1
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Peng JM, Liu H, Ying ZM. Rapid one-pot isothermal amplification reassembled of fluorescent RNA aptamer for SARS-CoV-2 detection. Talanta 2024; 276:126264. [PMID: 38761661 DOI: 10.1016/j.talanta.2024.126264] [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: 01/17/2024] [Revised: 04/22/2024] [Accepted: 05/14/2024] [Indexed: 05/20/2024]
Abstract
The outbreak of SARS-CoV-2 poses a serious threat to human life and health. A rapid nucleic acid tests can effectively curb the spread of the disease. With the advantages of fluorescent RNA aptamers, low background and high sensitivity. A variety of fluorescent RNA aptamer sensors have been developed for the detection of nucleic acid. Here, we report a hypersensitive detection platform in which SARS-CoV-2 initiates RTF-EXPAR to amplify trigger fragments. This activation leads to the reassembled of the SRB2 fluorescent RNA aptamer, restoring its secondary structure for SR-DN binding and turn-on fluorescence. The platform completes the assay in 30 min and all reactions occur in one tube. The detection limit is as low as 116 aM. Significantly, the platform's quantitative analyses were almost identical to qPCR results in simulated tests of positive samples. In conclusion, the platform is sensitive, accurate and provides a new protocol for point-of-care testing of viruses.
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Affiliation(s)
- Jia-Min Peng
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Hao Liu
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China
| | - Zhan-Ming Ying
- Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Key Laboratory of Environmentally Friendly Chemistry and Application of Ministry of Education, College of Chemistry, Xiangtan University, Xiangtan, 411105, China.
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2
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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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3
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Jeung JH, Han H, Jang SH, Lee CY, Ahn JK. One-pot, one-step, label-free miRNA detection method based on the structural transition of dumbbell probe. Talanta 2024; 274:125944. [PMID: 38537347 DOI: 10.1016/j.talanta.2024.125944] [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: 12/19/2023] [Revised: 02/15/2024] [Accepted: 03/16/2024] [Indexed: 05/04/2024]
Abstract
In this study, we present a one-pot, one-step, label-free miRNA detection method through a structural transition of a specially designed dumbbell-shape probe, initiating a rolling circle transition (RCT). In principle, target miRNA binds to right loop of the dumbbell probe (DP), which allows structural change of the DP to circular form, exposing a sequence complementary to the T7 promoter (T7p) previously hidden within the stem. This exposure allows T7 RNA polymerase to initiate RCT, producing a repetitive Mango aptamer sequence. TO1-biotin, fluorescent dye, binds to the aptamer, inducing a detectable enhancement of fluorescence intensity. Without miR-141, the DP stays closed, RCT is prevented, and the fluorescence intensity remains low. By employing this novel strategy, target miRNA was successfully identified with a detection of 73 pM and a dynamic linear range of 0-10 nM. Additionally, the method developed enables one-pot, one-step, and label-free detection of miRNA, demonstrating potential for point-of-care testing (POCT) applications. Furthermore, the practical application of the designed technique was demonstrated by reliably detecting the target miRNA in the human serum sample. We also believe that the conceived approach could be widely used to detect not only miRNAs but also diverse biomolecules by simply replacing the detection probe.
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Affiliation(s)
- Jae Hoon Jeung
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea; Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyogu Han
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea; Department of Chemistry, Gangneung-Wonju National University, Gangneung, 25457, Republic of Korea
| | - Se Hee Jang
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea; Department of Medical Device Engineering and Management, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea
| | - Chang Yeol Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Jun Ki Ahn
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea.
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4
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Zhao Y, Wang S. Experimental and biophysical modeling of transcription and translation dynamics in bacterial- and mammalian-based cell-free expression systems. SLAS Technol 2024; 29:100036. [PMID: 35231628 DOI: 10.1016/j.slast.2022.02.001] [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: 11/11/2021] [Revised: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 11/20/2022]
Abstract
Cell-free expression (CFE) systems have been used extensively in systems and synthetic biology as a promising platform for manufacturing proteins and chemicals. Currently, the most widely used CFE system is in vitro protein transcription and translation platform. As the rapidly increased applications and uses, it is crucial to have a standard biophysical model for quantitative studies of gene circuits, which will provide a fundamental understanding of basic working mechanisms of CFE systems. Current modeling approaches mainly focus on the characterization of E. coli-based CFE systems, a computational model that can be utilized for both bacterial- and mammalian-based CFE has not been investigated. Here, we developed a simple ODE (ordinary differential equation)-based biophysical model to simulate transcription and translation dynamics for both bacterial- and mammalian- based CFE systems. The key parameters were estimated and adjusted based on experimental results. We next tested four gene circuits to characterize kinetic dynamics of transcription and translation in E. coli- and HeLa-based CFE systems. The real-time transcription and translation were monitored using Broccoli aptamer, double stranded locked nucleic acid (dsLNA) probe and fluorescent protein. We demonstrated the difference of kinetic dynamics for transcription and translation in both systems, which will provide valuable information for quantitative genomic and proteomic studies. This simple biophysical model and the experimental data for both E. coli- and HeLa-based CFE will be useful for researchers that are interested in genetic engineering and CFE bio-manufacturing.
