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Yu CH, He X, Acero REP, Han X, Wang Y, Sczepanski JT. Interrogation of mirror-image l-RNA-protein interactions reveals key mechanisms of single-stranded G-rich l-RNA cytotoxicity and a potential mitigation strategy. Chem Sci 2025; 16:7560-7572. [PMID: 40171033 PMCID: PMC11955919 DOI: 10.1039/d5sc00596e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Accepted: 03/11/2025] [Indexed: 04/03/2025] Open
Abstract
l-Oligonucleotides (ONs), the synthetic enantiomers of native d-nucleic acids, are being increasingly utilized in the development of diverse biomedical technologies, including molecular imaging tools, diagnostic biosensors, and aptamer-based therapeutics. Nevertheless, our understanding of how l-ONs behave in living systems falls far short of native d-ONs. In particular, despite the potential for an abundant l-ON-protein interactome, the extent to which l-ONs bind to endogenous proteins and the consequences of these interactions are unknown, posing a major hurdle towards engineering functional l-ONs with predictable intracellular behaviours. Towards closing this knowledge gap, we now report the first l-ON-protein interactome, revealing that a wide-range of nuclear proteins have the potential to bind l-RNA. Importantly, by focusing our study on cytotoxic single-stranded G-rich l-RNA sequences, our data reveal key protein interactions that contribute to the cytotoxicity of these sequences. Furthermore, we show that introducing 2'-O-methyl modifications into single-stranded G-rich l-RNA can decrease its cytotoxicity through reducing l-RNA-protein interactions, thereby demonstrating that a well-established strategy for mitigating the cytotoxic effects of antisense ONs may translate across the chiral mirror. Overall, these findings greatly deepen our understanding of the intracellular behavior of l-ONs and provide valuable guidance for the future development of safe and effective l-ON-based biomedical technologies.
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Affiliation(s)
- Chen-Hsu Yu
- Department of Chemistry, Texas A&M University College Station Texas 77843 USA
| | - Xiaomei He
- Department of Chemistry, University of California Riverside Riverside California 92521-0403 USA
- Department of Biology, East Carolina University Greenville North Carolina 27858 USA
| | | | - Xuan Han
- Department of Chemistry, Texas A&M University College Station Texas 77843 USA
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside Riverside California 92521-0403 USA
| | - Jonathan T Sczepanski
- Department of Chemistry, Texas A&M University College Station Texas 77843 USA
- Department of Biochemistry and Biophysics, Texas A&M University College Station Texas 77843 USA
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2
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Lei X, Xia Y, Ma X, Wang L, Wu Y, Wu X, Yang Z, Wang S, Ren X. Illuminating RNA through fluorescent light-up RNA aptamers. Biosens Bioelectron 2025; 271:116969. [PMID: 39615220 DOI: 10.1016/j.bios.2024.116969] [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: 05/24/2024] [Revised: 11/13/2024] [Accepted: 11/18/2024] [Indexed: 01/06/2025]
Abstract
Visualizing RNA is critical for understanding RNA expression patterns and spatial organization within cells, offering valuable insights into gene regulation and cellular functions. High-resolution RNA imaging techniques are therefore indispensable for revealing the complexities of cellular pathways and physiological processes. Traditional RNA imaging methods, however, face significant limitations, such as high background noise resulting from labeling or cell fixation, which can impede the accurate tracking of RNA dynamics in live cells. Fluorescent light-up RNA aptamers (FLAPs) have emerged as a powerful alternative, distinguished by their capacity for enhanced fluorescence activation, reduced background interference, and advantages such as label-free imaging, small molecular size, and customizable structures. In this review, we provide an overview of the development of FLAPs, explore recent advancements in FLAP-based RNA imaging strategies, and discuss both the challenges and future directions in the field. Through this analysis, we aim to facilitate the further development and application of FLAPs in RNA research, fostering innovation and offering new perspectives in the study of RNA biology.
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Affiliation(s)
- Xin Lei
- College of Chemistry and Life Sciences, Beijing University of Technology, Beijing, China
| | - Yuqing Xia
- College of Chemistry and Life Sciences, Beijing University of Technology, Beijing, China
| | - Xiaochen Ma
- College of Chemistry and Life Sciences, Beijing University of Technology, Beijing, China
| | - Li Wang
- College of Chemistry and Life Sciences, Beijing University of Technology, Beijing, China
| | - Yifan Wu
- College of Chemistry and Life Sciences, Beijing University of Technology, Beijing, China
| | - Xin Wu
- College of Chemistry and Life Sciences, Beijing University of Technology, Beijing, China
| | - Zifu Yang
- College of Chemistry and Life Sciences, Beijing University of Technology, Beijing, China
| | - Shizheng Wang
- College of Chemistry and Life Sciences, Beijing University of Technology, Beijing, China
| | - Xiaojun Ren
- College of Chemistry and Life Sciences, Beijing University of Technology, Beijing, China.
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3
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Han X, Sczepanski JT. An expanded substrate scope for cross-chiral ligation enables efficient synthesis of long l-RNAs. RSC Chem Biol 2025; 6:209-217. [PMID: 39781247 PMCID: PMC11704760 DOI: 10.1039/d4cb00253a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Accepted: 12/26/2024] [Indexed: 01/12/2025] Open
Abstract
Despite the growing interest in mirror-image l-oligonucleotides, both as a robust nucleic acid analogue and as an artificial genetic polymer, their broader adoption in biochemical research and medicine remains hindered by challenges associated with the synthesis of long sequences, especially for l-RNA. Herein, we present a novel strategy for assembling long l-RNAs via the joining of two or more shorter fragments using cross-chiral ligase ribozymes together with new substrate activation chemistry. We show that 5'-monophosphorylated l-RNA, which is readily prepared by solid-phase synthesis, can be activated by chemical attachment of a 5'-adenosine monophosphate (AMP) or diphosphate (ADP), yielding 5'-adenosyl(di- or tri-)phosphate l-RNA. The activation reaction is performed in mild aqueous conditions, proceeds efficiently with short or large l-RNA, and, yielding few byproducts, requires little or no further purification after activation. Importantly, both groups, when added to l-RNA, are compatible with ribozyme-mediated ligation, with the 5'-adenosyltriphosphate permitting rapid and efficient joining of two long l-RNA strands. This is exemplified by the assembly of a 129-nt l-RNA molecule via a single cross-chiral ligation event. Overall, by relying on ribozymes that can be readily prepared by in vitro transcription and l-RNA substrates that can be activated through simple chemistry, these methods are expected to make long l-RNAs more accessible to a wider range of researchers and facilitate the expansion of l-ON-based technologies.
