subunits joined by an oxalyl diamide tether instead of a phosphate group. The synthetic strategy and oligomer design are optimized to easily obtain target substances without using protective groups. The dimers HOMorU-Ox-NHMorU, HOMorU-Ox-NHMorA, and uracil containing the hexamer HOMorU-(Ox-NHMorU)5 were synthesized. The structures of all substances were confirmed by 1H, 13C, NMR, and mass spectroscopy. Base stacking interactions in dimers were revealed by CD-spectra data.
Collapse
Affiliation(s)
- Tatiana V Abramova
- The Institute of Chemical Biology and Fundamental Medicine, Lavrent'ev Ave 8, Novosibirsk 630090, Russia.
| | | | | | | | | |
Collapse
|
23
|
Catry MA, Madder A. Synthesis of functionalised nucleosides for incorporation into nucleic acid-based serine protease mimics. Molecules 2007; 12:114-29. [PMID: 17693958 PMCID: PMC6149322 DOI: 10.3390/12010114] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 01/29/2007] [Accepted: 01/30/2006] [Indexed: 11/17/2022] Open
Abstract
The synthesis of nucleosides modified with an extra imidazole, carboxyl and hydroxyl group is described. These nucleosides can be incorporated into an oligonucleotide duplex, thus generating a novel type of serine protease mimic.
Collapse
Affiliation(s)
| | - Annemieke Madder
- Ghent University, Department of Organic Chemistry, Laboratory for Organic and Biomimetic Chemistry, Krijgslaan 281 (S4), B-9000 Gent, Belgium
| |
Collapse
|
24
|
Kovalev N, Burakova E, Silnikov V, Zenkova M, Vlassov V. Artificial ribonucleases: from combinatorial libraries to efficient catalysts of RNA cleavage. Bioorg Chem 2006; 34:274-86. [PMID: 16889817 DOI: 10.1016/j.bioorg.2006.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 06/21/2006] [Accepted: 06/21/2006] [Indexed: 11/23/2022]
Abstract
Combinatorial libraries of small organic compounds capable of cleaving RNA were synthesized. The compounds contain benzene ring substituted with two residues of bis quaternary salt of diazabicyclo[2.2.2]octane (DABCO) bearing hydrophobic fragments of different length and structure, attached to DABCO at the bridge position. These compounds, lacking traditional functionalities involved in transesterification reaction, exhibit pronounced RNA cleavage activity. To identify the most active artificial ribonucleases, sublibraries and truncated libraries, containing compounds lacking one of substituents were synthesized. Analysis of ribonuclease activity of truncated libraries resulted in identification of the most active compounds, which are characterized by the presence of at least one long oligomethylene substituent.
Collapse
Affiliation(s)
- N Kovalev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 8, Lavrentiev Ave., Novosibirsk, 630090, Russian Federation
| | | | | | | | | |
Collapse
|
25
|
Mironova NL, Pyshnyi DV, Stadler DV, Prokudin IV, Boutorine YI, Ivanova EM, Zenkova MA, Gross HJ, Vlassov VV. G-specific RNA-cleaving conjugates of short peptides and oligodeoxyribonucleotides. J Biomol Struct Dyn 2006; 23:591-602. [PMID: 16615805 DOI: 10.1080/07391102.2006.10507084] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Artificial ribonucleases, conjugates of short oligodeoxyribonucleotides and peptides built of arginine, leucine, proline, and serine, were synthesized and assessed in terms of ribonuclease activity and specificity of RNA cleavage. A specific group of the conjugates was identified that display T1-ribonuclease-like activity and cleave RNA predominantly at G-X sequences. Circular dichroism study of the structures of the most active conjugates, free peptide (LR)4G, and oligonucleotides revealed that conjugation of oligonucleotide to the peptide results in a specific peptide folding that possibly provides ribonuclease activity to the conjugate.
Collapse
Affiliation(s)
- Nadezhda L Mironova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev Avenue 8, Russian Federation, Novosibirsk, 630090
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Dioubankova NN, Malakhov AD, Stetsenko DA, Gait MJ, Korshun VA. Phosphoramidites and solid supports based on N-substituted 2,4-dihydroxybutyramides: universal reagents for synthesis of modified oligonucleotides. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
27
|
Abramova TV, Silnikov VN. 4-aminometyl-3-nitrobenzoic acid--a photocleavable linker for oligonucleotides containing combinatorial libraries. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:1333-43. [PMID: 16252670 DOI: 10.1080/15257770500230509] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
We detail the design, synthesis, and characterization of an o-nitrobenzyl-based photolabile linker containing amine and carboxyl anchor groups. A model nucleoside monomer modified with an imidazole residue and a precursor unit linked to a heterocyclic base through a photolabile tether is constructed Upon UV irradiation (313- 365 nm), the imidazole containing part of this molecule is released.
