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Liu X, Hu J, Ning Y, Xu H, Cai H, Yang A, Shi Z, Li Z. Aptamer Technology and Its Applications in Bone Diseases. Cell Transplant 2023; 32:9636897221144949. [PMID: 36591965 PMCID: PMC9811309 DOI: 10.1177/09636897221144949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Aptamers are single-stranded nucleic acids (DNA, short RNA, or other artificial molecules) produced by the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology, which can be tightly and specifically combined with desired targets. As a comparable alternative to antibodies, aptamers have many advantages over traditional antibodies such as a strong chemical stability and rapid bulk production. In addition, aptamers can bind targets in various ways, and are not limited like the antigen-antibody combination. Studies have shown that aptamers have tremendous potential to diagnose and treat clinical diseases. However, only a few aptamer-based drugs have been used because of limitations of the aptamers and SELEX technology. To promote the development and applications of aptamers, we present a review of the methods optimizing the SELEX technology and modifying aptamers to boost the selection success rate and improve aptamer characteristics. In addition, we review the application of aptamers to treat bone diseases.
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Affiliation(s)
- Xiangzhong Liu
- Department of Orthopaedics, Wuhan Third
Hospital, Tongren Hospital of Wuhan University, Wuhan, China
| | - Jing Hu
- Wuhan Children’s Hospital, Tongji
Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Yu Ning
- Department of Orthopaedics, Xiangyang
Hospital of Traditional Chinese Medicine Affiliated to Hubei University of Chinese
Medicine, Xiangyang, China
| | - Haijia Xu
- Department of Orthopaedics, Wuhan Third
Hospital, Tongren Hospital of Wuhan University, Wuhan, China
| | - Hantao Cai
- Department of Orthopaedics, Wenling
First People’s Hospital, Taizhou, China
| | - Aofei Yang
- Department of Orthopaedics, Hubei
Hospital of Traditional Chinese Medicine, Wuhan, China
| | - Zhengshuai Shi
- Department of Orthopaedics, Wuhan
Sports University, Wuhan, China
| | - Zhanghua Li
- Department of Orthopaedics, Wuhan Third
Hospital, Tongren Hospital of Wuhan University, Wuhan, China,Zhanghua Li, Department of Orthopaedics,
Wuhan Third Hospital, Tongren Hospital of Wuhan University, No. 216, Guanshan
Avenue, Hongshan District, Wuhan 430074, Hubei Province, China.
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Żydowicz-Machtel P, Dutkiewicz M, Swiatkowska A, Gurda-Woźna D, Ciesiołka J. Translation of human Δ133p53 mRNA and its targeting by antisense oligonucleotides complementary to the 5'-terminal region of this mRNA. PLoS One 2021; 16:e0256938. [PMID: 34492050 PMCID: PMC8423303 DOI: 10.1371/journal.pone.0256938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/18/2021] [Indexed: 11/18/2022] Open
Abstract
The p53 protein is expressed as at least twelve protein isoforms. Within intron 4 of the human TP53 gene, a P2 transcription initiation site is located and this transcript encodes two p53 isoforms: Δ133p53 and Δ160p53. Here, the secondary structure of the 5'-terminal region of P2-initiated mRNA was characterized by means of the SHAPE and Pb2+-induced cleavage methods and for the first time, a secondary structure model of this region was proposed. Surprisingly, only Δ133p53 isoform was synthetized in vitro from the P2-initiated p53 mRNA while translation from both initiation codons occurred after the transfection of vector-encoded model mRNA to HCT116 cells. Interestingly, translation performed in the presence of the cap analogue suggested that the cap-independent process contributes to the translation of P2-initiated p53 mRNA. Subsequently, several antisense oligonucleotides targeting the 5'-terminal region of P2-initiated p53 mRNA were designed. The selected oligomers were applied in in vitro translation assays as well as in cell lines and their impact on the Δ133p53 synthesis and on cell viability was investigated. The results show that these oligomers are attractive tools in the modulation of the translation of P2-initiated p53 mRNA through attacking the 5' terminus of the transcript. Since cell proliferation is also reduced by antisense oligomers that lower the level of Δ133p53, this demonstrates an involvement of this isoform in tumorigenesis.
