1
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Kaloudas D, Pavlova N, Penchovsky R. GHOST-NOT and GHOST-YES: Two programs for generating high-speed biosensors with randomized oligonucleotide binding sites with NOT or YES Boolean logic functions based on experimentally validated algorithms. J Biotechnol 2023; 373:82-89. [PMID: 37499876 DOI: 10.1016/j.jbiotec.2023.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 07/19/2023] [Indexed: 07/29/2023]
Abstract
High-speed allosteric hammerhead ribozymes can be engineered to distinguish well between a perfectly matching effector and the nucleic acid sequences with a few mismatches under physiologically relevant conditions. Such ribozymes can be designed to control the expression of exogenous mRNAs and can be used to develop new gene therapies, including anticancer treatments. The in vivo selection of such ribozymes is a complicated and lengthy procedure with no guarantee of success. Thus, in silico selection of high-speed ribozymes can be employed using secondary RNA structure computation based on the partition function of the RNA folding in combination with random search algorithms. This approach has already been proven very accurate in designing allosteric hammerhead ribozymes. Herein, we present two programs for the computational design of allosteric ribozymes sensing randomized oligonucleotides based on the extended version of the hammerhead ribozyme. A Generator for High-speed Oligonucleotide Sensing allosteric ribozymes with NOT logic function (GHOST-NOT) and a Generator for High-speed Oligonucleotide Sensing allosteric ribozymes with YES logic function (GHOST-YES) for computational design of high-speed allosteric ribozymes are described. The allosteric hammerhead ribozymes had a high self-cleavage rate of about 1.8 per minute and were very selective in sensing an effector sequence.
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Affiliation(s)
- Dimitrios Kaloudas
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 1164 Sofia, 8 Dragan Tsankov Blvd., Sofia, Bulgaria
| | - Nikolet Pavlova
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 1164 Sofia, 8 Dragan Tsankov Blvd., Sofia, Bulgaria
| | - Robert Penchovsky
- Laboratory of Synthetic Biology and Bioinformatics, Faculty of Biology, Sofia University, "St. Kliment Ohridski", 1164 Sofia, 8 Dragan Tsankov Blvd., Sofia, Bulgaria.
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2
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Ivanov KI, Samuilova OV, Zamyatnin AA. The emerging roles of long noncoding RNAs in lymphatic vascular development and disease. Cell Mol Life Sci 2023; 80:197. [PMID: 37407839 PMCID: PMC10322780 DOI: 10.1007/s00018-023-04842-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
Recent advances in RNA sequencing technologies helped uncover what was once uncharted territory in the human genome-the complex and versatile world of long noncoding RNAs (lncRNAs). Previously thought of as merely transcriptional "noise", lncRNAs have now emerged as essential regulators of gene expression networks controlling development, homeostasis and disease progression. The regulatory functions of lncRNAs are broad and diverse, and the underlying molecular mechanisms are highly variable, acting at the transcriptional, post-transcriptional, translational, and post-translational levels. In recent years, evidence has accumulated to support the important role of lncRNAs in the development and functioning of the lymphatic vasculature and associated pathological processes such as tumor-induced lymphangiogenesis and cancer metastasis. In this review, we summarize the current knowledge on the role of lncRNAs in regulating the key genes and pathways involved in lymphatic vascular development and disease. Furthermore, we discuss the potential of lncRNAs as novel therapeutic targets and outline possible strategies for the development of lncRNA-based therapeutics to treat diseases of the lymphatic system.
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Affiliation(s)
- Konstantin I Ivanov
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation.
- Department of Microbiology, University of Helsinki, Helsinki, Finland.
| | - Olga V Samuilova
- Department of Biochemistry, Sechenov First Moscow State Medical University, Moscow, Russian Federation
- HSE University, Moscow, Russian Federation
| | - Andrey A Zamyatnin
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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3
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An allosteric ribozyme generator and an inverse folding ribozyme generator: Two computer programs for automated computational design of oligonucleotide-sensing allosteric hammerhead ribozymes with YES Boolean logic function based on experimentally validated algorithms. Comput Biol Med 2022; 145:105469. [DOI: 10.1016/j.compbiomed.2022.105469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/26/2022] [Accepted: 03/27/2022] [Indexed: 11/18/2022]
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4
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Perrin D, Paul S, Wong AAWL, Liu LT. Selection of M2+-independent RNA-cleaving DNAzymes with Sidechains Mimicking Arginine and Lysine. Chembiochem 2021; 23:e202100600. [PMID: 34881502 DOI: 10.1002/cbic.202100600] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/04/2021] [Indexed: 11/07/2022]
Abstract
Sequence-specific cleavage of RNA by nucleic acid catalysts in the absence of a divalent metal cation (M 2+ ) has remained an important goal in biomimicry with potential therapeutic applications. Given the lack of functional group diversity in canonical nucleotides, modified nucleotides with amino acid-like side chains were used to enhance self-cleavage rates at a single embedded ribonucleoside site. Previous works relied on three functional groups: an amine, a guanidine and an imidazole ensconced on three different nucleosides. However, to date, few studies have systematically addressed the necessity of all three modifications, as the value of any single modified nucleoside is contextualized at the outset of selection. Herein, we report on the use of only two modified dNTPs, excluding an imidazole, i.e. 5-(3-guanidinoallyl)-2'-dUTP (dU ga TP) and 5-aminoallyl-2'-dCTP (dC aa TP), to select in-vitro self-cleaving DNAzymes that cleave in the absence of M 2+ in a pH-independent fashion. Cleavage shows biphasic kinetics with rate constants that are significantly higher than in unmodified DNAzymes and compare favorably to certain DNAzymes involving an imidazole. This work is the first report of a M2+-independent DNAzyme with two cationic modifications; as such it shows appreciable self-cleaving activity in the absence of an imidazole modification.
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Affiliation(s)
- David Perrin
- U. British Columbia, Chemistry, 2036 Main Mall, V6T-1Z1, Vancouver, CANADA
| | - Somdeb Paul
- The University of British Columbia, Chemistry, 2036 Main Mall, Vancouver, V6T1Z1, Vancouver, CANADA
| | - Antonio A W L Wong
- The University of British Columbia, Chemistry, 2036 Main Mall, Vancouver, V6T1Z1, Vancouver, CANADA
| | - Leo T Liu
- The University of British Columbia, Chemistry, 2036 Main Mall, UBC, Vancouver, V6T-1Z1, Vancouver, CANADA
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5
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Schneider N, Sundaresan Y, Gopalakrishnan P, Beryozkin A, Hanany M, Levanon EY, Banin E, Ben-Aroya S, Sharon D. Inherited retinal diseases: Linking genes, disease-causing variants, and relevant therapeutic modalities. Prog Retin Eye Res 2021; 89:101029. [PMID: 34839010 DOI: 10.1016/j.preteyeres.2021.101029] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022]
Abstract
Inherited retinal diseases (IRDs) are a clinically complex and heterogenous group of visual impairment phenotypes caused by pathogenic variants in at least 277 nuclear and mitochondrial genes, affecting different retinal regions, and depleting the vision of affected individuals. Genes that cause IRDs when mutated are unique by possessing differing genotype-phenotype correlations, varying inheritance patterns, hypomorphic alleles, and modifier genes thus complicating genetic interpretation. Next-generation sequencing has greatly advanced the identification of novel IRD-related genes and pathogenic variants in the last decade. For this review, we performed an in-depth literature search which allowed for compilation of the Global Retinal Inherited Disease (GRID) dataset containing 4,798 discrete variants and 17,299 alleles published in 31 papers, showing a wide range of frequencies and complexities among the 194 genes reported in GRID, with 65% of pathogenic variants being unique to a single individual. A better understanding of IRD-related gene distribution, gene complexity, and variant types allow for improved genetic testing and therapies. Current genetic therapeutic methods are also quite diverse and rely on variant identification, and range from whole gene replacement to single nucleotide editing at the DNA or RNA levels. IRDs and their suitable therapies thus require a range of effective disease modelling in human cells, granting insight into disease mechanisms and testing of possible treatments. This review summarizes genetic and therapeutic modalities of IRDs, provides new analyses of IRD-related genes (GRID and complexity scores), and provides information to match genetic-based therapies such as gene-specific and variant-specific therapies to the appropriate individuals.
