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Xiao L, Zhao Y, Yang M, Luan G, Du T, Deng S, Jia X. A promising nucleic acid therapy drug: DNAzymes and its delivery system. Front Mol Biosci 2023; 10:1270101. [PMID: 37753371 PMCID: PMC10518456 DOI: 10.3389/fmolb.2023.1270101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/29/2023] [Indexed: 09/28/2023] Open
Abstract
Based on the development of nucleic acid therapeutic drugs, DNAzymes obtained through in vitro selection technology in 1994 are gradually being sought. DNAzymes are single-stranded DNA molecules with catalytic function, which specifically cleave RNA under the action of metal ions. Various in vivo and in vitro models have recently demonstrated that DNAzymes can target related genes in cancer, cardiovascular disease, bacterial and viral infection, and central nervous system disease. Compared with other nucleic acid therapy drugs, DNAzymes have gained more attention due to their excellent cutting efficiency, high stability, and low cost. Here, We first briefly reviewed the development and characteristics of DNAzymes, then discussed disease-targeting inhibition model of DNAzymes, hoping to provide new insights and ways for disease treatment. Finally, DNAzymes were still subject to some restrictions in practical applications, including low cell uptake efficiency, nuclease degradation and interference from other biological matrices. We discussed the latest delivery strategy of DNAzymes, among which lipid nanoparticles have recently received widespread attention due to the successful delivery of the COVID-19 mRNA vaccine, which provides the possibility for the subsequent clinical application of DNAzymes. In addition, the future development of DNAzymes was prospected.
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Affiliation(s)
- Lang Xiao
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
| | - Yan Zhao
- Life Science and Engineering, Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Meng Yang
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
| | - Guangxin Luan
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
| | - Ting Du
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
| | - Shanshan Deng
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
| | - Xu Jia
- School of Basic Medical Sciences, Chengdu Medical College, Chengdu, Sichuan, China
- Sichuan Key Laboratory of Noncoding RNA and Drugs, Chengdu Medical College, Chengdu, Sichuan, China
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Fokina AA, Stetsenko DA, François JC. DNA enzymes as potential therapeutics: towards clinical application of 10-23 DNAzymes. Expert Opin Biol Ther 2015; 15:689-711. [PMID: 25772532 DOI: 10.1517/14712598.2015.1025048] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Ongoing studies on the inhibition of gene expression at the mRNA level have identified several types of specific inhibitors such as antisense oligonucleotides, small interfering RNA, ribozymes and DNAzymes (Dz). After its discovery in 1997, the 10-23 Dz (which can cleave RNA efficiently and site-specifically, has flexible design, is independent from cell mechanisms, does not require expensive chemical modifications for effective use in vivo) has been employed to downregulate a range of therapeutically important genes. Recently, 10-23 Dzs have taken their first steps into clinical trials. AREAS COVERED This review focuses predominantly on Dz applications as potential antiviral, antibacterial, anti-cancer and anti-inflammatory agents as well as for the treatment of cardiovascular disease and diseases of CNS, summarizing results of their clinical trials up to the present day. EXPERT OPINION In comparison with antisense oligonucleotides and small interfering RNAs, Dzs do not usually show off-target effects due to their high specificity and lack of immunogenicity in vivo. As more results of clinical trials carried out so far are gradually becoming available, Dzs may turn out to be safe and well-tolerated therapeutics in humans. Therefore, there is a good chance that we may witness a deoxyribozyme drug reaching the clinic in the near future.