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Affiliation(s)
| | - Mariola Dutkiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Agata Swiatkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Dorota Gurda-Woźna
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Jerzy Ciesiołka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- * E-mail:
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3
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Netter HJ, Barrios MH, Littlejohn M, Yuen LKW. Hepatitis Delta Virus (HDV) and Delta-Like Agents: Insights Into Their Origin. Front Microbiol 2021; 12:652962. [PMID: 34234753 PMCID: PMC8256844 DOI: 10.3389/fmicb.2021.652962] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 05/12/2021] [Indexed: 01/05/2023] Open
Abstract
Hepatitis delta virus (HDV) is a human pathogen, and the only known species in the genus Deltavirus. HDV is a satellite virus and depends on the hepatitis B virus (HBV) for packaging, release, and transmission. Extracellular HDV virions contain the genomic HDV RNA, a single-stranded negative-sense and covalently closed circular RNA molecule, which is associated with the HDV-encoded delta antigen forming a ribonucleoprotein complex, and enveloped by the HBV surface antigens. Replication occurs in the nucleus and is mediated by host enzymes and assisted by cis-acting ribozymes allowing the formation of monomer length molecules which are ligated by host ligases to form unbranched rod-like circles. Recently, meta-transcriptomic studies investigating various vertebrate and invertebrate samples identified RNA species with similarities to HDV RNA. The delta-like agents may be representatives of novel subviral agents or satellite viruses which share with HDV, the self-complementarity of the circular RNA genome, the ability to encode a protein, and the presence of ribozyme sequences. The widespread distribution of delta-like agents across different taxa with considerable phylogenetic distances may be instrumental in comprehending their evolutionary history by elucidating the transition from transcriptome to cellular circular RNAs to infectious subviral agents.
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Affiliation(s)
- Hans J Netter
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne Health, The Peter Doherty Institute, Melbourne, VIC, Australia.,School of Science, Royal Melbourne Institute of Technology (RMIT) University, Melbourne, VIC, Australia
| | - Marilou H Barrios
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne Health, The Peter Doherty Institute, Melbourne, VIC, Australia.,The Peter Doherty Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Margaret Littlejohn
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne Health, The Peter Doherty Institute, Melbourne, VIC, Australia
| | - Lilly K W Yuen
- Victorian Infectious Diseases Reference Laboratory (VIDRL), Melbourne Health, The Peter Doherty Institute, Melbourne, VIC, Australia
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4
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Kasprowicz A, Stokowa-Sołtys K, Jeżowska-Bojczuk M, Wrzesiński J, Ciesiołka J. Characterization of Highly Efficient RNA-Cleaving DNAzymes that Function at Acidic pH with No Divalent Metal-Ion Cofactors. ChemistryOpen 2016; 6:46-56. [PMID: 28168150 PMCID: PMC5288747 DOI: 10.1002/open.201600141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 11/29/2016] [Indexed: 12/02/2022] Open
Abstract
Here, we describe the characterization of new RNA‐cleaving DNAzymes that showed the highest catalytic efficiency at pH 4.0 to 4.5, and were completely inactive at pH values higher than 5.0. Importantly, these DNAzymes did not require any divalent metal ion cofactors for catalysis. This clearly suggests that protonated nucleic bases are involved in the folding of the DNAzymes into catalytically active structures and/or in the cleavage mechanism. The trans‐acting DNAzyme variants were also catalytically active. Mutational analysis revealed a conservative character of the DNAzyme catalytic core that underpins the high structural requirements of the cleavage mechanism. A significant advantage of the described DNAzymes is that they are inactive at pH values close to physiological pH and under a wide range of conditions in the presence of monovalent and divalent metal ions. These pH‐dependent DNAzymes could be used as molecular cassettes in biotechnology or nanotechnology, in molecular processes that consist of several steps. The results expand the repertoire of DNAzymes that are active under nonphysiological conditions and shed new light on the possible mechanisms of catalysis.