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Affiliation(s)
- Nina Schneider
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Yogapriya Sundaresan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Prakadeeswari Gopalakrishnan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Mor Hanany
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Shay Ben-Aroya
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel.
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6
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Dönmüş B, Ünal S, Kirmizitaş FC, Türkoğlu Laçin N. Virus-associated ribozymes and nano carriers against COVID-19. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2021; 49:204-218. [PMID: 33645342 DOI: 10.1080/21691401.2021.1890103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoo tonic, highly pathogenic virus. The new type of coronavirus with contagious nature spread from Wuhan (China) to the whole world in a very short time and caused the new coronavirus disease (COVID-19). COVID-19 has turned into a global public health crisis due to spreading by close person-to-person contact with high transmission capacity. Thus, research about the treatment of the damages caused by the virus or prevention from infection increases everyday. Besides, there is still no approved and definitive, standardized treatment for COVID-19. However, this disaster experienced by human beings has made us realize the significance of having a system ready for use to prevent humanity from viral attacks without wasting time. As is known, nanocarriers can be targeted to the desired cells in vitro and in vivo. The nano-carrier system targeting a specific protein, containing the enzyme inhibiting the action of the virus can be developed. The system can be used by simple modifications when we encounter another virus epidemic in the future. In this review, we present a potential treatment method consisting of a nanoparticle-ribozyme conjugate, targeting ACE-2 receptors by reviewing the virus-associated ribozymes, their structures, types and working mechanisms.
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Affiliation(s)
- Beyza Dönmüş
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Sinan Ünal
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Fatma Ceren Kirmizitaş
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
| | - Nelisa Türkoğlu Laçin
- Molecular Biology and Genetics Department, Yıldız Technical University, Istanbul, Turkey
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7
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Shen F, Mao S, Mathivanan J, Wu Y, Chandrasekaran AR, Liu H, Gan J, Sheng J. Short DNA Oligonucleotide as a Ag + Binding Detector. ACS OMEGA 2020; 5:28565-28570. [PMID: 33195907 PMCID: PMC7658945 DOI: 10.1021/acsomega.0c03372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/14/2020] [Indexed: 06/11/2023]
Abstract
Ag+ has been known to mediate several natural metallo-base pairs. Based on the unique structural information of a short 8-mer DNA strand (5'-GCACGCGC-3') induced by Ag+, we constructed several fluorescent DNA beacons for the detection of Ag+ according to the increase in the fluorescence emission on Ag+ binding. This Ag+ detection assay is quick, sensitive, and easy to adapt and can function in a wide range of temperatures from 5 to 65 °C.
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Affiliation(s)
- Fusheng Shen
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
| | - Song Mao
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
| | - Johnsi Mathivanan
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
| | - Ying Wu
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
| | - Arun Richard Chandrasekaran
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
| | - Hehua Liu
- Shanghai
Public Health Clinical Center, State Key Laboratory of Genetic Engineering,
Collaborative Innovation Center of Genetics and Development, School
of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianhua Gan
- Shanghai
Public Health Clinical Center, State Key Laboratory of Genetic Engineering,
Collaborative Innovation Center of Genetics and Development, School
of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jia Sheng
- Department
of Chemistry, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
- The
RNA Institute, University at Albany, State
University of New York, 1400 Washington Ave., Albany, New York 12222, United
States
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8
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Huang X, Zhao Y, Pu Q, Liu G, Peng Y, Wang F, Chen G, Sun M, Du F, Dong J, Cui X, Tang Z, Mo X. Intracellular selection of trans-cleaving hammerhead ribozymes. Nucleic Acids Res 2019; 47:2514-2522. [PMID: 30649474 PMCID: PMC6412130 DOI: 10.1093/nar/gkz018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 01/06/2019] [Accepted: 01/08/2019] [Indexed: 02/05/2023] Open
Abstract
Hammerhead ribozyme is the smallest and best characterized catalytic RNA-cleaving ribozyme. It has been reported as potential therapeutic tools to manipulate the expression of target genes. However, most of naturally occurring hammerhead ribozymes process self-cleavage rather than cleave substrate RNA in trans, and its high intracellular activity relies on the tertiary interaction of Loop II and steam I bulge, resulting in decreased performance as applied in gene silencing. We described a direct intracellular selection method to evolve hammerhead variants based on trans-cleavage mode via using a toxin gene as the reporter. And a dual fluorescence proteins system has also been established to quantitatively evaluate the efficiency of selected ribozymes in the cell. Based on this selection strategy, we obtained three mutants with enhanced intracellular cleaving activity compared to wide type hammerhead ribozyme. The best one, TX-2 was revealed to possess better and consistent gene knockdown ability at different positions on diverse targeted mRNA either in prokaryotic or eukaryotic cells than wild-type hammerhead ribozyme. These observations imply the efficiency of the intracellular selection method of the trans-acting ribozyme and the potentials of improved ribozyme variants for research and therapeutic purposes.
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Affiliation(s)
- Xin Huang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Yongyun Zhao
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P.R. China
| | - Qinlin Pu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Getong Liu
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Yan Peng
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Fei Wang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Gangyi Chen
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Meiling Sun
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Juan Dong
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Xin Cui
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institution of Biology, Chinese Academy of Science, Chengdu 610041, P.R. China
| | - Xianming Mo
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, P.R. China
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9
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Sonotaki S, Noguchi K, Yohda M, Murakami Y. A zeolite as a tool for successful refolding of PEGylated proteins and their reassembly with tertiary structures. Biotechnol Prog 2019; 35:e2853. [PMID: 31132320 DOI: 10.1002/btpr.2853] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/30/2019] [Accepted: 05/23/2019] [Indexed: 12/25/2022]
Abstract
In the present study, we demonstrated zeolites' potential contribution to establish a method for preparing successfully refolded and reassembled PEGylated protein nanoparticles without the use of protein denaturants through the proteins' reassembly process. At first, the PEGylated nanoparticles are disassembled into identical PEGylated protein subunits by means of protein denaturants, and then the denatured subunits are adsorbed to zeolites. After the complete removal of denaturants, high-molecular-weight poly(ethylene glycol) (PEG) molecules are added to a solution where the zeolites suspend. Consequently, the PEGylated proteins are gradually reassembled into nanoparticles because the subunits are desorbed from the zeolites by the steric hindrance of the added PEG molecules. The present study reveals that PEGylated encapsulin was reassembled and hollow encapsulin nanoparticles were obtained. The results clearly demonstrate the usefulness of zeolites as a tool for the successful refolding of PEGylated proteins and their reassembly with tertiary structures.
