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Zhou Y, Sheng P, Li J, Li Y, Xie M, Green AA. Conditional RNA interference in mammalian cells via RNA transactivation. Nat Commun 2024; 15:6855. [PMID: 39127751 PMCID: PMC11316766 DOI: 10.1038/s41467-024-50600-w] [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: 08/16/2023] [Accepted: 07/15/2024] [Indexed: 08/12/2024] Open
Abstract
RNA interference (RNAi) is a powerful tool for sequence-specific gene knockdown in therapeutic and research applications. However, spatiotemporal control of RNAi is required to decrease nonspecific targeting, potential toxicity, and allow targeting of essential genes. Herein we describe a class of de-novo-designed RNA switches that enable sequence-specific regulation of RNAi in mammalian cells. Using cis-repressing RNA elements, we engineer RNA devices that only initiate microRNA biogenesis when binding with cognate trigger RNAs. We demonstrate that this conditional RNAi system, termed Orthogonal RNA Interference induced by Trigger RNA (ORIENTR), provides up to 14-fold increases in artificial miRNA biogenesis upon activation in orthogonal libraries. We show that integration of ORIENTR triggers with dCas13d enhances dynamic range to up to 31-fold. We further demonstrate that ORIENTR can be applied to detect endogenous RNA signals and to conditionally knockdown endogenous genes, thus enabling regulatory possibilities including cell-type-specific RNAi and rewiring of transcriptional networks via RNA profile.
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Affiliation(s)
- Yu Zhou
- UF Center for NeuroGenetics (CNG), Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology (MGM), University of Florida, Gainesville, FL, USA
| | - Peike Sheng
- UF Center for NeuroGenetics (CNG), Gainesville, FL, USA
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), University of Florida, Gainesville, FL, USA
- UF Health Cancer Center, Gainesville, FL, USA
| | - Jiayi Li
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA, USA
| | - Yudan Li
- Biological Design Center, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Mingyi Xie
- UF Center for NeuroGenetics (CNG), Gainesville, FL, USA.
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), University of Florida, Gainesville, FL, USA.
- UF Health Cancer Center, Gainesville, FL, USA.
| | - Alexander A Green
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Biological Design Center, Boston University, Boston, MA, USA.
- Molecular Biology, Cell Biology and Biochemistry Program, Boston University, Boston, MA, USA.
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2
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Han SP, Scherer L, Gethers M, Salvador AM, Salah MBH, Mancusi R, Sagar S, Hu R, DeRogatis J, Kuo YH, Marcucci G, Das S, Rossi JJ, Goddard WA. Programmable siRNA pro-drugs that activate RNAi activity in response to specific cellular RNA biomarkers. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:797-809. [PMID: 35116191 PMCID: PMC8789579 DOI: 10.1016/j.omtn.2021.12.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022]
Abstract
Since Paul Ehrlich's introduction of the "magic bullet" concept in 1908, drug developers have been seeking new ways to target drug activity to diseased cells while limiting effects on normal tissues. In recent years, it has been proposed that coupling riboswitches capable of detecting RNA biomarkers to small interfering RNAs (siRNAs) to create siRNA pro-drugs could selectively activate RNA interference (RNAi) activity in specific cells. However, this concept has not been achieved previously. We report here that we have accomplished this goal, validating a simple and programmable new design that functions reliably in mammalian cells. We show that these conditionally activated siRNAs (Cond-siRNAs) can switch RNAi activity against different targets between clearly distinguished OFF and ON states in response to different cellular RNA biomarkers. Notably, in a rat cardiomyocyte cell line (H9C2), one version of our construct demonstrated biologically meaningful inhibition of a heart-disease-related target gene protein phosphatase 3 catalytic subunit alpha (PPP3CA) in response to increased expression of the pathological marker atrial natriuretic peptide (NPPA) messenger RNA (mRNA). Our results demonstrate the ability of synthetic riboswitches to regulate gene expression in mammalian cells, opening a new path for development of programmable siRNA pro-drugs.