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Affiliation(s)
- Aleksandra Kasprowicz
- Institute of Bioorganic Chemistry Polish Academy of Sciences Noskowskiego 12/14 61-704 Poznań Poland
| | | | | | - Jan Wrzesiński
- Institute of Bioorganic Chemistry Polish Academy of Sciences Noskowskiego 12/14 61-704 Poznań Poland
| | - Jerzy Ciesiołka
- Institute of Bioorganic Chemistry Polish Academy of Sciences Noskowskiego 12/14 61-704 Poznań Poland
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5
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Kasprowicz A, Stokowa-Sołtys K, Wrzesiński J, Jeżowska-Bojczuk M, Ciesiołka J. In vitro selection of deoxyribozymes active with Cd(2+) ions resulting in variants of DNAzyme 8-17. Dalton Trans 2016; 44:8138-49. [PMID: 25836771 DOI: 10.1039/c5dt00187k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In vitro selection was performed to search for RNA-cleaving DNAzymes catalytically active with Cd(2+) ions from the oligonucleotide combinatorial library with a 23-nucleotide random region. All the selected, catalytically active variants turned out to belong to the 8-17 type DNAzyme. Three DNAzymes were prepared in shortened, cis-acting versions which were subjected to a detailed study of the kinetic properties and metal ion preferences. Although the selection protocol was designed for Cd(2+)-dependent DNAzymes, the variants showed broader metal ion specificity. They preferred Cd(2+) but were also active with Mn(2+) and Zn(2+), suggesting that binding of the catalytic ion does not require an extremely specific coordination pattern. The unexpected decrease of the catalytic activity of the variants along with the temperature increase suggested that some changes occurred in their structures or the rate-limiting step of the reaction was changed. Two elements of the catalytic core of DNAzyme 1/VIIWS, the nucleotide at position 12 and the three-base-pair hairpin motif, were mutated. The presence of a purine residue at position 12 was crucial for the catalytic activity but the changes at that position had a relatively small influence on the metal ion preferences of this variant. The middle base pair of the three-base-pair hairpin was changed from A-T to C-G interaction. The catalytic activity of the mutated variant was increased with Zn(2+), decreased with Mn(2+), and was not changed in the presence of Cd(2+) ions. Clearly, this base pair was important for defining the metal ion preferences of the DNAzyme 1/VIIWS.
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Affiliation(s)
- Aleksandra Kasprowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland.
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6
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Stokowa-Sołtys K, Barbosa NA, Kasprowicz A, Wieczorek R, Gaggelli N, Gaggelli E, Valensin G, Wrzesiński J, Ciesiołka J, Kuliński T, Szczepanik W, Jeżowska-Bojczuk M. Studies of viomycin, an anti-tuberculosis antibiotic: copper(ii) coordination, DNA degradation and the impact on delta ribozyme cleavage activity. Dalton Trans 2016; 45:8645-58. [DOI: 10.1039/c6dt00245e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Viomycin is a basic peptide antibiotic, which is among the most effective agents against multidrug-resistant tuberculosis.
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Affiliation(s)
| | - N. A. Barbosa
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - A. Kasprowicz
- Institute of Bioorganic Chemistry
- Polish Academy of Sciences
- 61-704 Poznań
- Poland
| | - R. Wieczorek
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - N. Gaggelli
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena Via Aldo Moro
- 2-53100 Siena
- Italy
| | - E. Gaggelli
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena Via Aldo Moro
- 2-53100 Siena
- Italy
| | - G. Valensin
- Department of Biotechnology
- Chemistry and Pharmacy
- University of Siena Via Aldo Moro
- 2-53100 Siena
- Italy
| | - J. Wrzesiński
- Institute of Bioorganic Chemistry
- Polish Academy of Sciences
- 61-704 Poznań
- Poland
| | - J. Ciesiołka
- Institute of Bioorganic Chemistry
- Polish Academy of Sciences
- 61-704 Poznań
- Poland
| | - T. Kuliński
- Institute of Bioorganic Chemistry
- Polish Academy of Sciences
- 61-704 Poznań
- Poland
| | - W. Szczepanik
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
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7
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Ciesiołka J, Jeżowska-Bojczuk M, Wrzesiński J, Stokowa-Sołtys K, Nagaj J, Kasprowicz A, Błaszczyk L, Szczepanik W. Antibiotic bacitracin induces hydrolytic degradation of nucleic acids. Biochim Biophys Acta Gen Subj 2014; 1840:1782-9. [DOI: 10.1016/j.bbagen.2014.01.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/16/2014] [Accepted: 01/29/2014] [Indexed: 10/25/2022]
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Riccitelli N, Lupták A. HDV family of self-cleaving ribozymes. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2014; 120:123-71. [PMID: 24156943 DOI: 10.1016/b978-0-12-381286-5.00004-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The hepatitis delta virus (HDV) ribozymes are catalytic RNAs capable of cleaving their own sugar-phosphate backbone. The HDV virus possesses the ribozymes in both sense and antisense genomic transcripts, where they are essential for processing during replication. These ribozymes have been the subject of intense biochemical scrutiny and have yielded a wealth of mechanistic insights. In recent years, many HDV-like ribozymes have been identified in nearly all branches of life. The ribozymes are implicated in a variety of biological events, including episodic memory in mammals and retrotransposition in many eukaryotes. Detailed analysis of additional HDV-like ribozyme isolates will likely reveal many more biological functions and provide information about the evolution of this unique RNA.