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Affiliation(s)
- Yuwen Zhao
- Department of Chemistry, Chemical and Biomedical Engineering, Tagliatela College of Engineering, University of New Haven, West Haven, CT, 06516, United States; Department of Biomedical Engineering, Lehigh University, Bethlehem, PA, 18015, United States
| | - Shue Wang
- Department of Chemistry, Chemical and Biomedical Engineering, Tagliatela College of Engineering, University of New Haven, West Haven, CT, 06516, United States.
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5
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Herrera-Gutierrez J, Burden SJ, Kobernat SE, Shults NH, Smith M, Fologea D, Hayden EJ. Double-stemmed and split structural variants of fluorescent RNA Mango aptamers. RNA (NEW YORK, N.Y.) 2023; 29:1355-1364. [PMID: 37268327 PMCID: PMC10573287 DOI: 10.1261/rna.079651.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 05/01/2023] [Indexed: 06/04/2023]
Abstract
Aptamers with fluorogenic ligands are emerging as useful tools to quantify and track RNA molecules. The RNA Mango family of aptamers have a useful combination of tight ligand binding, bright fluorescence, and small size. However, the simple structure of these aptamers, with a single base-paired stem capped by a G-quadruplex, can limit the sequence and structural modifications needed for many use-inspired designs. Here we report new structural variants of RNA Mango that have two base-paired stems attached to the quadruplex. Fluorescence saturation analysis of one of the double-stemmed constructs showed a maximum fluorescence that is ∼75% brighter than the original single-stemmed Mango I. A small number of mutations to nucleotides in the tetraloop-like linker of the second stem were subsequently analyzed. The effect of these mutations on the affinity and fluorescence suggested that the nucleobases of the second linker do not directly interact with the fluorogenic ligand (TO1-biotin), but may instead induce higher fluorescence by indirectly altering the ligand properties in the bound state. The effects of the mutations in this second tetraloop-like linker indicate the potential of this second stem for rational design and reselection experiments. Additionally, we demonstrated that a bimolecular mango designed by splitting the double-stemmed Mango can function when two RNA molecules are cotranscribed from different DNA templates in a single in vitro transcription. This bimolecular Mango has potential application in detecting RNA-RNA interactions. Together, these constructs expand the designability of the Mango aptamers to facilitate future applications of RNA imaging.
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Affiliation(s)
| | - Steven J Burden
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, Idaho 83725, USA
| | - Sarah E Kobernat
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, Idaho 83725, USA
| | - Nicholas H Shults
- Department of Biological Sciences, Boise State University, Boise, Idaho 83725, USA
| | - Mark Smith
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, Idaho 83725, USA
| | - Daniel Fologea
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, Idaho 83725, USA
- Department of Physics, Boise State University, Boise, Idaho 83725, USA
| | - Eric J Hayden
- Biomolecular Sciences Graduate Programs, Boise State University, Boise, Idaho 83725, USA
- Department of Biological Sciences, Boise State University, Boise, Idaho 83725, USA
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6
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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: 2.0] [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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7
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Zhou Z, Lan X, Zhu L, Zhang Y, Chen K, Zhang W, Xu W. Portable dual-aptamer microfluidic chip biosensor for Bacillus cereus based on aptamer tailoring and dumbbell-shaped probes. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130545. [PMID: 36493638 DOI: 10.1016/j.jhazmat.2022.130545] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/21/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
As food-borne pathogens, Bacillus cereus not only produce toxins that contaminate food and threaten human health, but also rely on spores to resist extreme environments. At present, the detection of B. cereus is still at the genome level and it is not easily distinguished from other Bacilli of the same group. Herein, we obtained the aptamers of B. cereus in different phases through Cell-SELEX technology. Then, through step-by-step tailoring and molecular docking, the two best performing aptamers were ascertained and the interaction revealed between the repeated G bases in the aptamer and the polar amino acids in the α-helix of the epiprotein. Based on these aptamers, a multifunctional dumbbell-shaped probe and an ultrasensitive microfluidic chip biosensor were designed. Tests showed that the novel sensor is able to complete detection within 1 h with a limit of detection (LOD) of 9.27 CFU/mL. Moreover, the sensor can be used in complex food environments, such as milk and rice, is able to detect both vegetative cells and spores, and it can also distinguish B. thuringiensis from the same flora. This study can provide a reference for the future development of food-borne pathogenic bacteria aptamer selecting, target interaction analysis, detection methods and equipment.