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Affiliation(s)
- Alesya A Fokina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090 , Russia
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Gebbing M, Bergmann T, Schulz E, Ehrhardt A. Gene therapeutic approaches to inhibit hepatitis B virus replication. World J Hepatol 2015; 7:150-164. [PMID: 25729471 PMCID: PMC4342598 DOI: 10.4254/wjh.v7.i2.150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/23/2014] [Accepted: 11/19/2014] [Indexed: 02/06/2023] Open
Abstract
Acute and chronic hepatitis B virus (HBV) infections remain to present a major global health problem. The infection can be associated with acute symptomatic or asymptomatic hepatitis which can cause chronic inflammation of the liver and over years this can lead to cirrhosis and the development of hepatocellular carcinomas. Currently available therapeutics for chronically infected individuals aim at reducing viral replication and to slow down or stop the progression of the disease. Therefore, novel treatment options are needed to efficiently combat and eradicate this disease. Here we provide a state of the art overview of gene therapeutic approaches to inhibit HBV replication. We discuss non-viral and viral approaches which were explored to deliver therapeutic nucleic acids aiming at reducing HBV replication. Types of delivered therapeutic nucleic acids which were studied since many years include antisense oligodeoxynucleotides and antisense RNA, ribozymes and DNAzymes, RNA interference, and external guide sequences. More recently designer nucleases gained increased attention and were exploited to destroy the HBV genome. In addition we mention other strategies to reduce HBV replication based on delivery of DNA encoding dominant negative mutants and DNA vaccination. In combination with available cell culture and animal models for HBV infection, in vitro and in vivo studies can be performed to test efficacy of gene therapeutic approaches. Recent progress but also challenges will be specified and future perspectives will be discussed. This is an exciting time to explore such approaches because recent successes of gene therapeutic strategies in the clinic to treat genetic diseases raise hope to find alternative treatment options for patients chronically infected with HBV.
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Roy S, Gupta N, Subramanian N, Mondal T, Banerjea AC, Das S. Sequence-specific cleavage of hepatitis C virus RNA by DNAzymes: inhibition of viral RNA translation and replication. J Gen Virol 2008; 89:1579-1586. [PMID: 18559927 DOI: 10.1099/vir.0.83650-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
DNAzyme (Dz) molecules have been shown to be highly efficient inhibitors of virus replication. Hepatitis C virus RNA translation is mediated by an internal ribosome entry site (IRES) element located mostly in the 5' untranslated region (UTR), the mechanism of which is fundamentally different from cap-dependent translation of cellular mRNAs, and thus an attractive target for designing antiviral drugs. Inhibition of HCV IRES-mediated translation has drastic consequences for the replication of viral RNA as well. We have designed several Dzs, targeting different regions of HCV IRES specific for 1b and also sequences conserved across genotypes. The RNA cleavage and translation inhibitory activities of these molecules were tested in a cell-free system and in cell culture using transient transfections. The majority of Dzs efficiently inhibited HCV IRES-mediated translation. However, these Dz molecules did not show significant inhibition of coxsackievirus B3 IRES-mediated translation or cap-dependent translation of reporter gene, showing high level of specificity towards target RNA. Also, Northern blot hybridization analysis showed significant cleavage of HCV IRES by the Dz molecules in Huh7 cells transiently transfected with the HCV-FLuc monocistronic construct. Interestingly, one of the Dzs was more effective against genotype1b, whereas the other showed significant inhibition of viral RNA replication in Huh7 cells harbouring a HCV 2a monocistronic replicon. As expected, mutant-Dz failed to cleave RNA and inhibit HCV RNA translation, showing the specificity of inhibition. Taken together, these findings suggest that the Dz molecule can be used as selective and effective inhibitor of HCV RNA replication, which can be explored further for development of a potent therapeutic agent against HCV infection.