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Affiliation(s)
- Xuan Han
- Department of Chemistry, Texas A&M University College Station Texas 77843 USA
| | - Jonathan T Sczepanski
- Department of Chemistry, Texas A&M University College Station Texas 77843 USA
- Department of Biochemistry and Biophysics, Texas A&M University College Station Texas 77843 USA
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4
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Shearer V, Yu CH, Han X, Sczepanski JT. The clinical potential of l-oligonucleotides: challenges and opportunities. Chem Sci 2024; 15:d4sc05157b. [PMID: 39479156 PMCID: PMC11514577 DOI: 10.1039/d4sc05157b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Accepted: 10/19/2024] [Indexed: 11/02/2024] Open
Abstract
Chemically modified nucleotides are central to the development of biostable research tools and oligonucleotide therapeutics. In this context, l-oligonucleotides, the synthetic enantiomer of native d-nucleic acids, hold great promise. As enantiomers, l-oligonucleotides share the same physical and chemical properties as their native counterparts, yet their inverted l-(deoxy)ribose sugars afford them orthogonality towards the stereospecific environment of biology. Notably, l-oligonucleotides are highly resistant to degradation by cellular nucleases, providing them with superior biostability. As a result, l-oligonucleotides are being increasingly utilized for the development of diverse biomedical technologies, including molecular imaging tools, diagnostic biosensors, and aptamer-based therapeutics. Herein, we present recent such examples that highlight the clinical potential of l-oligonucleotides. Additionally, we provide our perspective on the remaining challenges and practical considerations currently associated with the use of l-oligonucleotides and explore potential solutions that will lead to the broader adoption of l-oligonucleotides in clinical applications.
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Affiliation(s)
- Victoria Shearer
- Department of Chemistry, Texas A&M University College Station Texas 77843 USA
| | - Chen-Hsu Yu
- Department of Chemistry, Texas A&M University College Station Texas 77843 USA
| | - Xuan Han
- Department of Chemistry, Texas A&M University College Station Texas 77843 USA
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5
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Kehrli J, Husser C, Ryckelynck M. Fluorogenic RNA-Based Biosensors of Small Molecules: Current Developments, Uses, and Perspectives. BIOSENSORS 2024; 14:376. [PMID: 39194605 DOI: 10.3390/bios14080376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/14/2024] [Accepted: 07/19/2024] [Indexed: 08/29/2024]
Abstract
Small molecules are highly relevant targets for detection and quantification. They are also used to diagnose and monitor the progression of disease and infectious processes and track the presence of contaminants. Fluorogenic RNA-based biosensors (FRBs) represent an appealing solution to the problem of detecting these targets. They combine the portability of molecular systems with the sensitivity and multiplexing capacity of fluorescence, as well as the exquisite ligand selectivity of RNA aptamers. In this review, we first present the different sensing and reporting aptamer modules currently available to design an FRB, together with the main methodologies used to discover modules with new specificities. We next introduce and discuss how both modules can be functionally connected prior to exploring the main applications for which FRB have been used. Finally, we conclude by discussing how using alternative nucleotide chemistries may improve FRB properties and further widen their application scope.
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Affiliation(s)
- Janine Kehrli
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Claire Husser
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
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6
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Wang X, Deng X, Zhang Y, Dong W, Rao Q, Huang Q, Tang F, Shen R, Xu H, Jin Z, Tang Y, Du D. A rapid and sensitive one-pot platform integrating fluorogenic RNA aptamers and CRISPR-Cas13a for visual detection of monkeypox virus. Biosens Bioelectron 2024; 257:116268. [PMID: 38636316 DOI: 10.1016/j.bios.2024.116268] [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: 02/18/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/20/2024]
Abstract
The recent global upsurge in Monkeypox virus (MPXV) outbreaks underscores the critical need for rapid and precise diagnostic solutions, particularly in resource-constrained settings. The gold standard diagnostic method, qRT-PCR, is hindered by its time-consuming nature, requirement for nucleic acid purification, expensive equipment, and the need for highly trained personnel. Traditional CRISPR/Cas fluorescence assays, relying on trans-cleavage of ssDNA/RNA reporters labeled with costly fluorophores and quenchers, pose challenges that limit their widespread application, especially for point-of-care testing (POCT). In this study, we utilized a cost-effective and stable fluorogenic RNA aptamer (Mango III), specifically binding and illuminating the fluorophore TO3-3 PEG-Biotin Fluorophore (TO3), as a reporter for Cas13a trans-cleavage activity. We propose a comprehensive strategy integrating RNA aptamer, recombinase-aided amplification (RAA), and CRISPR-Cas13a systems for the molecular detection of MPXV target. Leveraging the inherent collateral cleavage properties of the Cas13a system, we established high-sensitivity and specificity assays to distinguish MPXV from other Orthopoxviruses (OPVs). A streamlined one-pot protocol was developed to mitigate aerosol contamination risks. Our aptamer-coupled RAA-Cas13a one-pot detection method achieved a Limit of Detection (LoD) of 4 copies of target MPXV DNA in just 40 min. Validation using clinical MPX specimens confirmed the rapid and reliable application of our RAA-Cas13a-Apt assays without nucleic acid purification procedure, highlighting its potential as a point-of-care testing solution. These results underscore the user-friendliness and effectiveness of our one-pot RAA-Cas13a-Apt diagnostic platform, poised to revolutionize disease detection and management.
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Affiliation(s)
- Xiao Wang
- State Key Laboratory of Cellular Stress Biology, Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; Department of Stomatology, School of Medicine, Xiamen University, Xiamen 361102, China; Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
| | - Xiaobao Deng
- State Key Laboratory of Cellular Stress Biology, Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; Department of Stomatology, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Yidun Zhang
- Xiamen Center for Disease Control and Prevention, Xiamen 361021, China
| | - Weiyi Dong
- State Key Laboratory of Cellular Stress Biology, Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; Department of Stomatology, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Qiao Rao
- State Key Laboratory of Cellular Stress Biology, Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; Department of Stomatology, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Qingmei Huang
- Department of Stomatology, School of Medicine, Xiamen University, Xiamen 361102, China
| | - Fei Tang
- Xiamen Center for Disease Control and Prevention, Xiamen 361021, China
| | - Rong Shen
- State Key Laboratory of Cellular Stress Biology, Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Hongzhi Xu
- Department of Gastroenterology, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361004, China; Clinical Research Center for Gut Microbiota and Digestive Diseases of Fujian Province, Xiamen Key Laboratory of Intestinal Microbiome and Human Health, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361004, China
| | - Zhen Jin
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Youzhi Tang
- Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
| | - Dan Du
- State Key Laboratory of Cellular Stress Biology, Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China; Department of Stomatology, School of Medicine, Xiamen University, Xiamen 361102, China; Innovation Center for Cell Signaling Network, Xiamen University, Xiamen 361102, China; Department of Gastroenterology, The National Key Clinical Specialty, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361004, China; Clinical Research Center for Gut Microbiota and Digestive Diseases of Fujian Province, Xiamen Key Laboratory of Intestinal Microbiome and Human Health, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361004, China.