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Affiliation(s)
- Ziqi Zhou
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xinyue Lan
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yangzi Zhang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kehan Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Department of Mechanical Design and Manufacturing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Wenqiang Zhang
- Department of Mechanical Design and Manufacturing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China.
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8
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Huang Z, Guo X, Ma X, Wang F, Jiang JH. Genetically encodable tagging and sensing systems for fluorescent RNA imaging. Biosens Bioelectron 2023; 219:114769. [PMID: 36252312 DOI: 10.1016/j.bios.2022.114769] [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: 07/31/2022] [Revised: 09/24/2022] [Accepted: 09/28/2022] [Indexed: 10/06/2022]
Abstract
Live cell imaging of RNAs is crucial to interrogate their fundamental roles in various biological processes. The highly spatiotemporal dynamic nature of RNA abundance and localization has presented great challenges for RNA imaging. Genetically encodable tagging and sensing (GETS) systems that can be continuously produced in living systems have afforded promising tools for imaging and sensing RNA dynamics in live cells. Here we review the recent advances of GETS systems that have been developed for RNA tagging and sensing in live cells. We first describe the various GETS systems using MS2-bacteriophage-MS2 coat protein, pumilio homology domain and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9/13 for RNA labeling and tracking. The progresses of GETS systems for fluorogenic labeling and/or sensing RNAs by engineering light-up RNA aptamers, CRISPR-Cas9 systems and RNA aptamer stabilized fluorogenic proteins are then elaborated. The challenges and future perspectives in this field are finally discussed. With the continuing development, GETS systems will afford powerful tools to elucidate RNA biology in living systems.
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Affiliation(s)
- Zhimei Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Xiaoyan Guo
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Xianbo Ma
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China.
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9
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Wu LF, Liu Z, Roberts SJ, Su M, Szostak JW, Sutherland JD. Template-Free Assembly of Functional RNAs by Loop-Closing Ligation. J Am Chem Soc 2022; 144:13920-13927. [PMID: 35880790 PMCID: PMC9354263 DOI: 10.1021/jacs.2c05601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first ribozymes are thought to have emerged at a time when RNA replication proceeded via nonenzymatic template copying processes. However, functional RNAs have stable folded structures, and such structures are much more difficult to copy than short unstructured RNAs. How can these conflicting requirements be reconciled? Also, how can the inhibition of ribozyme function by complementary template strands be avoided or minimized? Here, we show that short RNA duplexes with single-stranded overhangs can be converted into RNA stem loops by nonenzymatic cross-strand ligation. We then show that loop-closing ligation reactions enable the assembly of full-length functional ribozymes without any external template. Thus, one can envisage a potential pathway whereby structurally complex functional RNAs could have formed at an early stage of evolution when protocell genomes might have consisted only of collections of short replicating oligonucleotides.
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Affiliation(s)
- Long-Fei Wu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom.,Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Ziwei Liu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Samuel J Roberts
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Meng Su
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
| | - Jack W Szostak
- Department of Molecular Biology and Center for Computational and Integrative Biology, Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States.,Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - John D Sutherland
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, United Kingdom
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10
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Citartan M. The dynamicity of light-up aptamers in one-pot in vitro diagnostic assays. Analyst 2021; 147:10-21. [PMID: 34860215 DOI: 10.1039/d1an01690c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Light-up aptamers are aptamers that ignite the fluorescence emission of certain dyes upon binding. Widely harnessed in in vivo imaging, the binding capacity of the light-up aptamers can also be deployed in in vitro diagnostic assays, engendering a mix-and-read format. Intrigued by this, I intend to provide an overview of the various formats of diagnostic assays developed using light-up aptamers from the direct modulation of the light-up aptamers, split aptamer-based configuration, strand displacement, in vitro transcription-based one-pot diagnostic assay, CRISPR-Cas system to the measurement of the ion reliance. The incorporation of the light-up aptamers into each configuration is expounded and further supported by describing the exemplary assays developed thus far. It is anticipated that the present study can be enlightening to any researchers who aspire to embark on the development of one-pot in vitro diagnostic assays based on light-up aptamers.