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Affiliation(s)
- Swagata Roy
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
| | - Nidhi Gupta
- National Institute of Immunology, Department of Virology, New Delhi-110067, India
| | - Nithya Subramanian
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
| | - Tanmoy Mondal
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
| | | | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India
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Pardo M, Bartolomé J, Carreño V. Current therapy of chronic hepatitis B. Arch Med Res 2007; 38:661-77. [PMID: 17613358 DOI: 10.1016/j.arcmed.2006.12.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2006] [Accepted: 12/04/2006] [Indexed: 12/24/2022]
Affiliation(s)
- Margarita Pardo
- Fundación para el Estudio de las Hepatitis Virales, Madrid, Spain
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Yuan BF, Xue Y, Luo M, Hao YH, Tan Z. Two DNAzymes targeting the telomerase mRNA with large difference in Mg2+ concentration for maximal catalytic activity. Int J Biochem Cell Biol 2007; 39:1119-29. [PMID: 17499543 DOI: 10.1016/j.biocel.2007.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2007] [Revised: 02/25/2007] [Accepted: 03/06/2007] [Indexed: 11/19/2022]
Abstract
The 10-23 RNA-cleaving DNAzymes require divalent metal ions, preferentially Mg(2+), for catalytic activity. For intracellular applications, it is important that a DNAzyme can perform maximal cleavage at physiological concentration of Mg(2+) (0.2-2mM). We designed DNAzymes targeting the mRNA of human telomere reverse transcriptase, two of them turned out to have large difference in Mg(2+) concentration requirement (1mM vs. 20mM) for maximal activity in vitro. When the two DNAzymes were transfected into HeLa cells, only the one requiring low Mg(2+) concentration showed inhibitory activity indicating that the in vitro property regarding Mg(2+) requirement was reserved in vivo. The cleavage of target RNA mainly involves two processes, that is hybridization of DNAzyme with substrate and cleavage of substrate in the DNAzyme-substrate duplex. To explore how the optimal Mg(2+) concentration was determined, we studied the effect of Mg(2+) on the two processes. For both DNAzymes, Mg(2+) enhanced hybridization over a range of concentration far beyond 1mM. Once the DNAzymes hybridized with their 19-mer substrates without flanking sequences, the cleavages showed little difference in Mg(2+) concentration-dependence. These facts suggest that the flanking sequences played a key role in determining the Mg(2+) concentration for maximal DNAzyme activity possibly via the formation of higher order structure in the DNAzyme-substrate duplex.
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Affiliation(s)
- Bi-Feng Yuan
- Laboratory of Biochemistry and Biophysics, College of Life Sciences, Wuhan University, Wuhan 430072, China
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Garibotti AV, Knudsen SM, Ellington AD, Seeman NC. Functional DNAzymes organized into two-dimensional arrays. NANO LETTERS 2006; 6:1505-7. [PMID: 16834439 PMCID: PMC2536694 DOI: 10.1021/nl0609955] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
DNAzymes are catalytically active DNA molecules, which have previously been described in solution. Here, we organize these molecules into a series of two-dimensional (2D) arrays using a periodic arrangement of DNA structures based on the DNA double crossover motif. We demonstrate by means of atomic force microscopy that the DNAzymes are organized according to the design and that they retain their activity when attached in linear strings within the context of the 2D array.
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Affiliation(s)
| | - Scott M. Knudsen
- Department of Chemistry & Biochemistry, University of Texas, Austin TX 78712, USA
| | - Andrew D. Ellington
- Department of Chemistry & Biochemistry, University of Texas, Austin TX 78712, USA
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Trepanier J, Tanner JE, Momparler RL, Le ONL, Alvarez F, Alfieri C. Cleavage of intracellular hepatitis C RNA in the virus core protein coding region by deoxyribozymes. J Viral Hepat 2006; 13:131-8. [PMID: 16436131 DOI: 10.1111/j.1365-2893.2005.00684.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hepatitis C virus (HCV) infection represents an important global health problem. Current antiviral therapeutics for HCV have proven inadequate in stemming the disease process. A novel therapeutic strategy involves the use of deoxyribozymes, also known as DNA enzymes or DNAzymes. These catalytic DNA molecules, designed to target and cleave specific RNA sequences, have shown promise in in vitro experimental models for various diseases and may serve as an alternative or adjunct to current HCV drug therapy. We designed and tested several deoxyribozymes that can bind and cleave highly conserved RNA sequences encoding the HCV core protein in in vitro systems. One of these deoxyribozymes reduced the level of our HCV RNA target by 32% and 48% after 24 h of cell exposure when tested in human hepatoma and epithelial cell lines, respectively. As this deoxyribozyme showed significant cleavage activity against HCV core protein target RNA in human cells, it may have potential as a therapeutic candidate for clinical trial in HCV infected patients.