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Affiliation(s)
- Nathan Riccitelli
- Department of Chemistry, University of California, Irvine, California, USA
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9
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Riccitelli NJ, Delwart E, Lupták A. Identification of minimal HDV-like ribozymes with unique divalent metal ion dependence in the human microbiome. Biochemistry 2014; 53:1616-26. [PMID: 24555915 DOI: 10.1021/bi401717w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
HDV-like self-cleaving ribozymes have been found in a wide variety of organisms, implicated in diverse biological processes, and their activity typically shows a strong divalent metal dependence, but little metal specificity. Recent studies suggested that very short variants of these ribozymes exist in nature, but their distribution and biochemical properties have not been established. To map out the distribution of small HDV-like ribozymes, the drz-Spur-3 sequence was minimized to yield a core construct for structure-based bioinformatic searches. These searches revealed several microbial ribozymes, particularly in the human microbiome. Kinetic profile of the smallest ribozyme revealed two distinct metal binding sites, only one of which promotes fast catalysis. Furthermore, this ribozyme showed markedly reduced activity in Ca(2+), even in the presence of physiological Mg(2+) concentrations. Our study substantially expands the number of microbial HDV-like ribozymes and provides an example of cleavage regulation by divalent metals.
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Affiliation(s)
- Nathan J Riccitelli
- Department of Chemistry, ∥Department of Pharmaceutical Sciences, and ⊥Department of Molecular Biology and Biochemistry, University of California-Irvine , Irvine, California 92697, United States
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Eickbush DG, Burke WD, Eickbush TH. Evolution of the R2 retrotransposon ribozyme and its self-cleavage site. PLoS One 2013; 8:e66441. [PMID: 24066021 PMCID: PMC3774820 DOI: 10.1371/journal.pone.0066441] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 05/07/2013] [Indexed: 12/23/2022] Open
Abstract
R2 is a non-long terminal repeat retrotransposon that inserts site-specifically in the tandem 28S rRNA genes of many animals. Previously, R2 RNA from various species of Drosophila was shown to self-cleave from the 28S rRNA/R2 co-transcript by a hepatitis D virus (HDV)-like ribozyme encoded at its 5' end. RNA cleavage was at the precise 5' junction of the element with the 28S gene. Here we report that RNAs encompassing the 5' ends of R2 elements from throughout its species range fold into HDV-like ribozymes. In vitro assays of RNA self-cleavage conducted in many R2 lineages confirmed activity. For many R2s, RNA self-cleavage was not at the 5' end of the element but at 28S rRNA sequences up to 36 nucleotides upstream of the junction. The location of cleavage correlated well with the types of endogenous R2 5' junctions from different species. R2 5' junctions were uniform for most R2s in which RNA cleavage was upstream in the rRNA sequences. The 28S sequences remaining on the first DNA strand synthesized during retrotransposition are postulated to anneal to the target site and uniformly prime second strand DNA synthesis. In species where RNA cleavage occurred at the R2 5' end, the 5' junctions were variable. This junction variation is postulated to result from the priming of second strand DNA synthesis by chance microhomologies between the target site and the first DNA strand. Finally, features of R2 ribozyme evolution, especially changes in cleavage site and convergence on the same active site sequences, are discussed.