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7
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Yan Z, Eshed A, Tang AA, Arevalos NR, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA. Rapid, Multiplexed, and Enzyme-Free Nucleic Acid Detection Using Programmable Aptamer-Based RNA Switches. Chem 2024; 10:2220-2244. [PMID: 39036067 PMCID: PMC11259118 DOI: 10.1016/j.chempr.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/23/2024]
Abstract
Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. We describe a class of aptamer-based RNA switches or aptaswitches that recognize target nucleic acid molecules and initiate folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide an intense fluorescent readout without intervening enzymes, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. Aptaswitches can be used to regulate folding of seven fluorogenic aptamers, providing a general means of controlling aptamers and an array of multiplexable reporter colors. Coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed all-in-one reactions against RNA from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that are readily integrated into rapid diagnostic assays.
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Affiliation(s)
- Zhaoqing Yan
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Amit Eshed
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Anli A. Tang
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Nery R. Arevalos
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Zachary M. Ticktin
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Soma Chaudhary
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | - Griffin McCutcheon
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yudan Li
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Kaiyue Wu
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
| | - Sanchari Saha
- Biodesign Center for Molecular Design and Biomimetics at
the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
| | | | | | | | - James J. Collins
- Department of Biological Engineering, Massachusetts
Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT,
Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA,
USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering,
Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School,
Boston, MA, USA
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University,
Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program,
Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA
02215, USA
- School of Molecular Sciences, Arizona State University,
Tempe, AZ, USA
- Lead contact
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8
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Emanuelson C, Bardhan A, Deiters A. DNA Logic Gates for Small Molecule Activation Circuits in Cells. ACS Synth Biol 2024; 13:538-545. [PMID: 38306634 PMCID: PMC10877608 DOI: 10.1021/acssynbio.3c00474] [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: 08/02/2023] [Revised: 01/09/2024] [Accepted: 01/09/2024] [Indexed: 02/04/2024]
Abstract
DNA-based devices such as DNA logic gates self-assemble into supramolecular structures, as dictated by the sequences of the constituent oligonucleotides and their predictable Watson-Crick base pairing interactions. The programmable nature of DNA-based devices permits the design and implementation of DNA circuits that interact in a dynamic and sequential manner capable of spatially arranging disparate DNA species. Here, we report the application of an activatable fluorescence reporter based on a proximity-driven inverse electron demand Diels-Alder (IEDDA) reaction and its robust integration with DNA strand displacement circuits. In response to specific DNA input patterns, sequential strand displacement reactions are initiated and culminate in the hybridization of two modified DNA strands carrying probes capable of undergoing an IEDDA reaction between a vinyl-ether-caged fluorophore and its reactive partner tetrazine, leading to the activation of fluorescence. This approach provides a major advantage for DNA computing in mammalian cells since circuit degradation does not induce fluorescence, in contrast to traditional fluorophore-quencher designs. We demonstrate the robustness and sensitivity of the reporter by testing its ability to serve as a readout for DNA logic circuits of varying complexity inside cells.
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Affiliation(s)
- Cole Emanuelson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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9
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Tang X, Chen T, Ma Y, Mao C, Hu S, Zhang R, Yan Y, Pan Q, Feng C, Zhu X. Enzyme Reaction-Assisted Programmable Transcriptional Switches for Bioactive Molecule Detection. Anal Chem 2024; 96:331-338. [PMID: 38127443 DOI: 10.1021/acs.analchem.3c04198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Bioactive molecules are highly worthwhile to recognize and explore the latent pathogenic mechanism. Conventional methods for bioactive molecule detection, including mass spectrometry and fluorescent probe imaging, are limited due to the complex processing and signal interference. Here, we designed enzyme-reaction-assisted programmable transcriptional switches for the detection of bioactive molecules. The approach is based on the use of programmable enzyme site-specific cleavage-assisted DNA triplex-based conformational switches that, upon responding to bioactive molecules, can trigger the transcription of fluorescent light-up aptamers. Thanks to the programmable nature of the sensing platform, the method can be adapted to different bioactive molecules, and we demonstrated the enzyme-small molecule catalytic reaction combination of myeloperoxidase (MPO)-hydrogen peroxide (H2O2) as a model that transcriptional switches was capable of detecting H2O2 and possessed the specificity and anti-interference ability in vitro. Furthermore, we successfully applied the switches into cells to observe the detection feasibility in vivo, and dynamically monitored changes of H2O2 in cellular oxidative stress levels. Therefore, we attempt to amalgamate the advantages of enzyme reaction with the pluripotency of programmable transcriptional switches, which can take both fields a step further, which may promote the research of biostimuli and the construction of DNA molecular devices.
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Affiliation(s)
- Xiaochen Tang
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Tianshu Chen
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Yonggeng Ma
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Changqing Mao
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Song Hu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Runchi Zhang
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Yilin Yan
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
| | - Qiuhui Pan
- Department of Clinical Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, P. R. China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai 200127, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, Shanghai Engineering Research Center of Organ Repair, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P. R. China
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10
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Lin B, Xiao F, Jiang J, Zhao Z, Zhou X. Engineered aptamers for molecular imaging. Chem Sci 2023; 14:14039-14061. [PMID: 38098720 PMCID: PMC10718180 DOI: 10.1039/d3sc03989g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/07/2023] [Indexed: 12/17/2023] Open
Abstract
Molecular imaging, including quantification and molecular interaction studies, plays a crucial role in visualizing and analysing molecular events occurring within cells or organisms, thus facilitating the understanding of biological processes. Moreover, molecular imaging offers promising applications for early disease diagnosis and therapeutic evaluation. Aptamers are oligonucleotides that can recognize targets with a high affinity and specificity by folding themselves into various three-dimensional structures, thus serving as ideal molecular recognition elements in molecular imaging. This review summarizes the commonly employed aptamers in molecular imaging and outlines the prevalent design approaches for their applications. Furthermore, it highlights the successful application of aptamers to a wide range of targets and imaging modalities. Finally, the review concludes with a forward-looking perspective on future advancements in aptamer-based molecular imaging.
