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Zhang Y, Shi Y, Khan MM, Xiao F, Chen W, Tao W, Yao K, Kong N. Ocular RNA nanomedicine: engineered delivery nanoplatforms in treating eye diseases. Trends Biotechnol 2024:S0167-7799(24)00121-5. [PMID: 38821834 DOI: 10.1016/j.tibtech.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/23/2024] [Accepted: 05/06/2024] [Indexed: 06/02/2024]
Abstract
Ocular disorders remain a major global health challenge with unmet medical needs. RNA nanomedicine has shown significant therapeutic benefits and safety profiles in patients with complex eye disorders, already benefiting numerous patients with gene-related eye disorders. The effective delivery of RNA to the unique structure of the eye is challenging owing to RNA instability, off-target effects, and ocular physiological barriers. Specifically tailored RNA medication, coupled with sophisticated engineered delivery platforms, is crucial to guide and advance developments in treatments for oculopathy. Herein we review recent advances in RNA-based nanomedicine, innovative delivery strategies, and current clinical progress and present challenges in ocular disease therapy.
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Affiliation(s)
- Yiming Zhang
- Liangzhu Laboratory, Zhejiang University Medical Center and Zhejiang Provincial Key Lab of Ophthalmology, Eye Center of The Second Affiliated Hospital, Zhejiang University, Hangzhou, China; Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yesi Shi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Muhammad M Khan
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Fan Xiao
- Liangzhu Laboratory, Zhejiang University Medical Center and Zhejiang Provincial Key Lab of Ophthalmology, Eye Center of The Second Affiliated Hospital, Zhejiang University, Hangzhou, China; Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wei Chen
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Ke Yao
- Liangzhu Laboratory, Zhejiang University Medical Center and Zhejiang Provincial Key Lab of Ophthalmology, Eye Center of The Second Affiliated Hospital, Zhejiang University, Hangzhou, China.
| | - Na Kong
- Liangzhu Laboratory, Zhejiang University Medical Center and Zhejiang Provincial Key Lab of Ophthalmology, Eye Center of The Second Affiliated Hospital, Zhejiang University, Hangzhou, China; Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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2
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Hertz LM, White EN, Kuznedelov K, Cheng L, Yu AM, Kakkaramadam R, Severinov K, Chen A, Lucks J. The effect of pseudoknot base pairing on cotranscriptional structural switching of the fluoride riboswitch. Nucleic Acids Res 2024; 52:4466-4482. [PMID: 38567721 PMCID: PMC11077080 DOI: 10.1093/nar/gkae231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 02/17/2024] [Accepted: 03/20/2024] [Indexed: 04/16/2024] Open
Abstract
A central question in biology is how RNA sequence changes influence dynamic conformational changes during cotranscriptional folding. Here we investigated this question through the study of transcriptional fluoride riboswitches, non-coding RNAs that sense the fluoride anion through the coordinated folding and rearrangement of a pseudoknotted aptamer domain and a downstream intrinsic terminator expression platform. Using a combination of Escherichia coli RNA polymerase in vitro transcription and cellular gene expression assays, we characterized the function of mesophilic and thermophilic fluoride riboswitch variants. We showed that only variants containing the mesophilic pseudoknot function at 37°C. We next systematically varied the pseudoknot sequence and found that a single wobble base pair is critical for function. Characterizing thermophilic variants at 65°C through Thermus aquaticus RNA polymerase in vitro transcription showed the importance of this wobble pair for function even at elevated temperatures. Finally, we performed all-atom molecular dynamics simulations which supported the experimental findings, visualized the RNA structure switching process, and provided insight into the important role of magnesium ions. Together these studies provide deeper insights into the role of riboswitch sequence in influencing folding and function that will be important for understanding of RNA-based gene regulation and for synthetic biology applications.