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Affiliation(s)
- Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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11
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Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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12
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Chang Z, Zhu B, Liu J, Zhu X, Xu M, Travas-Sejdic J. Electrochemical aptasensor for 17β-estradiol using disposable laser scribed graphene electrodes. Biosens Bioelectron 2021; 185:113247. [PMID: 33962157 DOI: 10.1016/j.bios.2021.113247] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/25/2021] [Accepted: 04/09/2021] [Indexed: 01/08/2023]
Abstract
17β-Estradiol (E2), the strongest of the three major physiological estrogens in females, is an important factor in the female reproductive system. The abnormal level of E2 causes health issues, such as weak bones, urinary tract infections and even depression. Here, we present a novel, sensitive and selective, electrochemical aptasensor for detection of 17β-estradiol (E2). The E2 recognition aptamer was split into two fragments: the first fragment, functionalised with adamantane, is attached to poly(β-cyclodextrin) (poly(β-CD))-modified electrode surface through host-guest interactions between the adamantane and poly(β-CD). The second fragment, labelled with gold nanoparticles, forms the stem-loop structure with the first fragment only in the presence of E2. That specific recognition process triggers the change in the electrochemical signal (a change in the peak current from reduction of AuNPs), recorded by means of differential pulse voltammetry (DPV). The feasibility of the sensing design was firstly investigated on the commercially available glass carbon electrodes (GCE), with achieved a linear detection range of 1.0 × 10-13 to 1.0 × 10-8 M and a limit of detection (LoD) 0.7 fM. The sensing methodology was then translated onto single-use, disposable, laser-scribed graphene electrodes (LSGE) on a plastic substrate. The dynamic sensing range of E2 on LSGE was found to be 1.0 × 10-13 to 1.0 × 10-9 M, with a LoD of 63.1 fM, comparable to these of GCE. The successful translation of the developed E2 aptasensor from GCE to low-cost, disposable LSGE highlights a potential of this sensing platform in commercial, portable sensing detection systems for E2 and similar targets of biological interest.
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Affiliation(s)
- Zhu Chang
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, Henan Province, PR China
| | - Bicheng Zhu
- Polymer Biointerface Centre, School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington, New Zealand
| | - JinJin Liu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, Henan Province, PR China
| | - Xu Zhu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, Henan Province, PR China
| | - Maotian Xu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, College of Chemistry and Chemical Engineering, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, Shangqiu Normal University, Shangqiu, 476000, Henan Province, PR China
| | - Jadranka Travas-Sejdic
- Polymer Biointerface Centre, School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, 1142, New Zealand; MacDiarmid Institute for Advanced Materials and Nanotechnology, Victoria University of Wellington, PO Box 600, Wellington, New Zealand.
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13
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Gu Y, Huang LJ, Zhao W, Zhang TT, Cui MR, Yang XJ, Zhao XL, Chen HY, Xu JJ. Living-Cell MicroRNA Imaging with Self-Assembling Fragments of Fluorescent Protein-Mimic RNA Aptamer. ACS Sens 2021; 6:2339-2347. [PMID: 34028262 DOI: 10.1021/acssensors.1c00453] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
As the cellular roles of RNA abundance continue to increase, there is an urgent need for the corresponding tools to elucidate native RNA functions and dynamics, especially those of short, low-abundance RNAs in live cells. Fluorescent RNA aptamers provide a useful strategy to create the RNA tag and biosensor devices. Corn, which binds with 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO), is a good candidate for the RNA tag because of its enhanced photostability and red-shifted spectrum. Herein, we report for the first time the utilization of Corn as a split aptamer system, combined with RNA-initiated fluorescence complementation (RIFC), for monitoring RNA self-assembly and sensing microRNA. In this platform, the 28-nt Corn was divided into two nonfunctional halves (named probe I and probe II), and an additional target RNA recognition and stem part was introduced in each probe. The target RNA can trigger the self-assembly reconstitution of the Corn's G-quadruplex scaffold for DFHO binding and turn-on fluorescence. These probes can be transfected stably into mammalian cells and deliver the light-up fluorescent response to microRNA-21 (miR-21). Significantly, the probes have good photostability, with minimal fluorescence loss after continuous irradiation, and can be used for imaging of miR-21 in living mammalian cells. The proposed method is universal and could be applied to the sensing of other tumor-associated RNAs, including messenger RNA and noncoding RNA, as well as for monitoring RNA/RNA interactions. The Corn-based splitting aptamers show promising potential in the real-time visualization and mechanistic analysis of nucleic acids.
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Affiliation(s)
- Yu Gu
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Institute for Materials Science and Engineering, School of Materials Sciences and Engineering, Suzhou University of Science and Technology, Suzhou 215011, China
| | - Li-Juan Huang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Ting-Ting Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Mei-Rong Cui
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xue-Jiao Yang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xue-Li Zhao
- College of Chemistry and Molecular Engineering, Zheng-Zhou University, Zhengzhou 450001, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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14
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RNA origami design tools enable cotranscriptional folding of kilobase-sized nanoscaffolds. Nat Chem 2021; 13:549-558. [PMID: 33972754 PMCID: PMC7610888 DOI: 10.1038/s41557-021-00679-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/08/2021] [Indexed: 12/18/2022]
Abstract
RNA origami is a framework for the modular design of nanoscaffolds that can be folded from a single strand of RNA, and used to organize molecular components with nanoscale precision. Design of genetically expressible RNA origami, which must cotranscriptionally fold, requires modeling and design tools that simultaneously consider thermodynamics, folding pathway, sequence constraints, and pseudoknot optimization. Here, we describe RNA Origami Automated Design software (ROAD), which builds origami models from a library of structural modules, identifies potential folding barriers, and designs optimized sequences. Using ROAD, we extend the scale and functional diversity of RNA scaffolds, creating 32 designs of up to 2360 nucleotides, five that scaffold two proteins, and seven that scaffold two small molecules at precise distances. Micrographic and chromatographic comparison of optimized and nonoptimized structures validates that our principles for strand routing and sequence design substantially improve yield. By providing efficient design of RNA origami, ROAD may simplify construction of custom RNA scaffolds for nanomedicine and synthetic biology.