Collapse
Affiliation(s)
- Tatiana V Abramova
- The Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia.
| | | |
Collapse
|
28
|
Putnam WC, Bashkin JK. Synthesis and evaluation of RNA transesterification efficiency using stereospecific serinol-terpyridine conjugates. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2005; 24:1309-23. [PMID: 16252668 DOI: 10.1080/15257770500230426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Six novel artificial ribonucleases were synthesized employing a stereochemically pure abasic serinol backbone residue for attachment of the RNA transesterification agent copper(II) terpyridine. These stereochemically pure abasic residues were synthesized as phosphoramidite building blocks from the parent L-serine and D-serine starting building blocks and incorporated into oligonucleotides via solid-phase DNA synthesis. These artificial ribonucleases were constructed to determine if the stereochemistry of the alpha carbon of an abasic serinol residue has influence over RNA transesterification through selective placement of a pendant transesterification agent in either the major or minor groove. The novel artificial ribonucleases and previously synthesized artificial ribonucleases were challenged with a 28-mer and 159-mer RNA substrate. It was determined that the stereochemistry of the carbon atom derived from the alpha-carbon of serine did not influence the extent of cleavage in these studies using copper(II) terpyridine conjugated artificial ribonucleases.
Collapse
Affiliation(s)
- William C Putnam
- Department of Chemistry, Washington University, St. Louis, Missouri, USA.
| | | |
Collapse
|
29
|
Holmes SC, Gait MJ. Syntheses and Oligonucleotide Incorporation of Nucleoside Analogues Containing Pendant Imidazolyl or Amino Functionalities - The Search for Sequence-Specific Artificial Ribonucleases. European J Org Chem 2005. [DOI: 10.1002/ejoc.200500413] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
30
|
Abstract
Mimicking the action of enzymes by simpler and more robust man-made catalysts has long inspired bioorganic chemists. During the past decade, mimics for RNA-cleaving enzymes, ribonucleases, or, more precisely, mimics of ribozymes that cleave RNA in sequence-selective rather than base-selective manner, have received special attention. These artificial ribonucleases are typically oligonucleotides (or their structural analogs) that bear a catalytically active conjugate group and catalyze sequence-selective hydrolysis of RNA phosphodiester bonds.
Collapse
Affiliation(s)
- Teija Niittymäki
- Department of Chemistry, University of Turku, FIN-20014, Turku, Finland
| | | |
Collapse
|
31
|
Ting R, Thomas JM, Lermer L, Perrin DM. Substrate specificity and kinetic framework of a DNAzyme with an expanded chemical repertoire: a putative RNaseA mimic that catalyzes RNA hydrolysis independent of a divalent metal cation. Nucleic Acids Res 2004; 32:6660-72. [PMID: 15625232 PMCID: PMC545449 DOI: 10.1093/nar/gkh1007] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2004] [Revised: 11/24/2004] [Accepted: 11/24/2004] [Indexed: 11/13/2022] Open
Abstract
This work addresses the binding, cleavage and dissociation rates for the substrate and products of a synthetic RNaseA mimic that was combinatorially selected using chemically modified nucleoside triphosphates. This trans-cleaving DNAzyme, 9(25)-11t, catalyzes sequence-specific ribophosphodiester hydrolysis in the total absence of a divalent metal cation, and in low ionic strength at pH 7.5 and in the presence of EDTA. It is the first such sequence capable of multiple turnover. 9(25)-11t consists of 31 bases, 18 of which form a catalytic domain containing 4 imidazole and 6 allylamino modified nucleotides. This sequence cleaves the 15 nt long substrate, S1, at one embedded ribocytosine at the eighth position to give a 5'-product terminating in a 2',3'-phosphodiester and a 3'-product terminating in a 5'-OH. Under single turnover conditions at 24 degrees C, 9(25)-11t displays a maximum first-order rate constant, k(cat), of 0.037 min(-1) and a catalytic efficiency, k(cat)/K(m), of 5.3 x 10(5) M(-1) min(-1). The measured value of k(cat) under catalyst excess conditions agrees with the value of k(cat) observed for steady-state multiple turnover, implying that slow product release is not rate limiting with respect to multiple turnover. The substrate specificity of 9(25)-11t was gauged in terms of k(cat) values for substrate sequence variants. Base substitutions on the scissile ribose and at the two bases immediately downstream decrease k(cat) values by a factor of 4 to 250, indicating that 9(25)-11t displays significant sequence specificity despite the lack of an apparent Watson-Crick base-pairing scheme for recognition.
Collapse
Affiliation(s)
- Richard Ting
- Chemistry Department, 2036 Main Mall, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | | | | | | |
Collapse
|