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Affiliation(s)
- Seiichi Sonotaki
- Department of Organic and Polymer Materials Chemistry, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Keiichi Noguchi
- Instrumentation Analysis Center, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
| | - Yoshihiko Murakami
- Department of Organic and Polymer Materials Chemistry, Tokyo University of Agriculture and Technology, Tokyo, Japan
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10
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Abstract
Recent advances in RNA engineering during the last two decades have supported the development of RNA-based therapeutics targeting a variety of human diseases. The broad scope of these emerging drugs clearly demonstrates the versatility of RNA. Ribozymes have been seen as promising candidates in this area. However, efficient intracellular application of ribozymes remains challenging, and other strategies appear to have outperformed ribozymes as molecular drugs. Nevertheless, trans-cleaving ribozymes have been applied for specific cleavage of target mRNAs in order to inhibit undesired gene expression. Furthermore, ribozymes have been engineered to allow site-directed RNA sequence alterations, enabling the correction of genetic misinformation at the RNA level. This chapter provides an overview of ribozyme-based strategies, highlighting the promises and pitfalls for potential therapeutic applications.
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Affiliation(s)
- Darko Balke
- University of Greifswald, Institute of Biochemistry Felix-Hausdorff-Str. 4 17487 Greifswald Germany
| | - Sabine Müller
- University of Greifswald, Institute of Biochemistry Felix-Hausdorff-Str. 4 17487 Greifswald Germany
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11
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Plashkevych O, Li Q, Chattopadhyaya J. How RNase HI (Escherichia coli) promoted site-selective hydrolysis works on RNA in duplex with carba-LNA and LNA substituted antisense strands in an antisense strategy context? MOLECULAR BIOSYSTEMS 2018; 13:921-938. [PMID: 28352859 DOI: 10.1039/c6mb00762g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A detailed kinetic study of 36 single modified AON-RNA heteroduplexes shows that substitution of a single native nucleotide in the antisense strand (AON) by locked nucleic acid (LNA) or by diastereomerically pure carba-LNA results in site-dependent modulation of RNase H promoted cleavage of complementary mRNA strands by 2 to 5 fold at 5'-GpN-3' cleavage sites, giving up to 70% of the RNA cleavage products. The experiments have been performed using RNase HI of Escherichia coli. The 2nd best cleavage site, being the 5'-ApN-3' sites, cleaves up to 23%, depending upon the substitution site in 36 isosequential complementary AONs. A comparison of the modified AON promoted RNA cleavage rates with that of the native AON shows that sequence-specificity is considerably enhanced as a result of modification. Clearly, relatively weaker 5'-purine (Pu)-pyrimidine (Py)-3' stacking in the complementary RNA strand is preferred (giving ∼90% of total cleavage products), which plays an important role in RNase H promoted RNA cleavage. A plausible mechanism of RNase H mediated cleavage of the RNA has been proposed to be two-fold, dictated by the balancing effect of the aromatic character of the purine aglycone: first, the locally formed 9-guanylate ion (pKa 9.3, ∼18-20% N1 ionized at pH 8) alters the adjoining sugar-phosphate backbone around the scissile phosphate, transforming its sugar N/S conformational equilibrium, to preferential S-type, causing preferential cleavage at 5'-GpN-3' sites around the center of 20 mer complementary mRNA. Second, the weaker nearest-neighbor strength of 5'-Pu-p-Py-3' stacking promotes preferential 5'-GpN-3' and 5'-ApN-3' cleavage, providing ∼90% of the total products, compared to ∼50% in that of the native one, because of the cLNA/LNA substituent effect on the neighboring 5'-Pu-p-Py-3' sites, providing both local steric flexibility and additional hydration. This facilitates both the water and water/Mg2+ ion availability at the cleavage site causing sequence-specific hydrolysis of the phosphodiester bond of scissile phosphate. The enhancement of the total rate of cleavage of the complementary mRNA strand by up to 25%, presented in this work, provides opportunities to engineer a single modification site in appropriately substituted AONs to design an effective antisense strategy based on the nucleolytic stability of the AON strand versus RNase H capability to cleave the complementary RNA strand.
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Affiliation(s)
- Oleksandr Plashkevych
- Chemical Biology Program, Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 581, SE-751 23 Uppsala, Sweden.
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12
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Liu H, Cai C, Haruehanroengra P, Yao Q, Chen Y, Yang C, Luo Q, Wu B, Li J, Ma J, Sheng J, Gan J. Flexibility and stabilization of HgII-mediated C:T and T:T base pairs in DNA duplex. Nucleic Acids Res 2017; 45:2910-2918. [PMID: 27998930 PMCID: PMC5389650 DOI: 10.1093/nar/gkw1296] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/14/2016] [Indexed: 12/17/2022] Open
Abstract
Owing to their great potentials in genetic code extension and the development of nucleic acid-based functional nanodevices, DNA duplexes containing HgII-mediated base pairs have been extensively studied during the past 60 years. However, structural basis underlying these base pairs remains poorly understood. Herein, we present five high-resolution crystal structures including one first-time reported C–HgII–T containing duplex, three T–HgII–T containing duplexes and one native duplex containing T–T pair without HgII. Our structures suggest that both C–T and T–T pairs are flexible in interacting with the HgII ion with various binding modes including N3–HgII–N3, N4–HgII–N3, O2–HgII–N3 and N3–HgII–O4. Our studies also reveal that the overall conformations of the C–HgII–T and T–HgII–T pairs are affected by their neighboring residues via the interactions with the solvent molecules or other metal ions, such as SrII. These results provide detailed insights into the interactions between HgII and nucleobases and the structural basis for the rational design of C–HgII–T or T–HgII–T containing DNA nanodevices in the future.
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Affiliation(s)
- Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chen Cai
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Baixing Wu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai 200433, China
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13
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Liu H, Shen F, Haruehanroengra P, Yao Q, Cheng Y, Chen Y, Yang C, Zhang J, Wu B, Luo Q, Cui R, Li J, Ma J, Sheng J, Gan J. A DNA Structure Containing AgI
-Mediated G:G and C:C Base Pairs. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201704891] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hehua Liu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Fusheng Shen
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yunshan Cheng
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jing Zhang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Baixing Wu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Ruixue Cui
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
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14
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Liu H, Shen F, Haruehanroengra P, Yao Q, Cheng Y, Chen Y, Yang C, Zhang J, Wu B, Luo Q, Cui R, Li J, Ma J, Sheng J, Gan J. A DNA Structure Containing AgI
-Mediated G:G and C:C Base Pairs. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/anie.201704891] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hehua Liu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Fusheng Shen
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Phensinee Haruehanroengra
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yunshan Cheng
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Yiqing Chen
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jing Zhang
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Baixing Wu
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Qiang Luo
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Ruixue Cui
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Biochemistry; School of Life Sciences; Fudan University; Shanghai 200433 China
| | - Jia Sheng
- Department of Chemistry and The RNA Institute; University at Albany; State University of New York; Albany NY 12222 USA
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering; Collaborative Innovation Center of Genetics and Development; Department of Physiology and Biophysics; School of Life Sciences; Fudan University; Shanghai 200433 China
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15
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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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16
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The structural stability and catalytic activity of DNA and RNA oligonucleotides in the presence of organic solvents. Biophys Rev 2016; 8:11-23. [PMID: 28510143 DOI: 10.1007/s12551-015-0188-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/03/2015] [Indexed: 01/02/2023] Open
Abstract
Organic solvents and apolar media are used in the studies of nucleic acids to modify the conformation and function of nucleic acids, to improve solubility of hydrophobic ligands, to construct molecular scaffolds for organic synthesis, and to study molecular crowding effects. Understanding how organic solvents affect nucleic acid interactions and identifying the factors that dominate solvent effects are important for the creation of oligonucleotide-based technologies. This review describes the structural and catalytic properties of DNA and RNA oligonucleotides in organic solutions and in aqueous solutions with organic cosolvents. There are several possible mechanisms underlying the effects of organic solvents on nucleic acid interactions. The reported results emphasize the significance of the osmotic pressure effect and the dielectric constant effect in addition to specific interactions with nucleic acid strands. This review will serve as a guide for the selection of solvent systems based on the purpose of the nucleic acid-based experiments.