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Affiliation(s)
- Si-ping Han
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - Lisa Scherer
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - Matt Gethers
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ane M. Salvador
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Marwa Ben Haj Salah
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - Rebecca Mancusi
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - Sahil Sagar
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - Robin Hu
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - Julia DeRogatis
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - Ya-Huei Kuo
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA
| | - Saumya Das
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John J. Rossi
- Department of Molecular and Cellular Biology, City of Hope, Duarte, CA 91010, USA
| | - William A. Goddard
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125, USA
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3
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Kabza AM, Kundu N, Zhong W, Sczepanski JT. Integration of chemically modified nucleotides with DNA strand displacement reactions for applications in living systems. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 14:e1743. [PMID: 34328690 DOI: 10.1002/wnan.1743] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/26/2021] [Accepted: 07/06/2021] [Indexed: 01/21/2023]
Abstract
Watson-Crick base pairing rules provide a powerful approach for engineering DNA-based nanodevices with programmable and predictable behaviors. In particular, DNA strand displacement reactions have enabled the development of an impressive repertoire of molecular devices with complex functionalities. By relying on DNA to function, dynamic strand displacement devices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation in living systems has been a slow process due to several persistent challenges, including nuclease degradation. To circumvent these issues, researchers are increasingly turning to chemically modified nucleotides as a means to increase device performance and reliability within harsh biological environments. In this review, we summarize recent progress toward the integration of chemically modified nucleotides with DNA strand displacement reactions, highlighting key successes in the development of robust systems and devices that operate in living cells and in vivo. We discuss the advantages and disadvantages of commonly employed modifications as they pertain to DNA strand displacement, as well as considerations that must be taken into account when applying modified oligonucleotide to living cells. Finally, we explore how chemically modified nucleotides fit into the broader goal of bringing dynamic DNA nanotechnology into the cell, and the challenges that remain. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Diagnostic Tools > Biosensing.
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Affiliation(s)
- Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Wenrui Zhong
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
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4
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Smart Nucleic Acids as Future Therapeutics. Trends Biotechnol 2021; 39:1289-1307. [PMID: 33980422 DOI: 10.1016/j.tibtech.2021.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/23/2021] [Accepted: 03/29/2021] [Indexed: 11/23/2022]
Abstract
Nucleic acid therapeutics (NATs) hold promise in treating undruggable diseases and are recognized as the third major category of therapeutics in addition to small molecules and antibodies. Despite the milestones that NATs have made in clinical translation over the past decade, one important challenge pertains to increasing the specificity of this class of drugs. Activating NATs exclusively in disease-causing cells is highly desirable because it will safely broaden the application of NATs to a wider range of clinical indications. Smart NATs are triggered through a photo-uncaging reaction or a specific molecular input such as a transcript, protein, or small molecule, thus complementing the current strategy of targeting cells and tissues with receptor-specific ligands to enhance specificity. This review summarizes the programmable modalities that have been incorporated into NATs to build in responsive behaviors. We discuss the various inputs, transduction mechanisms, and output response functions that have been demonstrated to date.
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5
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Zakrevsky P, Bindewald E, Humbertson H, Viard M, Dorjsuren N, Shapiro BA. A Suite of Therapeutically-Inspired Nucleic Acid Logic Systems for Conditional Generation of Single-Stranded and Double-Stranded Oligonucleotides. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E615. [PMID: 30991728 PMCID: PMC6526476 DOI: 10.3390/nano9040615] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 03/15/2019] [Accepted: 03/25/2019] [Indexed: 01/16/2023]
Abstract
Several varieties of small nucleic acid constructs are able to modulate gene expression via one of a number of different pathways and mechanisms. These constructs can be synthesized, assembled and delivered to cells where they are able to impart regulatory functions, presenting a potential avenue for the development of nucleic acid-based therapeutics. However, distinguishing aberrant cells in need of therapeutic treatment and limiting the activity of deliverable nucleic acid constructs to these specific cells remains a challenge. Here, we designed and characterized a collection of nucleic acids systems able to generate and/or release sequence-specific oligonucleotide constructs in a conditional manner based on the presence or absence of specific RNA trigger molecules. The conditional function of these systems utilizes the implementation of AND and NOT Boolean logic elements, which could ultimately be used to restrict the release of functionally relevant nucleic acid constructs to specific cellular environments defined by the high or low expression of particular RNA biomarkers. Each system is generalizable and designed with future therapeutic development in mind. Every construct assembles through nuclease-resistant RNA/DNA hybrid duplex formation, removing the need for additional 2'-modifications, while none contain any sequence restrictions on what can define the diagnostic trigger sequence or the functional oligonucleotide output.