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Affiliation(s)
- Bingqian Lin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Jinting Jiang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Zhengjia Zhao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Department of Hematology of Zhongnan Hospital, Taikang Center for Life and Medical Sciences, Wuhan University Wuhan 430072 China
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11
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Ma N, Xu S, Wu W, Liu J. Electrochemiluminescence Aptasensor with Dual Signal Amplification by Silica Nanochannel-Based Confinement Effect on Nanocatalyst and Efficient Emitter Enrichment for Highly Sensitive Detection of C-Reactive Protein. Molecules 2023; 28:7664. [PMID: 38005386 PMCID: PMC10675231 DOI: 10.3390/molecules28227664] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
The rapid and sensitive detection of the important biomarker C-reactive protein (CRP) is of great significance for monitoring inflammation and tissue damage. In this work, an electrochemiluminescence (ECL) aptasensor was fabricated based on dual signal amplification for the sensitive detection of CRP in serum samples. The sensor was constructed by modifying a silica nanochannel array film (SNF) on a cost-effective indium tin oxide (ITO) electrode using the Stöber solution growth method. Gold nanoparticles (AuNPs) were grown in situ within the nanochannels using a simple electrodeposition method as a nanocatalyst to enhance the active electrode area as well as the ECL signal. The negatively charged nanochannels also significantly enriched the positively charged ECL emitters, further amplifying the signal. The recognition aptamer was covalently immobilized on the outer surface of SNF after modification with epoxy groups, constructing the aptasensor. In the presence of CRP, the formation of complexes on the recognitive interface led to a decrease in the diffusion of ECL emitters and co-reactants to the supporting electrode, resulting in a reduction in the ECL signal. Based on this mechanism, ECL detection of CRP was achieved with a linear range of 10 pg/mL to 1 μg/mL and a low limit of detection (7.4 pg/mL). The ECL aptasensor developed in this study offers advantages such as simple fabrication and high sensitivity, making promising applications in biomarker detection.
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Affiliation(s)
- Ning Ma
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan 030032, China;
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shuai Xu
- School of Chemistry and Chemical Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China;
| | - Weidong Wu
- Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan 030032, China;
- Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jiyang Liu
- School of Chemistry and Chemical Engineering, Zhejiang Sci-Tech University, Hangzhou 310018, China;
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12
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Ji D, Feng H, Liew SW, Kwok CK. Modified nucleic acid aptamers: development, characterization, and biological applications. Trends Biotechnol 2023; 41:1360-1384. [PMID: 37302912 DOI: 10.1016/j.tibtech.2023.05.005] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/30/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Hengxin Feng
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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13
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Yan Z, Tang AA, Eshed A, Ticktin ZM, Chaudhary S, Ma D, McCutcheon G, Li Y, Wu K, Saha S, Alcantar-Fernandez J, Moreno-Camacho JL, Campos-Romero A, Collins JJ, Yin P, Green AA. Rapid and Multiplexed Nucleic Acid Detection using Programmable Aptamer-Based RNA Switches. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.02.23290873. [PMID: 37333364 PMCID: PMC10275000 DOI: 10.1101/2023.06.02.23290873] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Rapid, simple, and low-cost diagnostic technologies are crucial tools for combatting infectious disease. Here, we describe a class of aptamer-based RNA switches called aptaswitches that recognize specific target nucleic acid molecules and respond by initiating folding of a reporter aptamer. Aptaswitches can detect virtually any sequence and provide a fast and intense fluorescent readout, generating signals in as little as 5 minutes and enabling detection by eye with minimal equipment. We demonstrate that aptaswitches can be used to regulate folding of six different fluorescent aptamer/fluorogen pairs, providing a general means of controlling aptamer activity and an array of different reporter colors for multiplexing. By coupling isothermal amplification reactions with aptaswitches, we reach sensitivities down to 1 RNA copy/μL in one-pot reactions. Application of multiplexed one-pot reactions against RNA extracted from clinical saliva samples yields an overall accuracy of 96.67% for detection of SARS-CoV-2 in 30 minutes. Aptaswitches are thus versatile tools for nucleic acid detection that can be readily integrated into rapid diagnostic assays.
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Affiliation(s)
- Zhaoqing Yan
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- These authors contributed equally: Zhaoqing Yan, Anli A. Tang
| | - Anli A. Tang
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
- These authors contributed equally: Zhaoqing Yan, Anli A. Tang
| | - Amit Eshed
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Zackary M. Ticktin
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Soma Chaudhary
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Duo Ma
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | - Griffin McCutcheon
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yudan Li
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Kaiyue Wu
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Sanchari Saha
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
| | | | | | | | - James J. Collins
- Department of Biological Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
- Institute for Medical Engineering and Science, MIT, Cambridge, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, USA
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14
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Yu CH, Sczepanski JT. The influence of chirality on the behavior of oligonucleotides inside cells: revealing the potent cytotoxicity of G-rich l-RNA. Chem Sci 2023; 14:1145-1154. [PMID: 36756313 PMCID: PMC9891384 DOI: 10.1039/d2sc05511b] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/30/2022] [Indexed: 12/31/2022] Open
Abstract
Due to their intrinsic nuclease resistance, mirror image l-oligonucleotides are being increasingly employed in the development of biomedical research tools and therapeutics. Yet, the influence of chirality on the behavior of oligonucleotides in living systems, and specifically, the extent to which l-oligonucleotides interact with endogenous biomacromolecules and the resulting consequences remain unknown. In this study, we characterized the intracellular behavior of l-oligonucleotides for the first time, revealing important chirality-dependent effects on oligonucleotide cytotoxicity. We show that exogenously delivered l-oligonucleotides have the potential to be highly cytotoxic, which is dependent on backbone chemistry, sequence, and structure. Notably, for the sequences tested, we found that single-stranded G-rich l-RNAs are more cytotoxic than their d-DNA/RNA counterparts, exhibiting low nanomolar EC50 values. Importantly, RNA-seq analysis of differentially expressed genes suggests that G-rich l-RNAs stimulate an innate immune response and pro-inflammatory cytokine production. These data not only challenge the general perception that mirror image l-oligonucleotides are nontoxic and nonimmunogenic, but also reveal previously unrecognized therapeutic opportunities. Moreover, by establishing sequence/structure toxicity relationships, this work will guide how future l-oligonucleotide-based biotechnologies are designed and applied.