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Affiliation(s)
- Danna G. Eickbush
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - William D. Burke
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Thomas H. Eickbush
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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Stokowa-Sołtys K, Gaggelli N, Nagaj J, Szczepanik W, Ciesiołka J, Wrzesiński J, Górska A, Gaggelli E, Valensin G, Jeżowska-Bojczuk M. High affinity of copper(II) towards amoxicillin, apramycin and ristomycin. Effect of these complexes on the catalytic activity of HDV ribozyme. J Inorg Biochem 2013; 124:26-34. [DOI: 10.1016/j.jinorgbio.2013.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 02/28/2013] [Accepted: 03/04/2013] [Indexed: 12/18/2022]
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Wrzesinski J, Błaszczyk L, Wrońska M, Kasprowicz A, Stokowa-Sołtys K, Nagaj J, Szafraniec M, Kulinski T, Jeżowska-Bojczuk M, Ciesiołka J. Mapping the interactions of selected antibiotics and their Cu2+complexes with the antigenomic delta ribozyme. FEBS J 2013; 280:2652-64. [DOI: 10.1111/febs.12257] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/15/2013] [Accepted: 03/18/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Jan Wrzesinski
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznań; Poland
| | - Leszek Błaszczyk
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznań; Poland
| | | | | | | | | | - Milena Szafraniec
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznań; Poland
| | - Tadeusz Kulinski
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznań; Poland
| | | | - Jerzy Ciesiołka
- Institute of Bioorganic Chemistry; Polish Academy of Sciences; Poznań; Poland
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Wrońska M, Wrzesinski J, Jeżowska-Bojczuk M, Szczepanik W, Starosta R, Barys M, Ciunik Z, Ciesiołka J. The impact of isomers of hemiaminal-1,2,4-triazole conjugates differently substituted in the phenyl ring and their Cu2+ complexes on the catalytic activity of the antigenomic delta ribozyme. J Inorg Biochem 2012; 108:62-8. [PMID: 22266462 DOI: 10.1016/j.jinorgbio.2011.12.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 11/30/2011] [Accepted: 12/16/2011] [Indexed: 02/05/2023]
Abstract
The ability of four stable hemiaminals differently substituted in the phenyl ring and their complexes with Cu(2+) ions to inhibit catalytic cleavage of the antigenomic delta ribozyme was compared. The hemiaminals were novel chiral derivatives of 1,2,4-triazole [i.e. (2,4-dinitrophenyl)(4H-1,2,4-triazol-4-ylamino) methanol (2,4-dnbald), (2-nitrophenyl)(4H-1,2,4-triazol-4-ylamino) methanol (2-nbald), (3-nitrophenyl)(4H-1,2,4-triazol-4-ylamino) methanol (3-nbald) and (4-nitrophenyl)(4H-1,2,4-triazol-4-ylamino) methanol (4-nbald)]. The complexes of nbalds with Cu(2+) were characterized using UV and EPR methods and additionally, the formation of 2,4-dnbald-Cu(2+) complex with CuL(2) stoichiometry was confirmed by mass spectrometry. The data suggest that there are two ways in which nbalds and their Cu(2+) complexes can influence catalytic cleavage of antigenomic delta ribozyme. The coordinated Cu(2+) ions may play the role of new cationic ligands increasing the affinity of the complexes to the ribozyme. Such situation occurs in the case of 2- and 2,4-nbald. Their Cu(2+) complexes decrease ribozyme cleavage rates twice more efficiently than uncomplexed compounds. Moreover, the Cu(2+) complexes displace the catalytic divalent metal ions from their strong binding sites located in the ribozyme J4/2 region as shown by the Pb(2+)-induced cleavage approach. On the other hand, 3- and 4-nbald inhibit catalysis more strongly as compared to 2-nbald and 2,4-dnbald but the ribozyme cleavage rates are changed only slightly upon Cu(2+) complexation. The mechanism of ribozyme inhibition by interfering with the formation of a correct ribozyme tertiary structure seems to operate in this case.