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15
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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: 1.0] [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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16
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Liu LS, Wang F, Ge Y, Lo PK. Recent Developments in Aptasensors for Diagnostic Applications. ACS APPLIED MATERIALS & INTERFACES 2021; 13:9329-9358. [PMID: 33155468 DOI: 10.1021/acsami.0c14788] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Aptamers are exciting smart molecular probes for specific recognition of disease biomarkers. A number of strategies have been developed to convert target-aptamer binding into physically detectable signals. Since the aptamer sequence was first discovered, a large variety of aptamer-based biosensors have been developed, with considerable attention paid to their potential applications in clinical diagnostics. So far, a variety of techniques in combination with a wide range of functional nanomaterials have been used for the design of aptasensors to further improve the sensitivity and detection limit of target determination. In this paper, the advantages of aptamers over traditional antibodies as the molecular recognition components in biosensors for high-throughput screening target molecules are highlighted. Aptamer-target pairing configurations are predominantly single- or dual-site binding; the design of recognition modes of each aptamer-target pairing configuration is described. Furthermore, signal transduction strategies including optical, electrical, mechanical, and mass-sensitive modes are clearly explained together with examples. Finally, we summarize the recent progress in the development of aptamer-based biosensors for clinical diagnosis, including detection of cancer and disease biomarkers and in vivo molecular imaging. We then conclude with a discussion on the advanced development and challenges of aptasensors.
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Affiliation(s)
- Ling Sum Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Fei Wang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yonghe Ge
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
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17
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Kolpashchikov DM, Spelkov AA. Binary (Split) Light‐up Aptameric Sensors. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.201914919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dmitry M. Kolpashchikov
- Chemistry Department University of Central Florida Orlando FL 32816-2366 USA
- Burnett School of Biomedical Sciences University of Central Florida Orlando FL 32816 USA
| | - Alexander A. Spelkov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies ITMO University 9 Lomonosova Str. St. Petersburg 191002 Russian Federation
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18
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Bezerra AB, Kurian ASN, Easley CJ. Nucleic-Acid Driven Cooperative Bioassays Using Probe Proximity or Split-Probe Techniques. Anal Chem 2021; 93:198-214. [PMID: 33147015 PMCID: PMC7855502 DOI: 10.1021/acs.analchem.0c04364] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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Kolpashchikov DM, Spelkov AA. Binary (Split) Light-up Aptameric Sensors. Angew Chem Int Ed Engl 2020; 60:4988-4999. [PMID: 32208549 DOI: 10.1002/anie.201914919] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Indexed: 12/12/2022]
Abstract
This Minireview discusses the design and applications of binary (also known as split) light-up aptameric sensors (BLAS). BLAS consist of two RNA or DNA strands and a fluorogenic organic dye added as a buffer component. When associated, the two strands form a dye-binding site, followed by an increase in fluorescence of the aptamer-bound dye. The design is cost-efficient because it uses short oligonucleotides and does not require conjugation of organic dyes with nucleic acids. In some applications, BLAS design is preferable over monolithic sensors because of simpler assay optimization and improved selectivity. RNA-based BLAS can be expressed in cells and used for the intracellular monitoring of biological molecules. BLAS have been used as reporters of nucleic acid association events in RNA nanotechnology and nucleic-acid-based molecular computation. Other applications of BLAS include the detection of nucleic acids, proteins, and cancer cells, and potentially they can be tailored to report a broad range of biological analytes.