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17
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Rudchenko MN, Zamyatnin AA. Prospects for using self-assembled nucleic acid structures. BIOCHEMISTRY (MOSCOW) 2016; 80:391-9. [PMID: 25869355 DOI: 10.1134/s000629791504001x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
According to the central dogma in molecular biology, nucleic acids are assigned with key functions on storing and executing genetic information in any living cell. However, features of nucleic acids are not limited only with properties providing template-dependent biosynthetic processes. Studies of DNA and RNA unveiled unique features of these polymers able to make various self-assembled three-dimensional structures that, among other things, use the complementarity principle. Here, we review various self-assembled nucleic acid structures as well as application of DNA and RNA to develop nanomaterials, molecular automata, and nanodevices. It can be expected that in the near future results of these developments will allow designing novel next-generation diagnostic systems and medicinal drugs.
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Affiliation(s)
- M N Rudchenko
- Research Division, Hospital for Special Surgery, New York, NY 10021, USA.
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18
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Xing Z, Gao S, Duan Y, Han H, Li L, Yang Y, Li Q. Delivery of DNAzyme targeting aurora kinase A to inhibit the proliferation and migration of human prostate cancer. Int J Nanomedicine 2015; 10:5715-27. [PMID: 26425080 PMCID: PMC4583550 DOI: 10.2147/ijn.s90559] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Herein, a polyethylenimine derivative N-acetyl-l-leucine-polyethylenimine (N-Ac-l-Leu-PEI) was employed as a carrier to achieve the delivery of DNAzyme targeting aurora kinase A using PC-3 cell as a model. Flow cytometry and confocal laser scanning microscopy demonstrated that the derivative could realize the cellular uptake of nanoparticles in an energy-dependent and clathrin-mediated pathway and obtain a high DNAzyme concentration in the cytoplasm through further endosomal escape. After DNAzyme transfection, expression level of aurora kinase A would be downregulated at the protein level. Meanwhile, the inhibition of cell proliferation was observed through 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide and cell colony formation assay, attributing to the activation of apoptosis and cell cycle arrest. Through flow cytometric analysis, an early apoptotic ratio of 25.93% and G2 phase of 22.58% has been detected after N-Ac-l-Leu-PEI-mediated DNAzyme transfection. Finally, wound healing and Transwell migration assay showed that DNAzyme transfection could efficiently inhibit the cell migration. These results demonstrated that N-Ac-l-Leu-PEI could successfully mediate the DNAzyme delivery and downregulate the expression level of aurora kinase A, triggering a significant inhibitory effect of excessive proliferation and migration of tumor cells.
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Affiliation(s)
- Zhen Xing
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, People's Republic of China
| | - Sai Gao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, People's Republic of China
| | - Yan Duan
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, People's Republic of China
| | - Haobo Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, People's Republic of China
| | - Li Li
- Department of Clinic Library, Changchun Women and Children's Health, Changchun, People's Republic of China
| | - Yan Yang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, People's Republic of China
| | - Quanshun Li
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, People's Republic of China
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Liu Y, Liu G, Li Z, Rong W, Yu J, Zhou Y, Liu K, Zheng Z, He J. Studies on the effect of thymine-mercury-thymine stem as a structural or functional motif in DNAzymes. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 33:645-55. [PMID: 25222518 DOI: 10.1080/15257770.2014.912322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
T-Hg-T base pair formation has been demonstrated to be compatible with duplex DNA context, with considerable thermal stability contribution. Here, the T-Hg-T stem in two small DNAzymes 8-17 and 10-23 was studied for its structural and functional roles. The recognition arm 5' to the cleavage site of 10-23 DNAzyme complex and the stem in the catalytic loop of 8-17 DNAzyme could be replaced by consecutive T-Hg-T stem of different length. The linear relationship between the activity of the complex 10-23DZ-6T+D19-6T and the concentration of Hg(2+) demonstrated that the T-Hg-T stem contributes thermal stability of the recognition arm binding. The effect of T-Hg-T stem in the catalytic core of 8-17 DNAzyme and the position-dependent effect in 10-23 DNAzyme demonstrated that T-Hg-T base pair is not compatible with canonical base pairs in playing the functions of nucleic acids.
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Affiliation(s)
- Yang Liu
- a School of Pharmacological Sciences , Guangxi Medical University , 22 Shuangyong Road, Nanning , China
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20
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Dobrovolskaia MA, McNeil SE. Immunological and hematological toxicities challenging clinical translation of nucleic acid-based therapeutics. Expert Opin Biol Ther 2015; 15:1023-48. [PMID: 26017628 DOI: 10.1517/14712598.2015.1014794] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Nucleic acid-based therapeutics (NATs) are proven agents in correcting disorders caused by gene mutations, as treatments against cancer, microbes and viruses, and as vaccine adjuvants. Although many traditional small molecule NATs have been approved for clinical use, commercialization of macromolecular NATs has been considerably slower, and only a few have successfully reached the market. Preclinical and clinical evaluation of macromolecular NATs has revealed many assorted challenges in immunotoxicity, hematotoxicity, pharmacokinetics (PKs), toxicology and formulation. Extensive review has been given to the PK and toxicological concerns of NATs including approaches designed to overcome these issues. Immunological and hematological issues are a commonly reported side effect of NAT treatment; however, literature exploring the mechanistic background of these effects is sparse. AREAS COVERED This review focuses on the immunomodulatory properties of various types of therapeutic nucleic acid concepts. The most commonly observed immunological and hematological toxicities are described for various NAT classes, with citations of how to circumvent these toxicities. EXPERT OPINION Although some success with overcoming immunological and hematological toxicities of NATs has been achieved in recent years, immunostimulation remains the main dose-limiting factor challenging clinical translation of these promising therapies. Novel delivery vehicles should be considered to overcome this challenge.
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Affiliation(s)
- Marina A Dobrovolskaia
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Nanotechnology Characterization Laboratory, Cancer Research Technology Program , P.O. Box B, Frederick, MD 21702 , USA +1 301 846 6939 ; +1 301 846 6399 ;
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21
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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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Chitkara D, Mittal A, Mahato RI. miRNAs in pancreatic cancer: therapeutic potential, delivery challenges and strategies. Adv Drug Deliv Rev 2015; 81:34-52. [PMID: 25252098 DOI: 10.1016/j.addr.2014.09.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/18/2014] [Accepted: 09/15/2014] [Indexed: 02/08/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a severe pancreatic malignancy and is predicted to victimize 1.5% of men and women during their lifetime (Cancer statistics: SEER stat fact sheet, National Cancer Institute, 2014). miRNAs have emerged as a promising prognostic, diagnostic and therapeutic tool to fight against pancreatic cancer. miRNAs could modulate gene expression by imperfect base-pairing with target mRNA and hence provide means to fine-tune multiple genes simultaneously and alter various signaling pathways associated with the disease. This exceptional miRNA feature has provided a paradigm shift from the conventional one drug one target concept to one drug multiple target theory. However, in vivo miRNA delivery is not fully realized due to challenges posed by this special class of therapeutic molecules, which involves thorough understanding of the biogenesis and physicochemical properties of miRNA and delivery carriers along with the pathophysiology of the PDAC. This review highlights the delivery strategies of miRNA modulators (mimic/inhibitor) in cancer with special emphasis on PDAC since successful delivery of miRNA in vivo constitutes the major challenge in clinical translation of this promising class of therapeutics.