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14
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Szafraniec M, Stokowa-Sołtys K, Nagaj J, Kasprowicz A, Wrzesiński J, Jeżowska-Bojczuk M, Ciesiołka J. Capreomycin and hygromycin B modulate the catalytic activity of the delta ribozyme in a manner that depends on the protonation and complexation with Cu2+ ions of these antibiotics. Dalton Trans 2012; 41:9728-36. [DOI: 10.1039/c2dt30794d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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15
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Ruminski DJ, Webb CHT, Riccitelli NJ, Lupták A. Processing and translation initiation of non-long terminal repeat retrotransposons by hepatitis delta virus (HDV)-like self-cleaving ribozymes. J Biol Chem 2011; 286:41286-41295. [PMID: 21994949 DOI: 10.1074/jbc.m111.297283] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Many non-long terminal repeat (non-LTR) retrotransposons lack internal promoters and are co-transcribed with their host genes. These transcripts need to be liberated before inserting into new loci. Using structure-based bioinformatics, we show that several classes of retrotransposons in phyla-spanning arthropods, nematodes, and chordates utilize self-cleaving ribozymes of the hepatitis delta virus (HDV) family for processing their 5' termini. Ribozyme-terminated retrotransposons include rDNA-specific R2, R4, and R6, telomere-specific SART, and Baggins and RTE. The self-scission of the R2 ribozyme is strongly modulated by the insertion site sequence in the rDNA, with the most common insertion sequences promoting faster processing. The ribozymes also promote translation initiation of downstream open reading frames in vitro and in vivo. In some organisms HDV-like and hammerhead ribozymes appear to be dedicated to processing long and short interspersed elements, respectively. HDV-like ribozymes serve several distinct functions in non-LTR retrotransposition, including 5' processing, translation initiation, and potentially trans-templating.
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Affiliation(s)
- Dana J Ruminski
- Departments of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | - Chiu-Ho T Webb
- Departments of Molecular Biology and Biochemistry, University of California, Irvine, California 92697
| | | | - Andrej Lupták
- Departments of Molecular Biology and Biochemistry, University of California, Irvine, California 92697; Department of Chemistry, University of California, Irvine, California 92697; Department of Pharmaceutical Sciences, University of California, Irvine, California 92697.
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Abstract
HDV ribozymes catalyze their own scission from the transcript during rolling circle replication of the hepatitis delta virus. In vitro selection of self-cleaving ribozymes from a human genomic library revealed an HDV-like ribozyme in the second intron of the human CPEB3 gene and recent results suggest that this RNA affects episodic memory performance. Bioinformatic searches based on the secondary structure of the HDV/CPEB3 fold yielded numerous functional ribozymes in a wide variety of organisms. Genomic mapping of these RNAs suggested several biological roles, one of which is the 5' processing of non-LTR retrotransposons. The family of HDV-like ribozymes thus continues to grow in numbers and biological importance.
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Affiliation(s)
- Chiu-Ho T Webb
- Department of Molecular Biology, University of California, Irvine, CA, USA
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Luo X, McKeague M, Pitre S, Dumontier M, Green J, Golshani A, Derosa MC, Dehne F. Computational approaches toward the design of pools for the in vitro selection of complex aptamers. RNA (NEW YORK, N.Y.) 2010; 16:2252-62. [PMID: 20870801 PMCID: PMC2957063 DOI: 10.1261/rna.2102210] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
It is well known that using random RNA/DNA sequences for SELEX experiments will generally yield low-complexity structures. Early experimental results suggest that having a structurally diverse library, which, for instance, includes high-order junctions, may prove useful in finding new functional motifs. Here, we develop two computational methods to generate sequences that exhibit higher structural complexity and can be used to increase the overall structural diversity of initial pools for in vitro selection experiments. Random Filtering selectively increases the number of five-way junctions in RNA/DNA pools, and Genetic Filtering designs RNA/DNA pools to a specified structure distribution, whether uniform or otherwise. We show that using our computationally designed DNA pool greatly improves access to highly complex sequence structures for SELEX experiments (without losing our ability to select for common one-way and two-way junction sequences).
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Affiliation(s)
- Xuemei Luo
- School of Computer Science, Carleton University, Ottawa, Ontario K1S5B6, Canada
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Riccitelli NJ, Lupták A. Computational discovery of folded RNA domains in genomes and in vitro selected libraries. Methods 2010; 52:133-40. [PMID: 20554049 DOI: 10.1016/j.ymeth.2010.06.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Accepted: 06/03/2010] [Indexed: 10/19/2022] Open
Abstract
Structured functional RNAs are conserved on the level of secondary and tertiary structure, rather than at sequence level, and so traditional sequence-based searches often fail to identify them. Structure-based searches are increasingly used to discover known RNA motifs in sequence databases. We describe the application of the program RNABOB, which performs such searches by allowing the user to define a desired motif's sequence, paired and spacer elements and then scans a sequence file for regions capable of assuming the prescribed fold. Structure descriptors of stem-loops, internal loops, three-way junctions, kissing loops, and the hammerhead and hepatitis delta virus ribozymes are shown as examples of implementation of structure-based searches.