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Affiliation(s)
- Laura M Hertz
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Elise N White
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | | | - Luyi Cheng
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Angela M Yu
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Rivaan Kakkaramadam
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Alan Chen
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Julius B Lucks
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
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3
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Sumi S, Hamada M, Saito H. Deep generative design of RNA family sequences. Nat Methods 2024; 21:435-443. [PMID: 38238559 DOI: 10.1038/s41592-023-02148-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 12/07/2023] [Indexed: 03/13/2024]
Abstract
RNA engineering has immense potential to drive innovation in biotechnology and medicine. Despite its importance, a versatile platform for the automated design of functional RNA is still lacking. Here, we propose RNA family sequence generator (RfamGen), a deep generative model that designs RNA family sequences in a data-efficient manner by explicitly incorporating alignment and consensus secondary structure information. RfamGen can generate novel and functional RNA family sequences by sampling points from a semantically rich and continuous representation. We have experimentally demonstrated the versatility of RfamGen using diverse RNA families. Furthermore, we confirmed the high success rate of RfamGen in designing functional ribozymes through a quantitative massively parallel assay. Notably, RfamGen successfully generates artificial sequences with higher activity than natural sequences. Overall, RfamGen significantly improves our ability to design functional RNA and opens up new potential for generative RNA engineering in synthetic biology.
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Affiliation(s)
- Shunsuke Sumi
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Michiaki Hamada
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan.
- Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.
| | - Hirohide Saito
- Department of Life Science Frontiers, Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan.
- Graduate School of Medicine, Kyoto University, Kyoto, Japan.
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4
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Manna S, Kimoto M, Truong J, Bommisetti P, Peitz A, Hirao I, Hammond MC. Systematic Mutation and Unnatural Base Pair Incorporation Improves Riboswitch-Based Biosensor Response Time. ACS Sens 2023; 8:4468-4472. [PMID: 37878677 PMCID: PMC10749561 DOI: 10.1021/acssensors.3c01266] [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: 06/23/2023] [Accepted: 10/03/2023] [Indexed: 10/27/2023]
Abstract
Engineered RNAs have applications in diverse fields from biomedical to environmental. In many cases, the folding of the RNA is critical to its function. Here we describe a strategy to improve the response time of a riboswitch-based fluorescent biosensor. Systematic mutagenesis was performed to either make transpose or transition base pair mutants or introduce orthogonal base pairs. Both natural and unnatural base pair mutants were found to improve the biosensor response time without compromising fold turn-on or ligand affinity. These strategies can be transferred to improve the performance of other RNA-based tools.
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Affiliation(s)
- Sudeshna Manna
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Michiko Kimoto
- Institute
of Bioengineering and Bioimaging (IBB), A*STAR, 31 Biopolis
Way, The Nanos #07-01, 138669, Singapore
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, 118259, Singapore
| | - Johnny Truong
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Praneeth Bommisetti
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ava Peitz
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Ichiro Hirao
- Institute
of Bioengineering and Bioimaging (IBB), A*STAR, 31 Biopolis
Way, The Nanos #07-01, 138669, Singapore
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, 118259, Singapore
| | - Ming C. Hammond
- Department
of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
- Henry
Eyring Center for Cell & Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
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5
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Hertz LM, White EN, Kuznedelov K, Cheng L, Yu AM, Kakkaramadam R, Severinov K, Chen A, Lucks JB. The Effect of Pseudoknot Base Pairing on Cotranscriptional Structural Switching of the Fluoride Riboswitch. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570056. [PMID: 38106011 PMCID: PMC10723315 DOI: 10.1101/2023.12.05.570056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
A central question in biology is how RNA sequence changes influence dynamic conformational changes during cotranscriptional folding. Here we investigated this question through the study of transcriptional fluoride riboswitches, non-coding RNAs that sense the fluoride anion through the coordinated folding and rearrangement of a pseudoknotted aptamer domain and a downstream intrinsic terminator expression platform. Using a combination of E. coli RNA polymerase in vitro transcription and cellular gene expression assays, we characterized the function of mesophilic and thermophilic fluoride riboswitch variants. We showed that only variants containing the mesophilic pseudoknot function at 37 °C. We next systematically varied the pseudoknot sequence and found that a single wobble base pair is critical for function. Characterizing thermophilic variants at 65 °C through Thermus aquaticus RNA polymerase in vitro transcription showed the importance of this wobble pair for function even at elevated temperatures. Finally, we performed all-atom molecular dynamics simulations which supported the experimental findings, visualized the RNA structure switching process, and provided insight into the important role of magnesium ions. Together these studies provide deeper insights into the role of riboswitch sequence in influencing folding and function that will be important for understanding of RNA-based gene regulation and for synthetic biology applications.