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Affiliation(s)
- Dmitry M Kolpashchikov
- Chemistry Department, University of Central Florida, Orlando, FL, 32816-2366, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL, 32816, USA
| | - Alexander A Spelkov
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation
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20
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Trachman RJ, Cojocaru R, Wu D, Piszczek G, Ryckelynck M, Unrau PJ, Ferré-D'Amaré AR. Structure-Guided Engineering of the Homodimeric Mango-IV Fluorescence Turn-on Aptamer Yields an RNA FRET Pair. Structure 2020; 28:776-785.e3. [PMID: 32386573 DOI: 10.1016/j.str.2020.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 04/06/2020] [Accepted: 04/11/2020] [Indexed: 10/24/2022]
Abstract
Fluorescent RNA aptamers have been used in cells as biosensor reporters and tags for tracking transcripts. Recently, combined SELEX and microfluidic fluorescence sorting yielded three aptamers that activate fluorescence of TO1-Biotin: Mango-II, Mango-III, and Mango-IV. Of these, Mango-IV was best at imaging RNAs in both fixed and live mammalian cells. To understand how Mango-IV achieves activity in cells, we determined its crystal structure complexed with TO1-Biotin. The structure reveals a domain-swapped homodimer with two independent G-quadruplex fluorophore binding pockets. Structure-based analyses indicate that the Mango-IV core has relaxed fluorophore specificity, and a tendency to reorganize binding pocket residues. These molecular properties may endow it with robustness in the cellular milieu. Based on the domain-swapped structure, heterodimers between Mango-IV and the fluorescent aptamer iSpinach, joined by Watson-Crick base pairing, were constructed. These exhibited FRET between their respective aptamer-activated fluorophores, advancing fluorescent aptamer technology toward multi-color, RNA-based imaging of RNA coexpression and colocalization.
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Affiliation(s)
- Robert J Trachman
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Razvan Cojocaru
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Di Wu
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Grzegorz Piszczek
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA
| | - Michael Ryckelynck
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15 rue René Descartes, 67084 Strasbourg, France
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, 50 South Drive MSC 8012, Bethesda, MD 20892-8012, USA.
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21
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Debiais M, Lelievre A, Smietana M, Müller S. Splitting aptamers and nucleic acid enzymes for the development of advanced biosensors. Nucleic Acids Res 2020; 48:3400-3422. [PMID: 32112111 PMCID: PMC7144939 DOI: 10.1093/nar/gkaa132] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/12/2020] [Accepted: 02/18/2020] [Indexed: 12/16/2022] Open
Abstract
In analogy to split-protein systems, which rely on the appropriate fragmentation of protein domains, split aptamers made of two or more short nucleic acid strands have emerged as novel tools in biosensor set-ups. The concept relies on dissecting an aptamer into a series of two or more independent fragments, able to assemble in the presence of a specific target. The stability of the assembled structure can further be enhanced by functionalities that upon folding would lead to covalent end-joining of the fragments. To date, only a few aptamers have been split successfully, and application of split aptamers in biosensing approaches remains as promising as it is challenging. Further improving the stability of split aptamer target complexes and with that the sensitivity as well as efficient working modes are important tasks. Here we review functional nucleic acid assemblies that are derived from aptamers and ribozymes/DNAzymes. We focus on the thrombin, the adenosine/ATP and the cocaine split aptamers as the three most studied DNA split systems and on split DNAzyme assemblies. Furthermore, we extend the subject into split light up RNA aptamers used as mimics of the green fluorescent protein (GFP), and split ribozymes.
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Affiliation(s)
- Mégane Debiais
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Amandine Lelievre
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron, University of Montpellier, CNRS, ENCSM, Montpellier, France
| | - Sabine Müller
- University Greifswald, Institute for Biochemistry, Greifswald, Germany
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22
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Yuan B, Guo L, Yin K, Wang X, Liu Q, He M, Liu K, Zhao J. Highly sensitive and specific detection of tumor cells based on a split aptamer-triggered dual hybridization chain reaction. Analyst 2020; 145:2676-2681. [PMID: 32065595 DOI: 10.1039/c9an02476j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Highly sensitive and specific detection of rare tumor cells is urgently needed for early tumor diagnosis. Herein, a split aptamer-based dual hybridization chain reaction (dual-HCR) strategy with flow cytometry analysis was developed to meet this purpose. With the split aptamer pair as the recognition unit and HCR as the signal amplification technique, this strategy achieved an improved detection limit as low as 20 cells in 200 μL binding buffer. Meanwhile, this method was highly specific with distinct recognition of the target cells from the control cell and mixed cell samples. Furthermore, we succeeded in the specific detection of the target cells in 50% human serum, demonstrating that this method has great potential in clinical applications. In theory, this strategy can be used to detect different target cells by using different split aptamers. Therefore, this general, sensitive and specific tumor cell detection method may be helpful for early clinical diagnosis and cancer research.
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Affiliation(s)
- Baoyin Yuan
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China.