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Balke D, Zieten I, Strahl A, Müller O, Müller S. Design and Characterization of a Twin Ribozyme for Potential Repair of a Deletion Mutation within the OncogenicCTNNB1-ΔS45 mRNA. ChemMedChem 2014; 9:2128-37. [DOI: 10.1002/cmdc.201402166] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Indexed: 01/09/2023]
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Kondo J, Yamada T, Hirose C, Okamoto I, Tanaka Y, Ono A. Crystal structure of metallo DNA duplex containing consecutive Watson-Crick-like T-Hg(II)-T base pairs. Angew Chem Int Ed Engl 2014; 53:2385-8. [PMID: 24478025 DOI: 10.1002/anie.201309066] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 12/06/2013] [Indexed: 11/09/2022]
Abstract
The metallo DNA duplex containing mercury-mediated T-T base pairs is an attractive biomacromolecular nanomaterial which can be applied to nanodevices such as ion sensors. Reported herein is the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs. The Hg(II) ion occupies the center between two T residues. The N3-Hg(II) bond distance is 2.0 Å. The relatively short Hg(II)-Hg(II) distance (3.3 Å) observed in consecutive T-Hg(II)-T base pairs suggests that the metallophilic attraction could exist between them and may stabilize the B-form double helix. To support this, the DNA duplex is largely distorted and adopts an unusual nonhelical conformation in the absence of Hg(II). The structure of the metallo DNA duplex itself and the Hg(II)-induced structural switching from the nonhelical form to the B-form provide the basis for structure-based design of metal-conjugated nucleic acid nanomaterials.
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Affiliation(s)
- Jiro Kondo
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554 Tokyo (Japan).
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25
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Kondo J, Yamada T, Hirose C, Okamoto I, Tanaka Y, Ono A. Crystal Structure of Metallo DNA Duplex Containing Consecutive Watson-Crick-like T-HgII-T Base Pairs. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309066] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Hallett MA, Dalal P, Sweatman TW, Pourmotabbed T. The distribution, clearance, and safety of an anti-MMP-9 DNAzyme in normal and MMTV-PyMT transgenic mice. Nucleic Acid Ther 2013; 23:379-88. [PMID: 24083396 DOI: 10.1089/nat.2012.0348] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Catalytic oligonucleotides, known as DNAzymes, are a new class of nucleic acid-based gene therapy that have recently been used in preclinical animal studies to treat various cancers. In this study the systemic distribution, pharmacokinetics, and safety of intravenously administered anti-MMP (matrix metalloproteinase)-9 DNAzyme (AM9D) were determined in healthy FVB and in MMTV-polyoma virus middle T (PyMT) transgenic mice bearing mammary tumors. MMP-9 is known to be involved in tumor cell development, angiogenesis, invasion, and metastasis. Sulfur-35 ((35)S) labeled ([(35)S]-AM9D) administered intravenously, without the use of carrier molecules, to healthy and mammary tumor bearing MMTV-PyMT transgenic mice distributed to all major organs. The order of percentages of [(35)S]-AM9D accumulation in different organs of healthy and MMTV-PyMT mice were blood>liver>kidney>lung>spleen>heart and mammary tumor>blood≈liver>kidney>spleen>lung>heart, respectively. The amount of AM9D accumulated in mammary tumors 2 hours post injection was 0.6% and 0.2% higher than in either blood or liver, respectively, and its rate of initial clearance from mammary tissue was at least 50% slower than the other organs. Approximately 43% of the delivered dosage of [(35)S]-AM9D was cleared from the system via feces and urine over a period of 72 hours. No evidence of acute or chronic cytotoxicity, local or widespread, associated with AM9D treatment (up to 75 mg AM9D /kg of body weight) was observed in the organs examined. These data suggest that DNAzyme in general and AM9D in particular can be used systemically as a therapeutic agent to treat patients with breast cancer or other metastatic and surgically inaccessible tumors.
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Affiliation(s)
- Miranda A Hallett
- 1 Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center , Memphis Tennessee
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28
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Hollenstein M, Hipolito CJ, Lam CH, Perrin DM. Toward the combinatorial selection of chemically modified DNAzyme RNase A mimics active against all-RNA substrates. ACS COMBINATORIAL SCIENCE 2013; 15:174-82. [PMID: 23485334 DOI: 10.1021/co3001378] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The convenient use of SELEX and related combinatorial methods of in vitro selection provides a formidable gateway for the generation of DNA enzymes, especially in the context of improving their potential as gene therapeutic agents. Here, we report on the selection of DNAzyme 12-91, a modified nucleic acid catalyst adorned with imidazole, ammonium, and guanidinium groups that provide for efficient M(2+)-independent cleavage of an all-RNA target sequence (kobs = 0.06 min(-1)). While Dz12-91 was selected for intramolecular cleavage of an all-RNA target, it surprisingly cleaves a target containing a lone ribocytosine unit with even greater efficiency (kobs = 0.27 min(-1)) than Dz9-86 (kobs = 0.13 min(-1)). The sequence composition of Dz12-91 bears a marked resemblance to that of Dz9-86 (kobs = 0.0014 min(-1) with an all-RNA substrate) that was selected from the same library to cleave a target containing a single ribonucleotide. However, small alterations in the sequence composition have a profound impact on the substrate preference and catalytic properties. Indeed, Dz12-91 displays the highest known rate enhancement for the M(2+)-independent cleavage of all-RNA targets. Hence, Dz12-91 represents a step toward the generation of potentially therapeutically active DNAzymes and further underscores the usefulness of modified triphosphates in selection experiments.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - Christopher J. Hipolito
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - Curtis H. Lam
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
| | - David M. Perrin
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T
1Z1, Canada
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Abstract
This is a review of RNA as a target for small molecules (ribosomes, riboswitches, regulatory RNAs) and RNA-derived oligonucleotides as tools (antisense/small interfering RNA, ribozymes, aptamers/decoy RNA and microRNA). This review highlights the present state of research using RNA as a drug target or as a potential drug candidate and explains at which stage and to what extent rational design could eventually be involved. Special attention has been paid to the recent potential clinical applications of RNA either as drugs or drug targets. The review deals mainly with mechanistic approaches rather than with physicochemical or computational aspects of RNA-based drug design.
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Affiliation(s)
- Irene M Lagoja
- Katholieke Universiteit Leuven, Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, Minderbroedersstraat 10, B-3000 Leuven, Belgium +32 16 337396 ; +32 16 337340 ;
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Martínez T, Wright N, López-Fraga M, Jiménez AI, Pañeda C. Silencing human genetic diseases with oligonucleotide-based therapies. Hum Genet 2013; 132:481-93. [PMID: 23494242 DOI: 10.1007/s00439-013-1288-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 03/05/2013] [Indexed: 12/11/2022]
Abstract
RNA interference is an endogenous mechanism present in most eukaryotic cells that enables degradation of specific mRNAs. Pharmacological exploitation of this mechanism for therapeutic purposes attracted a whole amount of attention in its initial years, but was later hampered due to difficulties in delivery of the pharmacological agents to the appropriate organ or tissue. Advances in recent years have to a certain level started to address this specific issue. Genetic diseases are caused by aberrations in gene sequences or structure; these particular abnormalities are in theory easily addressable by RNAi therapeutics. Sequencing of the human genome has largely contributed to the identification of alterations responsible for genetic conditions, thus facilitating the design of compounds that can address these diseases. This review addresses the currently on-going programs with the aim of developing RNAi and other antisense compounds for the treatment of genetic conditions and the pros and cons that these products may encounter along the way. The authors have focused on those programs that have reached clinical trials or are very close to do so.