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Affiliation(s)
- Laura M Hertz
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Elise N White
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | | | - Luyi Cheng
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
| | - Angela M Yu
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Rivaan Kakkaramadam
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Konstantin Severinov
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ 08854, USA
| | - Alan Chen
- Department of Chemistry and the RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Julius B Lucks
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL 60208, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL 60208, USA
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6
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Pfeifer BA, Beitelshees M, Hill A, Bassett J, Jones CH. Harnessing synthetic biology for advancing RNA therapeutics and vaccine design. NPJ Syst Biol Appl 2023; 9:60. [PMID: 38036580 PMCID: PMC10689799 DOI: 10.1038/s41540-023-00323-3] [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: 06/01/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Recent global events have drawn into focus the diversity of options for combatting disease across a spectrum of prophylactic and therapeutic approaches. The recent success of the mRNA-based COVID-19 vaccines has paved the way for RNA-based treatments to revolutionize the pharmaceutical industry. However, historical treatment options are continuously updated and reimagined in the context of novel technical developments, such as those facilitated through the application of synthetic biology. When it comes to the development of genetic forms of therapies and vaccines, synthetic biology offers diverse tools and approaches to influence the content, dosage, and breadth of treatment with the prospect of economic advantage provided in time and cost benefits. This can be achieved by utilizing the broad tools within this discipline to enhance the functionality and efficacy of pharmaceutical agent sequences. This review will describe how synthetic biology principles can augment RNA-based treatments through optimizing not only the vaccine antigen, therapeutic construct, therapeutic activity, and delivery vector. The enhancement of RNA vaccine technology through implementing synthetic biology has the potential to shape the next generation of vaccines and therapeutics.
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Affiliation(s)
- Blaine A Pfeifer
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
| | | | - Andrew Hill
- Pfizer, 66 Hudson Boulevard, New York, NY, 10001, USA
| | - Justin Bassett
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, NY, USA
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7
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Escobar A, Diab-Liu A, Bosland K, Xu CQ. Microfluidic Device-Based Virus Detection and Quantification in Future Diagnostic Research: Lessons from the COVID-19 Pandemic. BIOSENSORS 2023; 13:935. [PMID: 37887128 PMCID: PMC10605122 DOI: 10.3390/bios13100935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023]
Abstract
The global economic and healthcare crises experienced over the past three years, as a result of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has significantly impacted the commonplace habits of humans around the world. SARS-CoV-2, the virus responsible for the coronavirus 2019 (COVID-19) phenomenon, has contributed to the deaths of millions of people around the world. The potential diagnostic applications of microfluidic devices have previously been demonstrated to effectively detect and quasi-quantify several different well-known viruses such as human immunodeficiency virus (HIV), influenza, and SARS-CoV-2. As a result, microfluidics has been further explored as a potential alternative to our currently available rapid tests for highly virulent diseases to better combat and manage future potential outbreaks. The outbreak management during COVID-19 was initially hindered, in part, by the lack of available quantitative rapid tests capable of confirming a person's active infectiousness status. Therefore, this review will explore the use of microfluidic technology, and more specifically RNA-based virus detection methods, as an integral part of improved diagnostic capabilities and will present methods for carrying the lessons learned from COVID-19 forward, toward improved diagnostic outcomes for future pandemic-level threats. This review will first explore the context of the COVID-19 pandemic and how diagnostic technology was shown to have required even greater advancements to keep pace with the transmission of such a highly infectious virus. Secondly, the historical significance of integrating microfluidic technology in diagnostics and how the different types of genetic-based detection methods may vary in their potential practical applications. Lastly, the review will summarize the past, present, and future potential of RNA-based virus detection/diagnosis and how it might be used to better prepare for a future pandemic.