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Affiliation(s)
- Paul Zakrevsky
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Eckart Bindewald
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Hadley Humbertson
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Mathias Viard
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
| | - Nomongo Dorjsuren
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Bruce A Shapiro
- RNA Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
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6
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Hochrein LM, Ge TJ, Schwarzkopf M, Pierce NA. Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology. ACS Synth Biol 2018; 7:2796-2802. [PMID: 30525469 PMCID: PMC6305621 DOI: 10.1021/acssynbio.8b00424] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Dynamic
RNA nanotechnology with small conditional RNAs (scRNAs)
offers a promising conceptual approach to introducing synthetic regulatory
links into endogenous biological circuits. Here, we use human cell
lysate containing functional Dicer and RNases as a testbed for engineering
scRNAs for conditional RNA interference (RNAi). scRNAs perform signal
transduction via conditional shape change: detection
of a subsequence of mRNA input X triggers formation of a Dicer substrate
that is processed to yield small interfering RNA (siRNA) output anti-Y
targeting independent mRNA Y for destruction. Automated sequence design
is performed using the reaction pathway designer within NUPACK to
encode this conditional hybridization cascade into the scRNA sequence
subject to the sequence constraints imposed by X and Y. Because it
is difficult for secondary structure models to predict which subsequences
of mRNA input X will be accessible for detection, here we develop
the RNAhyb method to experimentally determine accessible windows within
the mRNA that are provided to the designer as sequence constraints.
We demonstrate the programmability of scRNA regulators by engineering scRNAs for transducing
in both directions between two full-length mRNAs X and Y, corresponding
to either the forward molecular logic “if X then not Y”
(X Y) or
the reverse molecular logic “if Y then not X” (Y X). In human cell lysate, we
observe a strong OFF/ON conditional response with low crosstalk, corresponding
to a ≈20-fold increase in production of the siRNA output in
response to the cognate versus noncognate full-length mRNA input.
2′OMe-RNA chemical modifications protect signal transduction
reactants and intermediates against RNase degradation while enabling
Dicer processing of signal transduction products. Because diverse
biological pathways interact with RNA, scRNAs that transduce between
detection of endogenous RNA inputs and production of biologically
active RNA outputs hold great promise as a synthetic regulatory paradigm.
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Affiliation(s)
| | | | | | - Niles A. Pierce
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, United Kingdom
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7
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Kashida S, Saito H. Design of Ligand-Controlled Genetic Switches Based on RNA Interference. Synth Biol (Oxf) 2018. [DOI: 10.1002/9783527688104.ch8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Shunnichi Kashida
- Center for iPS Cell Research and Application, Kyoto University; Department of Life Science Frontiers; 53 Kawahara-cho, Shogoin, Sakyo-ku Kyoto 606-8507 Japan
- Ecole Normale Supérieure, UMR 8640 CNRS-ENS-UPMC Pasteur; Department of Chemistry; 24 rue Lhomond Paris 75005 France
| | - Hirohide Saito
- Center for iPS Cell Research and Application, Kyoto University; Department of Life Science Frontiers; 53 Kawahara-cho, Shogoin, Sakyo-ku Kyoto 606-8507 Japan
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8
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Zhang Y, Wang J, Cheng H, Sun N, Liu M, Wu Z, Pei R. Inducible Bcl-2 gene RNA interference mediated by aptamer-integrated HDV ribozyme switch. Integr Biol (Camb) 2017; 9:619-626. [PMID: 28548675 DOI: 10.1039/c7ib00029d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The regulation of RNA interference (RNAi) could be a powerful method for the study of temporal and dose dependent effects of gene expression. In this study, we designed the hepatitis delta virus (HDV) ribozyme with an embedded theophylline aptamer as the sensor domain and the pri-miRNA of endogenous gene Bcl-2 as the effector domain to engineer an RNAi-regulatory device in MCF-7 cells. The system allowed us to control gene expression by adding theophylline into the culture media in a dose dependent fashion. This is the pioneering application of ribozyme switches to activate RNAi for modulating endogenous genes in mammalian cells. The platform sets the stage for investigations of other endogenous genes that regulate various biological functions such as differentiation, cell division or cell death, and provides a promising interface with other universal RNAi-based decision-making circuits that operate in mammalian cells. It can be used to study more genes associated with cancer and screen for potential drug targets for gene therapy.
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Affiliation(s)
- Yuanyuan Zhang
- School of Life Science, Anhui Medical University, Hefei 230032, China and CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China. and CAS Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Jine Wang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
| | - Hui Cheng
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
| | - Na Sun
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
| | - Min Liu
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
| | - Zhengyan Wu
- CAS Key Laboratory of Ion Beam Bioengineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China.