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23
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Tjhung KF, Shokhirev MN, Horning DP, Joyce GF. An RNA polymerase ribozyme that synthesizes its own ancestor. Proc Natl Acad Sci U S A 2020; 117:2906-2913. [PMID: 31988127 PMCID: PMC7022166 DOI: 10.1073/pnas.1914282117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The RNA-based organisms from which modern life is thought to have descended would have depended on an RNA polymerase ribozyme to copy functional RNA molecules, including copying the polymerase itself. Such a polymerase must have been capable of copying structured RNAs with high efficiency and high fidelity to maintain genetic information across successive generations. Here the class I RNA polymerase ribozyme was evolved in vitro for the ability to synthesize functional ribozymes, resulting in the markedly improved ability to synthesize complex RNAs using nucleoside 5'-triphosphate (NTP) substrates. The polymerase is descended from the class I ligase, which contains the same catalytic core as the polymerase. The class I ligase can be synthesized by the improved polymerase as three separate RNA strands that assemble to form a functional ligase. The polymerase also can synthesize the complement of each of these three strands. Despite this remarkable level of activity, only a very small fraction of the assembled ligases retain catalytic activity due to the presence of disabling mutations. Thus, the fidelity of RNA polymerization should be considered a major impediment to the construction of a self-sustained, RNA-based evolving system. The propagation of heritable information requires both efficient and accurate synthesis of genetic molecules, a requirement relevant to both laboratory systems and the early history of life on Earth.
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Affiliation(s)
- Katrina F Tjhung
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute, La Jolla, CA 92037
| | - Maxim N Shokhirev
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute, La Jolla, CA 92037
| | - David P Horning
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute, La Jolla, CA 92037
| | - Gerald F Joyce
- Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute, La Jolla, CA 92037
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24
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Panigaj M, Johnson MB, Ke W, McMillan J, Goncharova EA, Chandler M, Afonin KA. Aptamers as Modular Components of Therapeutic Nucleic Acid Nanotechnology. ACS NANO 2019; 13:12301-12321. [PMID: 31664817 PMCID: PMC7382785 DOI: 10.1021/acsnano.9b06522] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Nucleic acids play a central role in all domains of life, either as genetic blueprints or as regulators of various biochemical pathways. The chemical makeup of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA), generally represented by a sequence of four monomers, also provides precise instructions for folding and higher-order assembly of these biopolymers that, in turn, dictate biological functions. The sequence-based specific 3D structures of nucleic acids led to the development of the directed evolution of oligonucleotides, SELEX (systematic evolution of ligands by exponential enrichment), against a chosen target molecule. Among the variety of functions, selected oligonucleotides named aptamers also allow targeting of cell-specific receptors with antibody-like precision and can deliver functional RNAs without a transfection agent. The advancements in the field of customizable nucleic acid nanoparticles (NANPs) opened avenues for the design of nanoassemblies utilizing aptamers for triggering or blocking cell signaling pathways or using aptamer-receptor combinations to activate therapeutic functionalities. A recent selection of fluorescent aptamers enables real-time tracking of NANP formation and interactions. The aptamers are anticipated to contribute to the future development of technologies, enabling an efficient assembly of functional NANPs in mammalian cells or in vivo. These research topics are of top importance for the field of therapeutic nucleic acid nanotechnology with the promises to scale up mass production of NANPs suitable for biomedical applications, to control the intracellular organization of biological materials to enhance the efficiency of biochemical pathways, and to enhance the therapeutic potential of NANP-based therapeutics while minimizing undesired side effects and toxicities.
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Affiliation(s)
- Martin Panigaj
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice 04154, Slovak Republic
| | - M. Brittany Johnson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Jessica McMillan
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Ekaterina A. Goncharova
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, St. Petersburg 191002, Russian Federation
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, North Carolina 28223, United States
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25
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Rodríguez-Serrano AF, Hsing IM. 110th Anniversary: Engineered Ribonucleic Acid Control Elements as Biosensors for in Vitro Diagnostics. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b03963] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alan F. Rodríguez-Serrano
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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Tracking RNA with light: selection, structure, and design of fluorescence turn-on RNA aptamers. Q Rev Biophys 2019; 52:e8. [PMID: 31423956 DOI: 10.1017/s0033583519000064] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescence turn-on aptamers, in vitro evolved RNA molecules that bind conditional fluorophores and activate their fluorescence, have emerged as RNA counterparts of the fluorescent proteins. Turn-on aptamers have been selected to bind diverse fluorophores, and they achieve varying degrees of specificity and affinity. These RNA-fluorophore complexes, many of which exceed the brightness of green fluorescent protein and their variants, can be used as tags for visualizing RNA localization and transport in live cells. Structure determination of several fluorescent RNAs revealed that they have diverse, unrelated overall architectures. As most of these RNAs activate the fluorescence of their ligands by restraining their photoexcited states into a planar conformation, their fluorophore binding sites have in common a planar arrangement of several nucleobases, most commonly a G-quartet. Nonetheless, each turn-on aptamer has developed idiosyncratic structural solutions to achieve specificity and efficient fluorescence turn-on. The combined structural diversity of fluorophores and turn-on RNA aptamers has already produced combinations that cover the visual spectrum. Further molecular evolution and structure-guided engineering is likely to produce fluorescent tags custom-tailored to specific applications.