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Affiliation(s)
- Andres Escobar
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Alex Diab-Liu
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Kamaya Bosland
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
| | - Chang-Qing Xu
- School of Biomedical Engineering, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
- Department of Engineering Physics, McMaster University, 1280 Main Street West, Hamilton, ON L8S 4L8, Canada
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8
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RNA-targeting strategies as a platform for ocular gene therapy. Prog Retin Eye Res 2023; 92:101110. [PMID: 35840489 DOI: 10.1016/j.preteyeres.2022.101110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/28/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023]
Abstract
Genetic medicine is offering hope as new therapies are emerging for many previously untreatable diseases. The eye is at the forefront of these advances, as exemplified by the approval of Luxturna® by the United States Food and Drug Administration (US FDA) in 2017 for the treatment of one form of Leber Congenital Amaurosis (LCA), an inherited blindness. Luxturna® was also the first in vivo human gene therapy to gain US FDA approval. Numerous gene therapy clinical trials are ongoing for other eye diseases, and novel delivery systems, discovery of new drug targets and emerging technologies are currently driving the field forward. Targeting RNA, in particular, is an attractive therapeutic strategy for genetic disease that may have safety advantages over alternative approaches by avoiding permanent changes in the genome. In this regard, antisense oligonucleotides (ASO) and RNA interference (RNAi) are the currently popular strategies for developing RNA-targeted therapeutics. Enthusiasm has been further fuelled by the emergence of clustered regularly interspersed short palindromic repeats (CRISPR)-CRISPR associated (Cas) systems that allow targeted manipulation of nucleic acids. RNA-targeting CRISPR-Cas systems now provide a novel way to develop RNA-targeted therapeutics and may provide superior efficiency and specificity to existing technologies. In addition, RNA base editing technologies using CRISPR-Cas and other modalities also enable precise alteration of single nucleotides. In this review, we showcase advances made by RNA-targeting systems for ocular disease, discuss applications of ASO and RNAi technologies, highlight emerging CRISPR-Cas systems and consider the implications of RNA-targeting therapeutics in the development of future drugs to treat eye disease.
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Li Y, Arce A, Lucci T, Rasmussen RA, Lucks JB. Dynamic RNA synthetic biology: new principles, practices and potential. RNA Biol 2023; 20:817-829. [PMID: 38044595 PMCID: PMC10730207 DOI: 10.1080/15476286.2023.2269508] [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: 10/28/2023] [Accepted: 08/23/2023] [Indexed: 12/05/2023] Open
Abstract
An increased appreciation of the role of RNA dynamics in governing RNA function is ushering in a new wave of dynamic RNA synthetic biology. Here, we review recent advances in engineering dynamic RNA systems across the molecular, circuit and cellular scales for important societal-scale applications in environmental and human health, and bioproduction. For each scale, we introduce the core concepts of dynamic RNA folding and function at that scale, and then discuss technologies incorporating these concepts, covering new approaches to engineering riboswitches, ribozymes, RNA origami, RNA strand displacement circuits, biomaterials, biomolecular condensates, extracellular vesicles and synthetic cells. Considering the dynamic nature of RNA within the engineering design process promises to spark the next wave of innovation that will expand the scope and impact of RNA biotechnologies.
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Affiliation(s)
- Yueyi Li
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Anibal Arce
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Tyler Lucci
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Rebecca A. Rasmussen
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
- Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, IL, USA
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10
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Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria. J Mol Biol 2022; 434:167689. [PMID: 35717997 DOI: 10.1016/j.jmb.2022.167689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 05/19/2022] [Accepted: 06/09/2022] [Indexed: 01/24/2023]
Abstract
RNA switches are versatile tools in synthetic biology for sensing and regulation applications. The discoveries of RNA-mediated translational and transcriptional control have facilitated the development of complexde novodesigns of RNA switches. Specifically, RNA toehold-mediated switches, in which binding to the toehold sensing domain controls the transition between switch states via strand displacement, have been extensively adapted for coupling systems responses to specifictrans-RNA inputs. This review highlights some of the challenges associated with applying these switches for native RNA detectionin vivo, including transferability between organisms. The applicability and design considerations of toehold-mediated switches are discussed by highlighting twelve recently developed switch designs. This review finishes with future perspectives to address current gaps in the field, particularly regarding the power of structural prediction algorithms for improved in vivo functionality of RNA switches.
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