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Affiliation(s)
- J Trepanier
- Department of Microbiology, Sainte-Justine Hospital Research Centre, University of Montreal, Montreal, Quebec, Canada
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Li J, Zhu D, Yi Z, He Y, Chun Y, Liu Y, Li N. DNAzymes Targeting theiclGene Inhibit ICL Expression and DecreaseMycobacterium tuberculosisSurvival in Macrophages. Oligonucleotides 2005; 15:215-22. [PMID: 16201909 DOI: 10.1089/oli.2005.15.215] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Latent infection with Mycobacterium tuberculosis presents a big obstacle for tuberculosis therapy. In this study, we investigated the effects of sequence-specific DNAzymes targeting the mRNA of isocitrate lyase (ICL), an enzyme playing a pivotal role in the metabolism of M. tuberculosis in the latent state, on the expression of ICL and survival of M. tuberculosis. In vitro studies showed that four of five designed DNAzymes, DZ1, DZ3, DZ4, and DZ5 could cleave icl mRNA efficiently and specifically. Treatment of virulent M. tuberculosis with 5microM DZ4 plus a subinhibitory concentration of isoniazid (INH) decreased ICL expression and the survival of M. tuberculosis in macrophages but had no obvious influence on the growth of M. tuberculosis in vitro. This study demonstrates that using INH to soften the cell wall of M. tuberculosis and help the entry of biomolecules is an efficient method of improving the uptake of DNAzymes. Silencing the icl gene by DNAzyme is a promising method to combat latent infection of tuberculosis.
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Affiliation(s)
- Junming Li
- Department of Microbiology and Immunology, Chongqing University of Medical Sciences, 1 Yixueyuan Road, Yuzhong District, Chongqing 400016, China.
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Phylactou LA, Kilpatrick MW. Potential therapy paradigms for Marfan syndrome. Expert Opin Investig Drugs 2005; 8:983-93. [PMID: 15992100 DOI: 10.1517/13543784.8.7.983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Marfan syndrome is the most common genetic disorder of the connective tissue with an estimated prevalence of 1:10,000. The disease is characterised by manifestations in the cardiovascular, skeletal and ocular systems. The most severe manifestations are those of the cardiovascular system: mitral valve prolapse and dilation of the aortic root, which may progress to aortic dissection, a common cause of mortality in patients. Marfan syndrome is a dominant genetic disorder caused by mutations in the gene coding for fibrillin-1, the FBN1 gene. Fibrillin, a 347 kDa glycoprotein, is found in most connective tissues and is a major component of the extracellular microfibrils. More than 100 different FBN1 mutations have been identified in individuals with Marfan syndrome, the majority of which are unique missense point mutations. Evidence suggests a dominant-negative mechanism of pathogenesis for the disorder, that is, the presence of the mutant fibrillin molecule interferes with the function of the normal protein. Therapies for dominant disorders such as Marfan syndrome (MFS) are likely to require both suppression of the disease allele expression and maintenance of expression of its wild-type counterpart. Thus, dominant genetic disorders present a unique therapeutic challenge. One approach to developing a therapy would be to use catalytic nucleic acid molecules. Antisense catalytic RNAs, or ribozymes, have been widely used to down-regulate or repair targeted gene expression respectively through the cleavage or trans-splicing of messenger RNA. Similarly, antisense DNA molecules or DNAzymes have been shown to be capable of cleaving target RNA molecules in a highly specific manner. This review will discuss the potential of catalytic nucleic acid molecules as therapeutic agents for MFS.
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Affiliation(s)
- L A Phylactou
- The Cyprus Institute of Neurology and Genetics, 6 International Airport Avenue, PO Box 23462, 1683 Nicosia, Cyprus.
