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Zhang K, Hodge J, Chatterjee A, Moon TS, Parker KM. Duplex Structure of Double-Stranded RNA Provides Stability against Hydrolysis Relative to Single-Stranded RNA. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8045-8053. [PMID: 34033461 DOI: 10.1021/acs.est.1c01255] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phosphodiester bonds in the backbones of double-stranded (ds)RNA and single-stranded (ss)RNA are known to undergo alkaline hydrolysis. Consequently, dsRNA agents used in emerging RNA interference (RNAi) products have been assumed to exhibit low chemical persistence in solutions. However, the impact of the duplex structure of dsRNA on alkaline hydrolysis has not yet been evaluated. In this study, we demonstrated that dsRNA undergoes orders-of-magnitude slower alkaline hydrolysis than ssRNA. Furthermore, we observed that dsRNA remains intact for multiple months at neutral pH, challenging the assumption that dsRNA is chemically unstable. In systems enabling both enzymatic degradation and alkaline hydrolysis of dsRNA, we found that increasing pH effectively attenuated enzymatic degradation without inducing alkaline hydrolysis that was observed for ssRNA. Overall, our findings demonstrated, for the first time, that key degradation pathways of dsRNA significantly differ from those of ssRNA. Consideration of the unique properties of dsRNA will enable greater control of dsRNA stability during the application of emerging RNAi technology and more accurate assessment of its fate in environmental and biological systems, as well as provide insights into broader application areas including dsRNA isolation, detection and inactivation of dsRNA viruses, and prebiotic molecular evolution.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joseph Hodge
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Dayeh DM, Cantara WA, Kitzrow JP, Musier-Forsyth K, Nakanishi K. Argonaute-based programmable RNase as a tool for cleavage of highly-structured RNA. Nucleic Acids Res 2018; 46:e98. [PMID: 29897478 PMCID: PMC6144825 DOI: 10.1093/nar/gky496] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/20/2018] [Accepted: 05/22/2018] [Indexed: 12/26/2022] Open
Abstract
The recent identification and development of RNA-guided enzymes for programmable cleavage of target nucleic acids offers exciting possibilities for both therapeutic and biotechnological applications. However, critical challenges such as expensive guide RNAs and inability to predict the efficiency of target recognition, especially for highly-structured RNAs, remain to be addressed. Here, we introduce a programmable RNA restriction enzyme, based on a budding yeast Argonaute (AGO), programmed with cost-effective 23-nucleotide (nt) single-stranded DNAs as guides. DNA guides offer the advantage that diverse sequences can be easily designed and purchased, enabling high-throughput screening to identify optimal recognition sites in the target RNA. Using this DNA-induced slicing complex (DISC) programmed with 11 different guide DNAs designed to span the sequence, sites of cleavage were identified in the 352-nt human immunodeficiency virus type 1 5'-untranslated region. This assay, coupled with primer extension and capillary electrophoresis, allows detection and relative quantification of all DISC-cleavage sites simultaneously in a single reaction. Comparison between DISC cleavage and RNase H cleavage reveals that DISC not only cleaves solvent-exposed sites, but also sites that become more accessible upon DISC binding. This study demonstrates the advantages of the DISC system for programmable cleavage of highly-structured, functional RNAs.
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Affiliation(s)
- Daniel M Dayeh
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
| | - William A Cantara
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
| | - Jonathan P Kitzrow
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
- Center for Retrovirus Research, The Ohio State University, Columbus, OH 43210, USA
| | - Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
- Center for RNA Biology, The Ohio State University, Columbus, OH 43210, USA
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA
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Skotte NH, Southwell AL, Østergaard ME, Carroll JB, Warby SC, Doty CN, Petoukhov E, Vaid K, Kordasiewicz H, Watt AT, Freier SM, Hung G, Seth PP, Bennett CF, Swayze EE, Hayden MR. Allele-specific suppression of mutant huntingtin using antisense oligonucleotides: providing a therapeutic option for all Huntington disease patients. PLoS One 2014; 9:e107434. [PMID: 25207939 PMCID: PMC4160241 DOI: 10.1371/journal.pone.0107434] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/11/2014] [Indexed: 01/10/2023] Open
Abstract
Huntington disease (HD) is an inherited, fatal neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene. The mutant protein causes neuronal dysfunction and degeneration resulting in motor dysfunction, cognitive decline, and psychiatric disturbances. Currently, there is no disease altering treatment, and symptomatic therapy has limited benefit. The pathogenesis of HD is complicated and multiple pathways are compromised. Addressing the problem at its genetic root by suppressing mutant huntingtin expression is a promising therapeutic strategy for HD. We have developed and evaluated antisense oligonucleotides (ASOs) targeting single nucleotide polymorphisms that are significantly enriched on HD alleles (HD-SNPs). We describe our structure-activity relationship studies for ASO design and find that adjusting the SNP position within the gap, chemical modifications of the wings, and shortening the unmodified gap are critical for potent, specific, and well tolerated silencing of mutant huntingtin. Finally, we show that using two distinct ASO drugs targeting the two allelic variants of an HD-SNP could provide a therapeutic option for all persons with HD; allele-specifically for roughly half, and non-specifically for the remainder.