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Affiliation(s)
- Tamara Martínez
- Sylentis, PCM C/Santiago Grisolía no 2, Tres Cantos, 28760, Madrid, Spain
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31
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Xiang Y, Wu P, Tan LH, Lu Y. DNAzyme-functionalized gold nanoparticles for biosensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 140:93-120. [PMID: 24026635 DOI: 10.1007/10_2013_242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent progress in using DNAzyme-functionalized gold nanoparticles (AuNPs) for biosensing is summarized in this chapter. A variety of methods, including those for attaching DNA on AuNPs, detecting metal ions and small molecules by DNAzyme-functionalized AuNPs, and intracellular applications of DNAzyme-functionalized AuNPs are discussed. DNAzyme-functionalized AuNPs will increasingly play more important roles in biosensing and many other multidisciplinary applications. This chapter covers the recent advancement in biosensing applications of DNAzyme-functionalized gold nanoparticles, including the detection of metal ions, small molecules, and intracellular imaging.
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Affiliation(s)
- Yu Xiang
- Department of Chemistry and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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32
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Singh N, Ranjan A, Sur S, Chandra R, Tandon V. Inhibition of HIV-1 Integrase gene expression by 10-23 DNAzyme. J Biosci 2012; 37:493-502. [PMID: 22750986 DOI: 10.1007/s12038-012-9216-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
HIV Integrase (IN) is an enzyme that is responsible for the integration of the proviral genome into the human genome, and this integration step is the first step of the virus hijacking the human cell machinery for its propagation and replication. 10-23 DNAzyme has the potential to suppress gene expressions through sequence-specific mRNA cleavage. We have designed three novel DNAzymes, DIN54, DIN116, and DIN152, against HIV-1 Integrase gene using Mfold software and evaluated them for target site cleavage activity on the in vitro transcribed mRNA. All DNAzymes were tested for its inhibition of expression of HIV Integrase protein in the transiently transfected cell lines. DIN116 and DIN152 inhibited IN-EGFP expression by 80 percent and 70 percent respectively.
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MESH Headings
- Base Pairing
- Base Sequence
- DNA, Catalytic/chemistry
- DNA, Catalytic/genetics
- DNA, Catalytic/metabolism
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- Gene Expression
- Green Fluorescent Proteins/biosynthesis
- Green Fluorescent Proteins/genetics
- HIV Integrase/biosynthesis
- HIV Integrase/genetics
- HeLa Cells
- Humans
- Models, Molecular
- Nucleic Acid Conformation
- RNA Cleavage
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Recombinant Fusion Proteins/biosynthesis
- Recombinant Fusion Proteins/genetics
- Software
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Affiliation(s)
- Nirpendra Singh
- Dr BR Ambedkar Center for Biomedical Research, University of Delhi, New Delhi 110 007, India
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33
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Catalytic cleavage activities of 10–23 DNAzyme analogs functionalized with an amino group in its catalytic core. Acta Pharm Sin B 2012. [DOI: 10.1016/j.apsb.2011.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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34
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Guga P, Koziołkiewicz M. Phosphorothioate nucleotides and oligonucleotides - recent progress in synthesis and application. Chem Biodivers 2012; 8:1642-81. [PMID: 21922655 DOI: 10.1002/cbdv.201100130] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Piotr Guga
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Department of Bioorganic Chemistry, Sienkiewicza 112, PL-90-363 Łódź.
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35
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Abstract
Small cis-acting ribozymes have been converted into trans-acting ribozymes possessing the ability to cleave RNA substrates. The Hepatitis Delta Virus (HDV) ribozyme is one of the rare examples of these that is derived from an RNA species that is found in human cells. Consequently, it possesses the natural ability to function in the presence of human proteins in addition to an outstanding stability in human cells, two significant advantages in its use. The development of an additional specific on/off adaptor (SOFA) has led to the production of a new generation of HDV ribozymes with improved specificities that provide a tool with significant potential for future development in the fields of both functional genomics and gene -therapy. SOFA-HDV ribozyme-based gene inactivation systems have been reported in both prokaryotic and eukaryotic cells. Here, a step-by-step approach for the efficient design of highly specific SOFA-HDV ribozymes with a minimum investment of time and effort is described.
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Affiliation(s)
- Michel V Lévesque
- Département de Biochimie, Université de Sherbrooke, Sherbrooke, QC, Canada
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36
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Grimpe B. Deoxyribozymes and bioinformatics: complementary tools to investigate axon regeneration. Cell Tissue Res 2011; 349:181-200. [PMID: 22190188 PMCID: PMC7087747 DOI: 10.1007/s00441-011-1291-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 11/17/2011] [Indexed: 11/28/2022]
Abstract
For over 100 years, scientists have tried to understand the mechanisms that lead to the axonal growth seen during development or the lack thereof during regeneration failure after spinal cord injury (SCI). Deoxyribozyme technology as a potential therapeutic to treat SCIs or other insults to the brain, combined with a bioinformatics approach to comprehend the complex protein-protein interactions that occur after such trauma, is the focus of this review. The reader will be provided with information on the selection process of deoxyribozymes and their catalytic sequences, on the mechanism of target digestion, on modifications, on cellular uptake and on therapeutic applications and deoxyribozymes are compared with ribozymes, siRNAs and antisense technology. This gives the reader the necessary knowledge to decide which technology is adequate for the problem at hand and to design a relevant agent. Bioinformatics helps to identify not only key players in the complex processes that occur after SCI but also novel or less-well investigated molecules against which new knockdown agents can be generated. These two tools used synergistically should facilitate the pursuit of a treatment for insults to the central nervous system.
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Affiliation(s)
- Barbara Grimpe
- Applied Neurobiology, Department of Neurology, Heinrich Heine University Düsseldorf, Moorenstrasse 5, 40225 Düsseldorf, Germany.
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37
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Müller S, Appel B, Krellenberg T, Petkovic S. The many faces of the hairpin ribozyme: Structural and functional variants of a small catalytic rna. IUBMB Life 2011; 64:36-47. [DOI: 10.1002/iub.575] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 08/18/2011] [Indexed: 12/15/2022]
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38
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Lévesque MV, Rouleau SG, Perreault JP. Selection of the most potent specific on/off adaptor-hepatitis delta virus ribozymes for use in gene targeting. Nucleic Acid Ther 2011; 21:241-52. [PMID: 21793786 DOI: 10.1089/nat.2011.0301] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The Hepatitis Delta Virus (HDV) ribozyme, which is well adapted to the environment of the human cell, is an excellent candidate for the future development of gene-inactivation systems. On top of this, a new generation of HDV ribozymes now exists that benefits from the addition of a specific on/off adaptor (specifically the SOFA-HDV ribozymes) which greatly increases both the ribozyme's specificity and its cleavage activity. Unlike RNAi and hammerhead ribozymes, the designing of SOFA-HDV ribozymes to cleave, in trans, given RNA species has never been the object of a systematic optimization study, even with their recent use for the gene knockdown of various targets. This report aims at both improving and clarifying the design process of SOFA-HDV ribozymes. Both the ribozyme and the targeted RNA substrate were analyzed in order to provide new criteria that are useful in the selection of the most potent SOFA-HDV ribozymes. The crucial features present in both the ribozyme's biosensor and blocker, as well as at the target site, were identified and characterized. Simple rules were derived and tested using hepatitis C virus NS5B RNA as a model target. Overall, this method should promote the use of the SOFA-HDV ribozymes in a plethora of applications in both functional genomics and gene therapy.