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Affiliation(s)
- Chen-Hsu Yu
- Department of Chemistry, Texas A&M University College Station Texas 77843 USA
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15
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López-Tena M, Chen SK, Winssinger N. Supernatural: Artificial Nucleobases and Backbones to Program Hybridization-Based Assemblies and Circuits. Bioconjug Chem 2023; 34:111-123. [PMID: 35856656 DOI: 10.1021/acs.bioconjchem.2c00292] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The specificity and predictability of hybridization make oligonucleotides a powerful platform to program assemblies and networks with logic-gated responses, an area of research which has grown into a field of its own. While the field has capitalized on the commercial availability of DNA oligomers with its four canonical nucleobases, there are opportunities to extend the capabilities of the hardware with unnatural nucleobases and other backbones. This Topical Review highlights nucleobases that favor hybridizations that are empowering for assemblies and networks as well as two chiral XNAs than enable orthogonal hybridization networks.
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Affiliation(s)
- Miguel López-Tena
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Si-Kai Chen
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
| | - Nicolas Winssinger
- University of Geneva, Department of Organic Chemistry, Faculty of Science, NCCR Chemical Biology, 30 Quai Ernest Ansermet, CH-1205 Geneva, Switzerland
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16
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Recent advance of RNA aptamers and DNAzymes for MicroRNA detection. Biosens Bioelectron 2022; 212:114423. [DOI: 10.1016/j.bios.2022.114423] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/19/2022] [Accepted: 05/23/2022] [Indexed: 02/02/2023]
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17
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Zon G. Recent advances in aptamer applications for analytical biochemistry. Anal Biochem 2022; 644:113894. [PMID: 32763306 PMCID: PMC7403853 DOI: 10.1016/j.ab.2020.113894] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/24/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022]
Abstract
Aptamers are typically defined as relatively short (20-60 nucleotides) single-stranded DNA or RNA molecules that bind with high affinity and specificity to various types of targets. Aptamers are frequently referred to as "synthetic antibodies" but are easier to obtain, less expensive to produce, and in several ways more versatile than antibodies. The beginnings of aptamers date back to 1990, and since then there has been a continual increase in aptamer publications. The intent of the present account was to focus on recent original research publications, i.e., those appearing in 2019 through April 2020, when this account was written. A Google Scholar search of this recent literature was performed for relevance-ranking of articles. New methods for selection of aptamers were not included. Nine categories of applications were organized and representative examples of each are given. Finally, an outlook is offered focusing on "faster, better, cheaper" application performance factors as key drivers for future innovations in aptamer applications.
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18
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Rahman MM, Lopa NS, Lee J. Advances in electrochemical aptasensing for cardiac biomarkers. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
| | - Nasrin Siraj Lopa
- Research Center for Photoenergy Harvesting & Conversion Technology (phct), Department of Energy and Materials Engineering Dongguk University Seoul South Korea
| | - Jae‐Joon Lee
- Research Center for Photoenergy Harvesting & Conversion Technology (phct), Department of Energy and Materials Engineering Dongguk University Seoul South Korea
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19
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Yu CH, Kabza AM, Sczepanski JT. Assembly of long L-RNA by native RNA ligation. Chem Commun (Camb) 2021; 57:10508-10511. [PMID: 34550128 DOI: 10.1039/d1cc04296c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to their intrinsic nuclease resistance, L-oligonucleotides are being increasingly utilized in the development of molecular tools and sensors. Yet, it remains challenging to synthesize long L-oligonucleotides, potential limiting future applications. Herein, we report straightforward and versitile approach to assemble long L-RNAs from two or more shorter fragments using T4 RNA ligase 1. We show that this approach is compatible with the assembly of several classes of functional L-RNA, which we highlight by generating a 124 nt L-RNA biosensor that functions in serum.
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Affiliation(s)
- Chen-Hsu Yu
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
| | - Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
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20
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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: 1.8] [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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21
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Ji D, Lyu K, Zhao H, Kwok CK. Circular L-RNA aptamer promotes target recognition and controls gene activity. Nucleic Acids Res 2021; 49:7280-7291. [PMID: 34233000 PMCID: PMC8287958 DOI: 10.1093/nar/gkab593] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 12/18/2022] Open
Abstract
Rational design of aptamers to incorporate unnatural nucleotides and special chemical moieties can expand their functional complexity and diversity. Spiegelmer (L-RNA aptamer) is a unique class of aptamer that is composed of unnatural L-RNA nucleotides, and so far there are limited L-RNA aptamer candidates and applications being reported. Moreover, the target binding properties of current L-RNA aptamers require significant improvement. Here, using L-Apt.4-1c as an example, we develop a simple and robust strategy to generate the first circular L-RNA aptamer, cycL-Apt.4-1c, quantitatively, demonstrate substantial enhancement in binding affinity and selectivity toward its target, and notably report novel applications of circular L-RNA aptamer in controlling RNA-protein interaction, and gene activity including telomerase activity and gene expression. Our approach and findings will be applicable to any L-RNA aptamers and open up a new avenue for diverse applications.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Kaixin Lyu
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Haizhou Zhao
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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22
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Abstract
DNA-based Boolean logic gates (for example, AND, OR, and NOT) can be assembled into complex computational circuits that generate an output signal in response to specific patterns of oligonucleotide inputs. However, the fundamental nature of NOT gates, which convert the absence of an input into an output, makes their implementation within DNA-based circuits difficult. Premature execution of a NOT gate before completion of its upstream computation introduces an irreversible error into the circuit. By utilizing photocaging groups, we developed a novel DNA gate design that prevents gate function until irradiation at a certain time point. Optical activation provides temporal control over circuit performance by preventing premature computation and is orthogonal to all other components of DNA computation devices. Using this approach, we designed NAND and NOR logic gates that respond to synthetic microRNA sequences. We further demonstrate the utility of the NOT gate within multilayer circuits in response to a specific pattern of four microRNAs.
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Affiliation(s)
- Cole Emanuelson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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23
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Kundu N, Young BE, Sczepanski JT. Kinetics of heterochiral strand displacement from PNA-DNA heteroduplexes. Nucleic Acids Res 2021; 49:6114-6127. [PMID: 34125895 PMCID: PMC8216467 DOI: 10.1093/nar/gkab499] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/06/2021] [Accepted: 05/27/2021] [Indexed: 12/19/2022] Open
Abstract
Dynamic DNA nanodevices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation remains challenging due to nuclease degradation and other cellular factors. Use of l-DNA, the nuclease resistant enantiomer of native d-DNA, provides a promising solution. On this basis, we recently developed a strand displacement methodology, referred to as ‘heterochiral’ strand displacement, that enables robust l-DNA nanodevices to be sequence-specifically interfaced with endogenous d-nucleic acids. However, the underlying reaction – strand displacement from PNA–DNA heteroduplexes – remains poorly characterized, limiting design capabilities. Herein, we characterize the kinetics of strand displacement from PNA–DNA heteroduplexes and show that reaction rates can be predictably tuned based on several common design parameters, including toehold length and mismatches. Moreover, we investigate the impact of nucleic acid stereochemistry on reaction kinetics and thermodynamics, revealing important insights into the biophysical mechanisms of heterochiral strand displacement. Importantly, we show that strand displacement from PNA–DNA heteroduplexes is compatible with RNA inputs, the most common nucleic acid target for intracellular applications. Overall, this work greatly improves the understanding of heterochiral strand displacement reactions and will be useful in the rational design and optimization of l-DNA nanodevices that operate at the interface with biology.