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Affiliation(s)
- Niels H. Skotte
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amber L. Southwell
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Jeffrey B. Carroll
- Behavioral Neuroscience Program, Department of Psychology, Western Washington University, Bellingham, Washington, United States of America
| | - Simon C. Warby
- Center for Advanced Research in Sleep Medicine, Department of Psychiatry, University of Montréal, Montréal, Quebec, Canada
| | - Crystal N. Doty
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Eugenia Petoukhov
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kuljeet Vaid
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Andrew T. Watt
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - Susan M. Freier
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - Gene Hung
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - Punit P. Seth
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - C. Frank Bennett
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - Eric E. Swayze
- ISIS Pharmaceuticals, Carlsbad, California, United States of America
| | - Michael R. Hayden
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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Hsiao C, Lenz TK, Peters JK, Fang PY, Schneider DM, Anderson EJ, Preeprem T, Bowman JC, O'Neill EB, Lie L, Athavale SS, Gossett JJ, Trippe C, Murray J, Petrov AS, Wartell RM, Harvey SC, Hud NV, Williams LD. Molecular paleontology: a biochemical model of the ancestral ribosome. Nucleic Acids Res 2013; 41:3373-85. [PMID: 23355613 PMCID: PMC3597689 DOI: 10.1093/nar/gkt023] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Ancient components of the ribosome, inferred from a consensus of previous work, were constructed in silico, in vitro and in vivo. The resulting model of the ancestral ribosome presented here incorporates ∼20% of the extant 23S rRNA and fragments of five ribosomal proteins. We test hypotheses that ancestral rRNA can: (i) assume canonical 23S rRNA-like secondary structure, (ii) assume canonical tertiary structure and (iii) form native complexes with ribosomal protein fragments. Footprinting experiments support formation of predicted secondary and tertiary structure. Gel shift, spectroscopic and yeast three-hybrid assays show specific interactions between ancestral rRNA and ribosomal protein fragments, independent of other, more recent, components of the ribosome. This robustness suggests that the catalytic core of the ribosome is an ancient construct that has survived billions of years of evolution without major changes in structure. Collectively, the data here support a model in which ancestors of the large and small subunits originated and evolved independently of each other, with autonomous functionalities.
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Affiliation(s)
- Chiaolong Hsiao
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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Abstract
A brief historical introduction describes early attempts to silence specific genes using the antisense oligonucleotides that flourished in the 1980s. Early aspirations for therapeutic applications were almost extinguished by the unexpected complexity of oligonucleotide pharmacology. Once the biochemistry and molecular biology behind some of the pharmacology was worked out, new approaches became apparent for using oligonucleotides to treat disease. The biochemistry of small nucleic acids is outlined in Section 2. Various approaches employing oligonucleotides to control cellular functions are reviewed in Section 3. These include antisense oligonucleotides and siRNA that bind to RNA, antigene oligonucleotides that bind to DNA, and aptamers, decoys, and CpG oligonucleotides that bind to proteins.