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Torresi J, Locarnini SA. New therapeutic strategies in the treatment of hepatitis B virus infection. Expert Opin Investig Drugs 2005; 8:289-305. [PMID: 15992079 DOI: 10.1517/13543784.8.3.289] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Principally, because of the association of the chronic carrier state with the development of cirrhotic liver disease and hepatocellular carcinoma, chronic hepatitis B infection is a public health problem of global significance. In the main, therapy for chronic hepatitis B is limited to the use of alpha interferon for a limited number of chronic hepatitis B virus (HBV) carriers who have chronic hepatitis with active viral replication. The development of antiviral nucleoside analogues for the herpes viruses and human immunodeficiency virus (HIV) has resulted in the identification of several compounds which also have activity against HBV. Unfortunately, these agents have not been associated with the clearance of hepatitis B infection, but rather only the suppression of active infection while the patient is receiving medication. In addition, the development of drug-resistance to these agents by the virus will most likely limit their long-term efficacy. Gene therapy has recently been applied to HBV both in vitro and in vivo. This has included the use of antisense oligodeoxynucleotides and RNA, ribozymes, dominant negative mutants and therapeutic HBV vaccines. These newer therapeutic modalities may hold promise as effective treatments for chronic hepatitis B, but to date, have been limited by the problem of delivery to the target cell population or infected organ in vivo. Combination nucleoside analogue therapy may also provide an important treatment modality for chronic hepatitis B, although this will require further investigation.
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Affiliation(s)
- J Torresi
- Victorian Infectious Diseases Reference Laboratory, 10 Wreckyn Street, North Melbourne, Victoria, 3051, Australia.
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Abstract
Liver transplantation has become a well-recognized therapy for hepatic failure resulting from acute or chronic liver disease. It also plays a role in the treatment of certain inborn errors of metabolism that do not directly injure the liver. In fact, the liver maintains a central role in many inherited and acquired genetic disorders. There has been a considerable effort to develop new and more effective gene therapy approaches, in part, to overcome the need for transplantation as well as the shortage of donor livers. Traditional gene therapy involves the delivery of a piece of DNA to replace the faulty gene. More recently, there has been a growing interest in the use of gene repair to correct certain genetic defects. In fact, targeted gene repair has many advantages over conventional replacement strategies. In this review, we will describe a variety of viral and nonviral strategies that are now available to the liver. The ever-growing list includes viral vectors, antisense and ribozyme technology, and the Sleeping Beauty transposon system. In addition, targeted gene repair with RNA/DNA oligonucleotides, small-fragment homologous replacement, and triplex-forming and single-stranded oligonucleotides is a long-awaited and potentially exciting approach. Although each method uses different mechanisms for gene repair and therapy, they all share a basic requirement for the efficient delivery of DNA.
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Affiliation(s)
- Betsy T Kren
- Department of Medicine, University of Minnesota School of Medicine, Minneapolis, MN 55455, USA
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Smith RM, Walton CM, Wu CH, Wu GY. Secondary structure and hybridization accessibility of hepatitis C virus 3'-terminal sequences. J Virol 2002; 76:9563-74. [PMID: 12208936 PMCID: PMC136501 DOI: 10.1128/jvi.76.19.9563-9574.2002] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The 3'-terminal sequences of hepatitis C virus (HCV) positive- and negative-strand RNAs contribute cis-acting functions essential for viral replication. The secondary structure and protein-binding properties of these highly conserved regions are of interest not only for the further elucidation of HCV molecular biology, but also for the design of antisense therapeutic constructs. The RNA structure of the positive-strand 3' untranslated region has been shown previously to influence binding by various host and viral proteins and is thus thought to promote HCV RNA synthesis and genome stability. Recent studies have attributed analogous functions to the negative-strand 3' terminus. We evaluated the HCV negative-strand secondary structure by enzymatic probing with single-strand-specific RNases and thermodynamic modeling of RNA folding. The accessibility of both 3'-terminal sequences to hybridization by antisense constructs was evaluated by RNase H cleavage mapping in the presence of combinatorial oligodeoxynucleotide libraries. The mapping results facilitated identification of antisense oligodeoxynucleotides and a 10-23 deoxyribozyme active against the positive-strand 3'-X region RNA in vitro.