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Affiliation(s)
- Michel V Lévesque
- RNA Group/Groupe ARN, Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke , Sherbrooke, Québec, Canada
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39
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Kaur H, Scaria V, Maiti S. “Locked onto the target”: increasing the efficiency of antagomirzymes using locked nucleic acid modifications. Biochemistry 2011; 49:9449-56. [PMID: 20879750 DOI: 10.1021/bi101185k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study highlights the effect of incorporation of locked nucleic acid (LNA) on improving the functional efficacy of DNAzymes against microRNAs (antagomirzymes). DNAzymes were designed against two different sites of miR-27a, which were encompassed both within the precursor and mature form of miRNA. The cleavage and functional activities of these DNAzymes have been compared to those of LNA-modified counterparts, containing LNA modification in each of the substrate binding arms. Preliminary examination based on in vitro cleavage demonstrated LNAzyme to be much more effective in the ensuing cleavage of target miRNA under both single- and multiple-turnover conditions. Evaluation of kinetic parameters indicated almost 5-fold higher cleavage efficiency, kobs, for LNAzymes than for DNAzymes, leading to more efficient cleavage of the substrate. We attribute this enhancement in cleavage efficiency to the LNA-mediated improvement in the hybridization of the antagomirzyme·target complex. Functional validation of the relative activities was accomplished through the luciferase reporter assay and quantitative real-time polymerase chain reaction (qRT-PCR). Both the unmodified and LNA-modified antagomirzymes were very active in ensuing efficient miRNA knockdown; however, compared to the DNAzymes, the LNAzymes were almost 25% more active. A direct quantitative estimate of miRNA cleavage, conducted using qRT-PCR, further substantiated the data by indicating that LNAzyme effectively downregulated the levels of mature miRNA (up to 50%) versus the corresponding DNAzymes. Our data thus provide formative evidence of the successful employment of LNA-based antagomirzymes against miRNA.
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Affiliation(s)
- Harleen Kaur
- Institute of Genomics and Integrative Biology, CSIR, Delhi, India
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40
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Yi J, Liu C. Efficient silencing of gene expression by an ASON-bulge-DNAzyme complex. PLoS One 2011; 6:e18629. [PMID: 21490924 PMCID: PMC3072403 DOI: 10.1371/journal.pone.0018629] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 03/14/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND DNAzymes are DNA molecules that can directly cleave cognate mRNA, and have been developed to silence gene expression for research and clinical purposes. The advantage of DNAzymes over ribozymes is that they are inexpensive to produce and exhibit good stability. The "10-23 DNA enzyme" is composed of a catalytic domain of 15 deoxynucleotides, flanked by two substrate-recognition domains of approximately eight nucleotides in each direction, which provides the complementary sequence required for specific binding to RNA substrates. However, these eight nucleotides might not afford sufficient binding energy to hold the RNA substrate along with the DNAzyme, which would interfere with the efficiency of the DNAzyme or cause side effects, such as the cleavage of non-cognate mRNAs. METHODOLOGY In this study, we inserted a nonpairing bulge at the 5' end of the "10-23 DNA enzyme" to enhance its efficiency and specificity. Different sizes of bulges were inserted at different positions in the 5' end of the DNAzyme. The non-matching bulge will avoid strong binding between the DNAzyme and target mRNA, which may interfere with the efficiency of the DNAzyme. CONCLUSIONS Our novel DNAzyme constructs could efficiently silence the expression of target genes, proving a powerful tool for gene silencing. The results showed that the six oligo bulge was the most effective when the six oligo bulge was 12-15 bp away from the core catalytic domain.
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Affiliation(s)
- Jianzhong Yi
- Institute of Animal Husbandry Veterinary Sciences, Shanghai Academy of Agricultural Sciences, Shanghai, China.
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41
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Liu Y, Xu J, Karimiahmadabadi M, Zhou C, Chattopadhyaya J. Synthesis of 2',4'-propylene-bridged (carba-ENA) thymidine and its analogues: the engineering of electrostatic and steric effects at the bottom of the minor groove for nuclease and thermodynamic stabilities and elicitation of RNase H. J Org Chem 2011; 75:7112-28. [PMID: 20929200 DOI: 10.1021/jo101207d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
2',4'-Propylene-bridged thymidine (carba-ENA-T) and five 8'-Me/NH(2)/OH modified carba-ENA-T analogues have been prepared through intramolecular radical addition to C═N of the tethered oxime-ether. These carba-ENA nucleosides have been subsequently incorporated into 15mer oligodeoxynucleotides (AON), and their affinity toward cDNA and RNA, nuclease resistance, and RNase H recruitment capability have been investigated in comparison with those of the native and ENA counterparts. These carba-ENAs modified AONs are highly RNA-selective since all of them led to slight thermal stabilization effect for the AON:RNA duplex, but quite large destabilization effect for the AON:DNA duplex. It was found that different C8' substituents (at the bottom of the minor groove) on carba-ENA-T only led to rather small variation of thermal stability of the AON:RNA duplexes. We, however, observed that the parent carba-ENA-T modified AONs exhibited higher nucleolytic stability than those of the ENA-T modified counterparts. The nucleolytic stability of carba-ENA-T modified AONs can be further modulated by C8' substituent to variable extents depending on not only the chemical nature but also the stereochemical orientation of the C8' substituents: Thus, (1) 8'S-Me on carba-ENA increases the nucleolytic stability but 8'R-Me leads to a decreased effect; (2) 8'R-OH on carba-ENA had little, if any, effect on nuclease resistance but 8'S-OH resulted in significantly decreased nucleolytic stability; and (3) 8'-NH(2) substituted carba-ENA leads to obvious loss in the nuclease resistance. The RNA strand in all of the carba-ENA derivatives modified AON:RNA hybrid duplexes can be digested by RNase H1 with high efficiency, even at twice the rate of those of the native and ENA modified counterpart.
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Affiliation(s)
- Yi Liu
- Bioorganic Chemistry Program, Department of Cell and Molecular Biology, Box 581, Biomedical Center, Uppsala University, SE-751 23 Uppsala, Sweden
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42
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Sugiyama R, Hayafune M, Habu Y, Yamamoto N, Takaku H. HIV-1 RT-dependent DNAzyme expression inhibits HIV-1 replication without the emergence of escape viruses. Nucleic Acids Res 2011; 39:589-98. [PMID: 20833635 PMCID: PMC3025543 DOI: 10.1093/nar/gkq794] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Revised: 08/18/2010] [Accepted: 08/23/2010] [Indexed: 12/12/2022] Open
Abstract
DNAzymes are easier to prepare and less sensitive to chemical and enzymatic degradation than ribozymes; however, a DNA enzyme expression system has not yet been developed. In this study, we exploited the mechanism of HIV-1 reverse transcription (RT) in a DNA enzyme expression system. We constructed HIV-1 RT-dependent lentiviral DNAzyme expression vectors including the HIV-1 primer binding site, the DNA enzyme, and either a native tRNA (Lys-3), tR(M)DtR(L), or one of two truncated tRNAs (Lys-3), tR(M)DΔARMtR(L) or tR(M)D3'-endtR(L). Lentiviral vector-mediated DNAzyme expression showed high levels of inhibition of HIV-1 replication in SupT1 cells. We also demonstrated the usefulness of this approach in a long-term assay, in which we found that the DNAzymes prevented escape from inhibition of HIV. These results suggest that HIV-1 RT-dependent lentiviral vector-derived DNAzymes prevent the emergence of escape mutations.