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Affiliation(s)
- Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Brian E Young
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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24
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Ryckelynck M. Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More. Methods Mol Biol 2021; 2166:73-102. [PMID: 32710404 DOI: 10.1007/978-1-0716-0712-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The central role of RNA in living systems made it highly desirable to have noninvasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-fluorescent molecules called "fluorogens" that become fluorescent upon binding to genetically encodable RNAs called "light-up aptamers." Yet, the development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications is presented and discussed.
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Affiliation(s)
- Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.
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25
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Zhong W, Sczepanski JT. Direct Comparison of d-DNA and l-DNA Strand-Displacement Reactions in Living Mammalian Cells. ACS Synth Biol 2021; 10:209-212. [PMID: 33347747 DOI: 10.1021/acssynbio.0c00527] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To overcome technical challenges associated with the use of DNA strand-displacement circuits in vivo, including degradation by cellular nucleases, researchers are increasingly turning to bio-orthogonal l-DNA. Although enhanced stability and improved performance of l-DNA-based circuits within living cells are often implied, direct experimental evidence has not been provided. Herein, we directly compare the functional stability and kinetics of d-DNA and l-DNA strand-displacement in live cells for the first time. We show that l-DNA strand-displacement reaction systems have minimal "leak", fast reaction kinetics, and prolonged stability inside living cells as compared to conventional d-DNA. Furthermore, using "heterochiral" strand-displacement, we demonstrate that biostable l-DNA reaction components can be easily interfaced with native DNA inside cells. Overall, our results strongly support the broader adoption of l-DNA in the field of DNA molecular circuitry, especially for in vivo applications.
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Affiliation(s)
- Wenrui Zhong
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Jonathan T. Sczepanski
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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26
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Schaudy E, Somoza MM, Lietard J. l-DNA Duplex Formation as a Bioorthogonal Information Channel in Nucleic Acid-Based Surface Patterning. Chemistry 2020; 26:14310-14314. [PMID: 32515523 PMCID: PMC7702103 DOI: 10.1002/chem.202001871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Indexed: 01/02/2023]
Abstract
Photolithographic in situ synthesis of nucleic acids enables extremely high oligonucleotide sequence density as well as complex surface patterning and combined spatial and molecular information encoding. No longer limited to DNA synthesis, the technique allows for total control of both chemical and Cartesian space organization on surfaces, suggesting that hybridization patterns can be used to encode, display or encrypt informative signals on multiple chemically orthogonal levels. Nevertheless, cross-hybridization reduces the available sequence space and limits information density. Here we introduce an additional, fully independent information channel in surface patterning with in situ l-DNA synthesis. The bioorthogonality of mirror-image DNA duplex formation prevents both cross-hybridization on chimeric l-/d-DNA microarrays and also results in enzymatic orthogonality, such as nuclease-proof DNA-based signatures on the surface. We show how chimeric l-/d-DNA hybridization can be used to create informative surface patterns including QR codes, highly counterfeiting resistant authenticity watermarks, and concealed messages within high-density d-DNA microarrays.
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Affiliation(s)
- Erika Schaudy
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Mark M. Somoza
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
- Chair of Food Chemistry and Molecular and Sensory ScienceTechnical University of MunichLise-Meitner-Straße 3485354FreisingGermany
- Leibniz-Institute for Food Systems BiologyTechnical University of MunichLise-Meitner-Straße 3485354FreisingGermany
| | - Jory Lietard
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
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27
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Bertucci A, Porchetta A, Del Grosso E, Patiño T, Idili A, Ricci F. Protein‐Controlled Actuation of Dynamic Nucleic Acid Networks by Using Synthetic DNA Translators**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Alessandro Bertucci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Alessandro Porchetta
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Erica Del Grosso
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Tania Patiño
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Andrea Idili
- Catalan Institute of Nanoscience and Nanotechnology (ICN2) Campus UAB Bellaterra 08193 Barcelona Spain
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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28
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Umar MI, Kwok CK. Specific suppression of D-RNA G-quadruplex-protein interaction with an L-RNA aptamer. Nucleic Acids Res 2020; 48:10125-10141. [PMID: 32976590 PMCID: PMC7544233 DOI: 10.1093/nar/gkaa759] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/28/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023] Open
Abstract
G-quadruplexes (G4s) are nucleic acid structure motifs that are of significance in chemistry and biology. The function of G4s is often governed by their interaction with G4-binding proteins. Few categories of G4-specific tools have been developed to inhibit G4-protein interactions; however, until now there is no aptamer tool being developed to do so. Herein, we present a novel L-RNA aptamer that can generally bind to D-RNA G-quadruplex (rG4) structure, and interfere with rG4-protein interaction. Using hTERC rG4 as the target for in vitro selection, we report the shortest L-aptamer being developed so far, with only 25 nucleotides. Notably, this new aptamer, L-Apt.4-1c, adopts a stem-loop structure with the loop folding into an rG4 motif with two G-quartet, demonstrates preferential binding toward rG4s over non-G4s and DNA G-quadruplexes (dG4s), and suppresses hTERC rG4-nucleolin interactions. We also show that inhibition of rG4-protein interaction using L-RNA aptamer L-Apt.4-1c is comparable to or better than G4-specific ligands such as carboxypyridostatin and QUMA-1 respectively, highlighting that our approach and findings expand the current G4 toolbox, and open a new avenue for diverse applications.
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Affiliation(s)
- Mubarak I Umar
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
| | - Chun Kit Kwok
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong SAR, China
- Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China
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29
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Bertucci A, Porchetta A, Del Grosso E, Patiño T, Idili A, Ricci F. Protein-Controlled Actuation of Dynamic Nucleic Acid Networks by Using Synthetic DNA Translators*. Angew Chem Int Ed Engl 2020; 59:20577-20581. [PMID: 32737920 DOI: 10.1002/anie.202008553] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/22/2020] [Indexed: 12/20/2022]
Abstract
Integrating dynamic DNA nanotechnology with protein-controlled actuation will expand our ability to process molecular information. We have developed a strategy to actuate strand displacement reactions using DNA-binding proteins by engineering synthetic DNA translators that convert specific protein-binding events into trigger inputs through a programmed conformational change. We have constructed synthetic DNA networks responsive to two different DNA-binding proteins, TATA-binding protein and Myc-Max, and demonstrated multi-input activation of strand displacement reactions. We achieved protein-controlled regulation of a synthetic RNA and of an enzyme through artificial DNA-based communication, showing the potential of our molecular system in performing further programmable tasks.