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Affiliation(s)
- Robert M Smith
- Division of Gastroenterology-Hepatology, Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut 06030, USA
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Delaney W, Bartholomeusz A, Locarnini SA. Evolving therapies for the treatment of chronic hepatitis B virus infection. Expert Opin Investig Drugs 2002; 11:169-87. [PMID: 11829711 DOI: 10.1517/13543784.11.2.169] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Despite the availability of prophylactic vaccines lamivudine and IFN-alpha, chronic hepatitis B remains an enormous global health problem. Several promising nucleosides/nucleotides are undergoing clinical trials, including adefovir dipivoxil, the latter of which is active against lamivudine-resistant hepatitis B virus (HBV). In addition to nucleosides/nucleotides, it will be important to develop new agents with different modes of action. Novel small molecule inhibitors, as well as gene therapy approaches, have produced encouraging results in vitro and in animal models. Additional immunomodulatory therapies, including thymosin-alpha 1, IL-12 and several therapeutic vaccines, are also being explored. Combination therapy with multiple nucleosides/nucleotides and other agents will play an important role in the treatment of hepatitis and may help achieve complete viral suppression, host-mediated elimination of infected cells and lasting immunity.
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Affiliation(s)
- William Delaney
- Victorian Infectious Diseases Reference Laboratory, Carlton South, VIC 3053, Australia
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Li J, Zheng W, Kwon AH, Lu Y. In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme. Nucleic Acids Res 2000; 28:481-8. [PMID: 10606646 PMCID: PMC102519 DOI: 10.1093/nar/28.2.481] [Citation(s) in RCA: 338] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A group of highly efficient Zn(II)-dependent RNA-cleaving deoxyribozymes has been obtained through in vitro selection. They share a common motif with the '8-17' deoxyribozyme isolated under different conditions, including different design of the random pool and metal ion cofactor. We found that this commonly selected motif can efficiently cleave both RNA and DNA/RNA chimeric substrates. It can cleave any substrate containing rNG (where rN is any ribo-nucleotide base and G can be either ribo- or deoxy-ribo-G). The pH profile and reaction products of this deoxyribozyme are similar to those reported for hammerhead ribozyme. This deoxyribozyme has higher activity in the presence of transition metal ions compared to alkaline earth metal ions. At saturating concentrations of Zn(2+), the cleavage rate is 1.35 min(-1)at pH 6.0; based on pH profile this rate is estimated to be at least approximately 30 times faster at pH 7.5, where most assays of Mg(2+)-dependent DNA and RNA enzymes are carried out. This work represents a comprehensive characterization of a nucleic acid-based endonuclease that prefers transition metal ions to alkaline earth metal ions. The results demonstrate that nucleic acid enzymes are capable of binding transition metal ions such as Zn(2+)with high affinity, and the resulting enzymes are more efficient at RNA cleavage than most Mg(2+)-dependent nucleic acid enzymes under similar conditions.
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Affiliation(s)
- J Li
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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Abstract
BACKGROUND/AIMS The aim of this study was to determine whether DNA analogs of ribozymes could be prepared to inhibit hepatitis C virus (HCV) gene expression. METHODS Two DNA ribonucleases, Dz2 and Dz4, were designed with varying arm lengths, to cleave at the 5'-noncoding region (NCR) just upstream from the translation start site, and core region of HCV genome, respectively. A reporter vector was prepared to contain target HCV regulatory sequences controlling a downstream luciferase gene. DNA ribonucleases with normal phosphodiester, as well as with terminal phosphorothioate linkages, were administered to Huh7 cells, and luciferase activity was measured. RESULTS DNA ribonucleases were highly active in cleaving HCV RNA targets. Enzymes with longer arms had consistently higher cleavage activity compared to enzymes with shorter arms under cell-free conditions. Furthermore, in Huh7 cells, terminal phosphorothioate derivatives, Dz2 and Dz4, significantly suppressed HCV-luciferase fusion gene expression up to 45% and 67% of controls, respectively. Interestingly, phosphorothioate-modified DNA ribonucleases had greater inhibitory effects on target gene expression than their unmodified counterparts. In contrast, DNA ribonucleases with point mutations in the catalytic domain had significantly lower inhibitory effects compared to wild-type DNA ribonucleases. However, activity was not eliminated, suggesting that some antisense contribution was present. CONCLUSIONS DNA ribonucleases directed against the HCV genome can specifically cleave target HCV RNA. Modifications of the extreme 3'- and 5'-termini protect against nuclease degradation without appreciable reduction in inhibitory activity against viral gene expression under intracellular conditions.
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Affiliation(s)
- M Oketani
- Department of Medicine, University of Connecticut Health Center, Farmington 06030, USA
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