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Affiliation(s)
- Ryuichi Sugiyama
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Masaaki Hayafune
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Yuichiro Habu
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Norio Yamamoto
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
| | - Hiroshi Takaku
- Department of Life and Environmental Science, High Technology Research Center, Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino-shi, Chiba 275-0016, Japan, Department of Microbiology, Immunology and Pathology 1619 Campus Delivery, Colorado State University, Fort Collins, CO 80523-161, USA and Influenza Virus Research Center, National Institute of Infectious Diseases, 4-7-1 Musashimurayama-shi, Tokyo 208-0011, Japan
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43
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Drude I, Strahl A, Galla D, Müller O, Müller S. Design of hairpin ribozyme variants with improved activity for poorly processed substrates. FEBS J 2010; 278:622-33. [DOI: 10.1111/j.1742-4658.2010.07983.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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44
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Chien MP, Thompson MP, Gianneschi NC. DNA-nanoparticle micelles as supramolecular fluorogenic substrates enabling catalytic signal amplification and detection by DNAzyme probes. Chem Commun (Camb) 2010; 47:167-9. [PMID: 20830351 DOI: 10.1039/c0cc02291h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Catalytic DNA molecules have tremendous potential in propagating detection events via nucleic acid sequence selective signal amplification. However, they suffer from product inhibition limiting their widespread utility. Herein, this limitation is overcome utilizing a novel fluorogenic substrate design consisting of cooperatively assembled DNA-nanoparticle micelles.
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Affiliation(s)
- Miao-Ping Chien
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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45
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Zhou M, Liang X, Mochizuki T, Asanuma H. A light-driven DNA nanomachine for the efficient photoswitching of RNA digestion. Angew Chem Int Ed Engl 2010; 49:2167-70. [PMID: 20175178 DOI: 10.1002/anie.200907082] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Mengguang Zhou
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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46
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Gerasimova YV, Cornett E, Kolpashchikov DM. RNA-cleaving deoxyribozyme sensor for nucleic acid analysis: the limit of detection. Chembiochem 2010; 11:811-7, 729. [PMID: 20301161 PMCID: PMC2949061 DOI: 10.1002/cbic.201000006] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Indexed: 12/31/2022]
Abstract
Along with biocompatibility, chemical stability, and simplicity of structural prediction and modification, deoxyribozyme-based molecular sensors have the potential of an improved detection limit due to their ability to catalytically amplify signal. This study contributes to the understanding of the factors responsible for the limit of detection (LOD) of RNA-cleaving deoxyribozyme sensors. A new sensor that detects specific DNA/RNA sequences was designed from deoxyribozyme OA-II [Chiuman, W.; Li, Y. (2006) J. Mol. Biol. 357, 748-754]. The sensor architecture allows for a unique combination of high selectivity, low LOD and the convenience of fluorescent signal monitoring in homogeneous solution. The LOD of the sensor was found to be approximately 1.6 x 10(-10) M after 3 h of incubation. An equation that allows estimation of the lowest theoretical LOD using characteristics of parent deoxyribozymes and their fluorogenic substrates was derived and experimentally verified. According to the equation, "catalytically perfect" enzymes can serve as scaffolds for the design of sensors with the LOD not lower than approximately 2 x 10(-15) M after 3 h of incubation. A new value termed the detection efficiency (DE) is suggested as a time-independent characteristic of a sensor's sensitivity. The expressions for the theoretical LOD and DE can be used to evaluate nucleic acid and protein enzymes for their application as biosensing platforms.
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Affiliation(s)
| | | | - Dmitry M. Kolpashchikov
- Dr. Y. V. Gerasimova, E. Cornett, Dr. D. M. Kolpashchikov Chemistry Department, University of Central Florida 4000 Central Florida Blvd, Orlando, FL 32816-2366 (USA)
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47
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Zhou M, Liang X, Mochizuki T, Asanuma H. A Light-Driven DNA Nanomachine for the Efficient Photoswitching of RNA Digestion. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907082] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Hollenstein M, Hipolito CJ, Lam CH, Perrin DM. A self-cleaving DNA enzyme modified with amines, guanidines and imidazoles operates independently of divalent metal cations (M2+). Nucleic Acids Res 2009; 37:1638-49. [PMID: 19153138 PMCID: PMC2655665 DOI: 10.1093/nar/gkn1070] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 12/18/2008] [Accepted: 12/19/2008] [Indexed: 12/04/2022] Open
Abstract
The selection of modified DNAzymes represents an important endeavor in expanding the chemical and catalytic properties of catalytic nucleic acids. Few examples of such exist and to date, there is no example where three different modified bases have been simultaneously incorporated for catalytic activity. Herein, dCTP, dATP and dUTP bearing, respectively, a cationic amine, an imidazole and a cationic guanidine, were enzymatically polymerized on a DNA template for the selection of a highly functionalized DNAzyme, called DNAzyme 9-86, that catalyzed (M(2+))-independent self-cleavage under physiological conditions at a single ribo(cytosine)phosphodiester linkage with a rate constant of (0.134 +/- 0.026) min(-1). A pH rate profile analysis revealed pK(a)'s of 7.4 and 8.1, consistent with both general acid and base catalysis. The presence of guanidinium cations permits cleavage at significantly higher temperatures than previously observed for DNAzymes with only amines and imidazoles. Qualitatively, DNAzyme 9-86 presents an unprecedented ensemble of synthetic functionalities while quantitatively it expresses one of the highest reported values for any self-cleaving nucleic acid when investigated under M(2+)-free conditions at 37 degrees C.
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Affiliation(s)
| | | | | | - David M. Perrin
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver BC, V6T 1Z1, Canada
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49
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Affiliation(s)
- Jens Kurreck
- Institut für Industrielle Genetik, Universität Stuttgart, Allmandring 31, 70569 Stuttgart (Deutschland), Fax: (+49) 711‐685 66973 http://www.uni‐stuttgart.de/iig/institut/staff/kurreck/index.html
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50
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Stobart MJ, Simon SLR, Plews M, Lamoureux L, Knox JD. Efficient knockdown of human prnp mRNA expression levels using hybrid hammerhead ribozymes. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2009; 72:1034-1039. [PMID: 19697238 DOI: 10.1080/15287390903084314] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Prion diseases are invariably fatal infectious diseases of the central nervous system. The prion protein has been identified as the underlying causative agent as PrP knockout mice (prnp(0/0)) are resistant to infection. This suggests that a significant reduction in the expression levels of PrP(c) should interrupt disease progression. Accomplishing this in vivo, upon presentation of symptoms, requires a mechanism that significantly reduces prnp mRNA levels while lacking potential side effects that may be cytotoxic or lethal to the host. Hybrid hammerhead ribozymes (HyHamRzs) include both a helicase recruitment signal and a tRNA(Val) promoter. HyHamRzs offer a means of highly specific and significant mRNA cleavage. In this study, data demonstrate increased activity granted to HamRzs by the addition of the helicase recruitment signal. Results show that three different HyHamRzs, targeting different locations along the full length prnp mRNA, reduced expression levels by greater than 95% relative to the control. It is postulated that HyHamRzs, modified to enhance serum stability and delivered intravenously to neurons by forming a complex with the modified rabies virus G protein (RVG), may offer a potential gene therapy strategy.
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Affiliation(s)
- Michael J Stobart
- Division of Prion Diseases Program, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, Winnipeg, Manitoba, Canada
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