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Affiliation(s)
- Alessandro Bertucci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Erica Del Grosso
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Tania Patiño
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Andrea Idili
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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30
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Mallette TL, Stojanovic MN, Stefanovic D, Lakin MR. Robust Heterochiral Strand Displacement Using Leakless Translators. ACS Synth Biol 2020; 9:1907-1910. [PMID: 32551499 DOI: 10.1021/acssynbio.0c00131] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Molecular computing offers a powerful framework for in situ biosensing and signal processing at the nanoscale. However, for in vivo applications, the use of conventional DNA components can lead to false positive signals being generated due to degradation of circuit components by nuclease enzymes. Here, we use hybrid chiral molecules, consisting of both l- and d-nucleic acid domains, to implement leakless signal translators that enable d-nucleic acid signals to be detected by hybridization and then translated into a robust l-DNA signal for further analysis. We show that our system is robust to false positive signals even if the d-DNA components are degraded by nucleases, thanks to circuit-level robustness. This work thus broadens the scope and applicability of DNA-based molecular computers for practical, in vivo applications.
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Affiliation(s)
- Tracy L. Mallette
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Milan N. Stojanovic
- Division of Experimental Therapeutics, Department of Medicine, Columbia University Medical Center, New York, New York 10032, United States
- Departments of Biomedical Engineering and Systems Biology, Columbia University, New York, New York 10027, United States
| | - Darko Stefanovic
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
- Department of Computer Science, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Matthew R. Lakin
- Center for Biomedical Engineering, University of New Mexico, Albuquerque, New Mexico 87131, United States
- Department of Computer Science, University of New Mexico, Albuquerque, New Mexico 87131, United States
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31
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Broch F, Gautier A. Illuminating Cellular Biochemistry: Fluorogenic Chemogenetic Biosensors for Biological Imaging. Chempluschem 2020; 85:1487-1497. [PMID: 32644262 DOI: 10.1002/cplu.202000413] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/18/2020] [Indexed: 12/19/2022]
Abstract
Cellular activity is defined by the precise spatiotemporal regulation of various components, such as ions, small molecules, or proteins. Studying cell physiology consequently requires the optical recording of these processes, notably by using fluorescent biosensors. The recent development of various fluorogenic systems greatly expanded the palette of reporters to be included in these sensors design. Fluorogenic reporters consist of a protein or RNA tag that can complex either an endogenous or a synthetic fluorogenic dye (so-called fluorogen). The intrinsic nature of these tags, along with the high tunability of their cognate chromophore provide interesting features such as far-red to near-infrared emission, oxygen independence, or unprecedented color versatility. These engineered photoreceptors, self-labelling proteins, or noncovalent aptamers and protein tags were rapidly identified as promising reporters to observe biological events. This Minireview focuses on the new perspectives they offer to design unique and innovative biosensors, thus pushing the boundaries of cellular imaging.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France.,Institut Universitaire de France, France
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32
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Gautier A, Tebo AG. Sensing cellular biochemistry with fluorescent chemical-genetic hybrids. Curr Opin Chem Biol 2020; 57:58-64. [PMID: 32580134 DOI: 10.1016/j.cbpa.2020.04.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/19/2020] [Accepted: 04/08/2020] [Indexed: 11/26/2022]
Abstract
Fluorescent biosensors are powerful tools for the detection of biochemical events inside cells with high spatiotemporal resolution. Biosensors based on fluorescent proteins often suffer from issues with photostability and brightness. On the other hand, hybrid, chemical-genetic systems present unique opportunities to combine the strengths of synthetic, organic chemistry with biological macromolecules to generate exquisitely tailored semisynthetic sensors.
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Affiliation(s)
- Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France; Institut Universitaire de France, France.
| | - Alison G Tebo
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France.
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33
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Kabza AM, Sczepanski JT. l-DNA-Based Catalytic Hairpin Assembly Circuit. Molecules 2020; 25:molecules25040947. [PMID: 32093258 PMCID: PMC7070954 DOI: 10.3390/molecules25040947] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 02/18/2020] [Accepted: 02/19/2020] [Indexed: 11/16/2022] Open
Abstract
Isothermal, enzyme-free amplification methods based on DNA strand-displacement reactions show great promise for applications in biosensing and disease diagnostics but operating such systems within biological environments remains extremely challenging due to the susceptibility of DNA to nuclease degradation. Here, we report a catalytic hairpin assembly (CHA) circuit constructed from nuclease-resistant l-DNA that is capable of unimpeded signal amplification in the presence of 10% fetal bovine serum (FBS). The superior biostability of the l-DNA CHA circuit relative to its native d-DNA counterpart was clearly demonstrated through a direct comparison of the two systems (d versus l) under various conditions. Importantly, we show that the l-CHA circuit can be sequence-specifically interfaced with an endogenous d-nucleic acid biomarker via an achiral peptide nucleic acid (PNA) intermediary, enabling catalytic detection of the target in FBS. Overall, this work establishes a blueprint for the detection of low-abundance nucleic acids in harsh biological environments and provides further impetus for the construction of DNA nanotechnology using l-oligonucleotides.
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34
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Guan B, Zhang X. Aptamers as Versatile Ligands for Biomedical and Pharmaceutical Applications. Int J Nanomedicine 2020; 15:1059-1071. [PMID: 32110008 PMCID: PMC7035142 DOI: 10.2147/ijn.s237544] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/10/2020] [Indexed: 12/14/2022] Open
Abstract
Aptamers are a class of targeting ligands that bind exclusively to biomarkers of interest. Aptamers have been identified as candidates for the construction of various smart systems for therapy, diagnosis, bioimaging, and drug delivery due to their high target affinity and specificity. Aptamers are accounted as chemical antibodies that can be readily linked to drugs, sensors, signal enhancers, or nanocarriers for functionalization. Use of aptamer-guided medications, especially nanomedicines, has resulted in encouraging outcomes compared to those use of aptamer-free counterparts. This article reviews recent advances in the use of aptamers as targeting ligands for various biomedical and pharmaceutical purposes. Special interests focus on aptamer-based theranostics, biosensing, bioimaging, drug potentiation, and targeted drug delivery.