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Wrzesinski J, Wichłacz A, Nijakowska D, Rebowska B, Nawrot B, Ciesiołka J. Phosphate residues of antigenomic HDV ribozyme important for catalysis that are revealed by phosphorothioate modification. NEW J CHEM 2010. [DOI: 10.1039/b9nj00727j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Dutkiewicz M, Swiatkowska A, Figlerowicz M, Ciesiołka J. Structural domains of the 3'-terminal sequence of the hepatitis C virus replicative strand. Biochemistry 2008; 47:12197-207. [PMID: 18947238 DOI: 10.1021/bi800348g] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Here we present the results of a structural analysis of the 3'-terminal region of the replicative strand of hepatitis C virus (HCV), IRES(-), by the Pb (2+)-induced cleavage approach and partial digestion with T1 ribonuclease. Oligoribonucleotides that represent selected domains of the earlier proposed in the literature secondary structure models of this region were also synthesized, their structures were analyzed in solution, and the results were compared to those obtained with the full-length molecule. Such "structural fingerprinting" gave better insight into the structure of the IRES(-) region. We showed that in the case of the IRES(-) fragment, which consists of 374 nucleotides, its three domains, D3 (nucleotides 1-104), DM (nucleotides 105-222), and D5 (nucleotides 223-374), independently fold on one another. However, when the IRES(-) molecule is extended by 25 nucleotides of the upstream viral sequence, domains D3 and DM fold autonomously, but a part of domain D5 interacts with that additional RNA stretch. Analysis in silico suggests that similar interactions involving the IRES(-) region and upstream sequences are also possible in other fragments of viral RNA, several hundreds of nucleotides in length. The results of experimental probing are supported by secondary structure predictions in silico and phylogenetic analysis.
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Affiliation(s)
- Mariola Dutkiewicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań 61-704, Poland.
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Nehdi A, Perreault J, Beaudoin JD, Perreault JP. A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme. Nucleic Acids Res 2007; 35:6820-31. [PMID: 17933779 PMCID: PMC2175327 DOI: 10.1093/nar/gkm674] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
A bioinformatic covariation analysis of a collection of 119 novel variants of the antigenomic, self-cleaving hepatitis delta virus (HDV) RNA motif supported the formation of all of the Watson–Crick base pairs (bp) of the catalytic centre except the C19–G81 pair located at the bottom of the P2 stem. In fact, a novel Watson–Crick bp between C19 and G80 is suggested by the data. Both chemical and enzymatic probing demonstrated that initially the C19–G81 pair is formed in the ribozyme (Rz), but upon substrate (S) binding and the formation of the P1.1 pseudoknot C19 switches its base-pairing partner from G81 to G80. As a result of this finding, the secondary structure of this ribozyme has been redrawn. The formation of the C19–G80 bp results in a J4/2 junction composed of four nucleotides, similar to that seen in the genomic counterpart, thereby increasing the similarities between these two catalytic RNAs. Additional mutagenesis, cleavage activity and probing experiments yield an original characterization of the structural features involving the residues of the J4/2 junction.
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Affiliation(s)
- Atef Nehdi
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
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Ultrasensitive monitoring of ribozyme cleavage product using molecular-beacon-ligation system. ACTA ACUST UNITED AC 2007. [DOI: 10.1007/s11434-007-0074-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Salehi-Ashtiani K, Lupták A, Litovchick A, Szostak JW. A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene. Science 2006; 313:1788-92. [PMID: 16990549 DOI: 10.1126/science.1129308] [Citation(s) in RCA: 209] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ribozymes are thought to have played a pivotal role in the early evolution of life, but relatively few have been identified in modern organisms. We performed an in vitro selection aimed at isolating self-cleaving RNAs from the human genome. The selection yielded several ribozymes, one of which is a conserved mammalian sequence that resides in an intron of the CPEB3 gene, which belongs to a family of genes regulating messenger RNA polyadenylation. The CPEB3 ribozyme is structurally and biochemically related to the human hepatitis delta virus (HDV) ribozymes. The occurrence of this ribozyme exclusively in mammals suggests that it may have evolved as recently as 200 million years ago. We postulate that HDV arose from the human transcriptome.
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Affiliation(s)
- Kourosh Salehi-Ashtiani
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology (CCIB), 7215 Simches Research Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
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