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MESH Headings
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/pharmacology
- Aptamers, Nucleotide/therapeutic use
- Communicable Diseases/drug therapy
- Communicable Diseases/pathology
- CpG Islands
- DNA/chemistry
- DNA/metabolism
- DNA, Catalytic/chemistry
- DNA, Catalytic/pharmacology
- DNA, Catalytic/therapeutic use
- Diabetes Mellitus/drug therapy
- Diabetes Mellitus/pathology
- Humans
- MicroRNAs/chemistry
- MicroRNAs/pharmacology
- MicroRNAs/therapeutic use
- Molecular Targeted Therapy/methods
- Neoplasms/drug therapy
- Neoplasms/pathology
- Neurodegenerative Diseases/drug therapy
- Neurodegenerative Diseases/pathology
- Nucleic Acid Hybridization
- Oligonucleotides/chemistry
- Oligonucleotides/pharmacology
- Oligonucleotides/therapeutic use
- Oligonucleotides, Antisense/chemistry
- Oligonucleotides, Antisense/pharmacology
- Oligonucleotides, Antisense/therapeutic use
- RNA, Catalytic/chemistry
- RNA, Catalytic/pharmacology
- RNA, Catalytic/therapeutic use
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/pharmacology
- RNA, Small Interfering/therapeutic use
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Affiliation(s)
- John Goodchild
- Department of Chemistry, Worcester State University, Worcester, MA 01602-2597, USA.
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Zhang J, Zhang J, Liu LH, Zhou Y, Li YP, Shao ZH, Wu YJ, Li MJ, Fan YY, Shi HJ. Effects of miR-541 on neurite outgrowth during neuronal differentiation. Cell Biochem Funct 2011; 29:279-86. [PMID: 21452340 DOI: 10.1002/cbf.1747] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 02/06/2011] [Accepted: 02/10/2011] [Indexed: 12/20/2022]
Abstract
MicroRNA (miRNAs) are short non-coding RNA molecules that downregulate gene expression at post-transcriptional level. miRNAs are post-transcriptional regulators of gene expression important for neuron development and function. This report demonstrated that a putative and chemically synthesized miRNA rno-mir-541 played an important role in the neuron development. Differentiation of PC12 cells with nerve growth factor (NGF) is associated with neurite outgrowth, a process that involves upregulation of Synapsin I. We predicted, detected and assessed the expression levels of a number of possible miRNAs for synapsin I in rats and our outcomes showed that rno-mir-541 was associated with rat synapsin I expression. miR-541, a brain specific miRNA, plays an important role in repressing neurite extension in cultured PC12 neurons. The neurites of PC12 cells was shortened drasticly as a result of the overexpression of rno-mir-541. In contrast, the neurites of PC12 cell developed well after the knockdown of rno-mir-541 by RNA interference. Our study showed that rno-mir-541 played an important role in neuron-cell proliferation and neurite outgrowth through suppressing the expression of its target gene synapsin I. Furthermore, the introduction of NGF causes downregulation of miR-541, de-repression of its target, Synapsin-I and allows for neuritogenesis. Thus, miR-541 functions in neuronal precursors as an endogenous conditional component between NGF and Synapsin-I.
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Affiliation(s)
- Jun Zhang
- Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai, China.
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Liang R, Kierzek E, Kierzek R, Turner DH. Comparisons between chemical mapping and binding to isoenergetic oligonucleotide microarrays reveal unexpected patterns of binding to the Bacillus subtilis RNase P RNA specificity domain. Biochemistry 2010; 49:8155-68. [PMID: 20557101 PMCID: PMC2938832 DOI: 10.1021/bi100286n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 06/16/2010] [Indexed: 11/29/2022]
Abstract
Microarrays with isoenergetic pentamer and hexamer 2'-O-methyl oligonucleotide probes with LNA (locked nucleic acid) and 2,6-diaminopurine substitutions were used to probe the binding sites on the RNase P RNA specificity domain of Bacillus subtilis. Unexpected binding patterns were revealed. Because of their enhanced binding free energies, isoenergetic probes can break short duplexes, merge adjacent loops, and/or induce refolding. This suggests new approaches to the rational design of short oligonucleotide therapeutics but limits the utility of microarrays for providing constraints for RNA structure determination. The microarray results are compared to results from chemical mapping experiments, which do provide constraints. Results from both types of experiments indicate that the RNase P RNA folds similarly in 1 M Na(+) and 10 mM Mg(2+).
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Affiliation(s)
- Ruiting Liang
- Department of Chemistry, University of Rochester, Rochester, New York 14627
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-714 Poznan, Noskowskiego 12/14, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-714 Poznan, Noskowskiego 12/14, Poland
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, New York 14627
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