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9
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Guo Y, Wei B, Xiao S, Yao D, Li H, Xu H, Song T, Li X, Liang H. Recent advances in molecular machines based on toehold-mediated strand displacement reaction. QUANTITATIVE BIOLOGY 2017. [DOI: 10.1007/s40484-017-0097-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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10
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Chen YJ, Groves B, Muscat RA, Seelig G. DNA nanotechnology from the test tube to the cell. NATURE NANOTECHNOLOGY 2015; 10:748-60. [PMID: 26329111 DOI: 10.1038/nnano.2015.195] [Citation(s) in RCA: 417] [Impact Index Per Article: 46.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 07/29/2015] [Indexed: 05/18/2023]
Abstract
The programmability of Watson-Crick base pairing, combined with a decrease in the cost of synthesis, has made DNA a widely used material for the assembly of molecular structures and dynamic molecular devices. Working in cell-free settings, researchers in DNA nanotechnology have been able to scale up system complexity and quantitatively characterize reaction mechanisms to an extent that is infeasible for engineered gene circuits or other cell-based technologies. However, the most intriguing applications of DNA nanotechnology - applications that best take advantage of the small size, biocompatibility and programmability of DNA-based systems - lie at the interface with biology. Here, we review recent progress in the transition of DNA nanotechnology from the test tube to the cell. We highlight key successes in the development of DNA-based imaging probes, prototypes of smart therapeutics and drug delivery systems, and explore the future challenges and opportunities for cellular DNA nanotechnology.
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Affiliation(s)
- Yuan-Jyue Chen
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Benjamin Groves
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Richard A Muscat
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Georg Seelig
- Department of Electrical Engineering, University of Washington, Seattle, Washington 98195, USA
- Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
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11
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Andries O, Kitada T, Bodner K, Sanders NN, Weiss R. Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: a propositional review. Expert Rev Vaccines 2015; 14:313-31. [DOI: 10.1586/14760584.2015.997714] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Hochrein LM, Schwarzkopf M, Shahgholi M, Yin P, Pierce NA. Conditional Dicer substrate formation via shape and sequence transduction with small conditional RNAs. J Am Chem Soc 2013; 135:17322-30. [PMID: 24219616 PMCID: PMC3842090 DOI: 10.1021/ja404676x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) enables knockdown of a gene of choice, executing the logical operation: silence gene Y. The fact that the siRNA is constitutively active is a significant limitation, making it difficult to confine knockdown to a specific locus and time. To achieve spatiotemporal control over silencing, we seek to engineer small conditional RNAs (scRNAs) that mediate 'conditional RNAi' corresponding to the logical operation: if gene X is transcribed, silence independent gene Y. By appropriately selecting gene X, knockdown of gene Y could then be restricted in a tissue- and time-specific manner. To implement the logic of conditional RNAi, our approach is to engineer scRNAs that, upon binding to mRNA 'detection target' X, perform shape and sequence transduction to form a Dicer substrate targeting independent mRNA 'silencing target' Y, with subsequent Dicer processing yielding an siRNA targeting mRNA Y for destruction. Toward this end, here we design and experimentally validate diverse scRNA mechanisms for conditional Dicer substrate formation. Test tube studies demonstrate strong OFF/ON conditional response, with at least an order of magnitude increase in Dicer substrate production in the presence of the cognate mRNA detection target. By appropriately dimensioning and/or chemically modifying the scRNAs, only the product of signal transduction, and not the reactants or intermediates, is efficiently processed by Dicer, yielding siRNAs. These mechanism studies explore diverse design principles for engineering scRNA signal transduction cascades including reactant stability vs metastability, catalytic vs noncatalytic transduction, pre- vs post-transcriptional transduction, reactant and product molecularity, and modes of molecular self-assembly and disassembly.
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Affiliation(s)
- Lisa M Hochrein
- Department of Chemical Engineering, ‡Department of Biology, ∥Department of Chemistry, §Department of Bioengineering, and ⊥Department of Computing and Mathematical Sciences, California Institute of Technology , Pasadena, California 91125, United States
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13
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Synthetic biology with RNA: progress report. Curr Opin Chem Biol 2012; 16:278-84. [DOI: 10.1016/j.cbpa.2012.05.192] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Revised: 05/09/2012] [Accepted: 05/14/2012] [Indexed: 11/20/2022]
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14
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Engineering biological systems with synthetic RNA molecules. Mol Cell 2011; 43:915-26. [PMID: 21925380 DOI: 10.1016/j.molcel.2011.08.023] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 08/16/2011] [Accepted: 08/21/2011] [Indexed: 01/08/2023]
Abstract
RNA molecules play diverse functional roles in natural biological systems. There has been growing interest in designing synthetic RNA counterparts for programming biological function. The design of synthetic RNA molecules that exhibit diverse activities, including sensing, regulatory, information processing, and scaffolding activities, has highlighted the advantages of RNA as a programmable design substrate. Recent advances in implementing these engineered RNA molecules as key control elements in synthetic genetic networks are highlighting the functional relevance of this class of synthetic elements in programming cellular behaviors.
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