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Affiliation(s)
- Baozhang Guan
- Department of Nephrology, The First Affiliated Hospital of Jinan University, Guangzhou 510630, People's Republic of China
| | - Xingwang Zhang
- Department of Pharmaceutics, College of Pharmacy, Jinan University, Guangzhou 510632, People's Republic of China
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35
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Young BE, Sczepanski JT. Heterochiral DNA Strand-Displacement Based on Chimeric d/l-Oligonucleotides. ACS Synth Biol 2019; 8:2756-2759. [PMID: 31670930 DOI: 10.1021/acssynbio.9b00335] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Heterochiral DNA strand-displacement reactions enable sequence-specific interfacing of oligonucleotide enantiomers, making it possible to interface native d-nucleic acids with molecular circuits built using nuclease-resistant l-DNA. To date, all heterochiral reactions have relied on peptide nucleic acid (PNA), which places potential limits on the scope and utility of this approach. Herein, we now report heterochiral strand-displacement in the absence of PNA, instead utilizing chimeric d/l-DNA complexes to interface oligonucleotides of the opposite chirality. We show that these strand-displacement reactions can be easily integrated into multicomponent heterochiral circuits, are compatible with both DNA and RNA inputs, and can be engineered to function in serum-supplemented medium. We anticipate that these new reactions will lead to a wider application of heterochiral strand-displacement, especially in the design of biocompatible nucleic acid circuits that can reliably operate within living systems.
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Affiliation(s)
- Brian E. Young
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jonathan T. Sczepanski
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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36
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Péresse T, Gautier A. Next-Generation Fluorogen-Based Reporters and Biosensors for Advanced Bioimaging. Int J Mol Sci 2019; 20:E6142. [PMID: 31817528 PMCID: PMC6940837 DOI: 10.3390/ijms20246142] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
Our ability to observe biochemical events with high spatial and temporal resolution is essential for understanding the functioning of living systems. Intrinsically fluorescent proteins such as the green fluorescent protein (GFP) have revolutionized the way biologists study cells and organisms. The fluorescence toolbox has been recently extended with new fluorescent reporters composed of a genetically encoded tag that binds endogenously present or exogenously applied fluorogenic chromophores (so-called fluorogens) and activates their fluorescence. This review presents the toolbox of fluorogen-based reporters and biosensors available to biologists. Various applications are detailed to illustrate the possible uses and opportunities offered by this new generation of fluorescent probes and sensors for advanced bioimaging.
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Affiliation(s)
- Tiphaine Péresse
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
- Institut Universitaire de France (IUF), 1 rue Descartes, 75005 Paris, France
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37
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Hong S, Zhang X, Lake RJ, Pawel GT, Guo Z, Pei R, Lu Y. A photo-regulated aptamer sensor for spatiotemporally controlled monitoring of ATP in the mitochondria of living cells. Chem Sci 2019; 11:713-720. [PMID: 34123044 PMCID: PMC8145946 DOI: 10.1039/c9sc04773e] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Fluorescent aptamer sensors have shown enormous potential for intracellular imaging of small molecule metabolites. Since metabolites distribute differently at different subcellular locations and their concentrations and locations fluctuate with time, methods are needed for spatiotemporally controlled monitoring of these metabolites. Built upon previous success in temporal control of aptamer-based sensors, we herein report an aptamer sensor containing a photocleavable linker and using DQAsomes to target mitochondria for spatiotemporally controlled monitoring of ATP in the mitochondria of living cells. The photocleavable modification on the DNA ATP aptamer sensor can prevent sensor activation before reaching mitochondria and the sensor can then be activated upon light irradiation. The sensor has a detection limit of 3.7 μM and high selectivity against other nucleotides, allowing detection of ATP concentration fluctuations in mitochondria induced by Ca2+ or oligomycin. This work represents the first successful delivery of a DNA aptamer sensor to mitochondria, providing a new platform for targeted delivery to subcellular organelles for monitoring energy producing processes, as well as mitochondrial dysfunction-related diseases in different cells. A photo-regulated ATP sensor coupled with cationic DQAsomes is developed for spatiotemporally controlled imaging of ATP in the mitochondria of living cells.![]()
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Affiliation(s)
- Shanni Hong
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences Suzhou 215123 China .,Department of Chemistry, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Xiaoting Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210093 China
| | - Ryan J Lake
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana IL 61801 USA .,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Gregory T Pawel
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana IL 61801 USA .,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University Nanjing 210093 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
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign Urbana IL 61801 USA .,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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38
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Development of a histamine aptasensor for food safety monitoring. Sci Rep 2019; 9:16659. [PMID: 31723193 PMCID: PMC6853955 DOI: 10.1038/s41598-019-52876-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022] Open
Abstract
Histamine produced by bacteria through decarboxylation of histidine in spoiled foods such as fish is known to cause food poisoning. Therefore, accurate and facile measurement of histamine is of practical importance. Using the recently discovered RNA aptamer that specifically recognizes histamine (A1-949 aptamer), we developed an aptasensor based on the structure-switching mechanism. Specifically, the aptamer A1-949 was fluorescently labeled at the 5′ end and hybridized with a short quencher DNA strand that is partially complementary to the aptamer. The quencher strand was modified with a fluorescence quencher at its 3′ terminus. Displacement of the quencher strand upon histamine binding results in an increased fluorescence. After optimizing the assay condition, the enantiomeric version of the aptasensor (L-RNA and L-DNA) was synthesized which could detect the achiral analyte with identical sensitivity and improved biochemical stability. The aptasensor performance was validated by measuring fish samples spiked with known concentrations of histamine. Finally, histamine content in spoiled fish samples was measured, and the results were compared with the measurements using a commercial enzymatic assay kit.
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39
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Abstract
The programmability of DNA/RNA-based molecular circuits provides numerous opportunities in the field of synthetic biology. However, the stability of nucleic acids remains a major concern when performing complex computations in biological environments. Our solution to this problem is L-(deoxy)ribose nucleic acids (L-DNA/RNA), which are mirror images (i.e. enantiomers) of natural D-nucleotides. L-oligonucleotides have the same physical and chemical properties as their natural counterparts, yet they are completely invisible to the stereospecific environment of biology. We recently reported a novel strand-displacement methodology for transferring sequence information between oligonucleotide enantiomers (which are incapable of base pairing with each other), enabling bio-orthogonal L-DNA/RNA circuits to be easily interfaced with living systems. In this perspective, we summarize these so-called "heterochiral" circuits, provide a viewpoint on their potential applications in synthetic biology, and discuss key problems that must be solved before achieving the ultimate goal of engineering complex and reliable functionality.
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