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28
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Truong L, Ferré-D'Amaré AR. From fluorescent proteins to fluorogenic RNAs: Tools for imaging cellular macromolecules. Protein Sci 2019; 28:1374-1386. [PMID: 31017335 DOI: 10.1002/pro.3632] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/23/2019] [Indexed: 01/01/2023]
Abstract
The explosion in genome-wide sequencing has revealed that noncoding RNAs are ubiquitous and highly conserved in biology. New molecular tools are needed for their study in live cells. Fluorescent RNA-small molecule complexes have emerged as powerful counterparts to fluorescent proteins, which are well established, universal tools in the study of proteins in cell biology. No naturally fluorescent RNAs are known; all current fluorescent RNA tags are in vitro evolved or engineered molecules that bind a conditionally fluorescent small molecule and turn on its fluorescence by up to 5000-fold. Structural analyses of several such fluorescence turn-on aptamers show that these compact (30-100 nucleotides) RNAs have diverse molecular architectures that can restrain their photoexcited fluorophores in their maximally fluorescent states, typically by stacking between planar nucleotide arrangements, such as G-quadruplexes, base triples, or base pairs. The diversity of fluorogenic RNAs as well as fluorophores that are cell permeable and bind weakly to endogenous cellular macromolecules has already produced RNA-fluorophore complexes that span the visual spectrum and are useful for tagging and visualizing RNAs in cells. Because the ligand binding sites of fluorogenic RNAs are not constrained by the need to autocatalytically generate fluorophores as are fluorescent proteins, they may offer more flexibility in molecular engineering to generate photophysical properties that are tailored to experimental needs.
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Affiliation(s)
- Lynda Truong
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland, 20892-8012
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland, 20892-8012
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29
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Wang Z, Liu W, Fan C, Chen N. Visualizing mRNA in live mammalian cells. Methods 2019; 161:16-23. [DOI: 10.1016/j.ymeth.2019.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 03/10/2019] [Accepted: 03/12/2019] [Indexed: 01/06/2023] Open
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30
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Chandler M, Afonin KA. Smart-Responsive Nucleic Acid Nanoparticles (NANPs) with the Potential to Modulate Immune Behavior. NANOMATERIALS (BASEL, SWITZERLAND) 2019; 9:E611. [PMID: 31013847 PMCID: PMC6523571 DOI: 10.3390/nano9040611] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 03/29/2019] [Accepted: 04/08/2019] [Indexed: 12/24/2022]
Abstract
Nucleic acids are programmable and biocompatible polymers that have beneficial uses in nanotechnology with broad applications in biosensing and therapeutics. In some cases, however, the development of the latter has been impeded by the unknown immunostimulatory properties of nucleic acid-based materials, as well as a lack of functional dynamicity due to stagnant structural design. Recent research advancements have explored these obstacles in tandem via the assembly of three-dimensional, planar, and fibrous cognate nucleic acid-based nanoparticles, called NANPs, for the conditional activation of embedded and otherwise quiescent functions. Furthermore, a library of the most representative NANPs was extensively analyzed in human peripheral blood mononuclear cells (PBMCs), and the links between the programmable architectural and physicochemical parameters of NANPs and their immunomodulatory properties have been established. This overview will cover the recent development of design principles that allow for fine-tuning of both the physicochemical and immunostimulatory properties of dynamic NANPs and discuss the potential impacts of these novel strategies.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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31
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Fraser LA, Cheung YW, Kinghorn AB, Guo W, Shiu SCC, Jinata C, Liu M, Bhuyan S, Nan L, Shum HC, Tanner JA. Microfluidic Technology for Nucleic Acid Aptamer Evolution and Application. ACTA ACUST UNITED AC 2019; 3:e1900012. [PMID: 32627415 DOI: 10.1002/adbi.201900012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/12/2019] [Indexed: 12/18/2022]
Abstract
The intersection of microfluidics and aptamer technologies holds particular promise for rapid progress in a plethora of applications across biomedical science and other areas. Here, the influence of microfluidics on the field of aptamers, from traditional capillary electrophoresis approaches through innovative modern-day approaches using micromagnetic beads and emulsion droplets, is reviewed. Miniaturizing aptamer-based bioassays through microfluidics has the potential to transform diagnostics and embedded biosensing in the coming years.
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Affiliation(s)
- Lewis A Fraser
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Yee-Wai Cheung
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Andrew B Kinghorn
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Wei Guo
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), China
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Chandra Jinata
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Mengping Liu
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Soubhagya Bhuyan
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
| | - Lang Nan
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), China
| | - Ho Cheung Shum
- Department of Mechanical Engineering, Faculty of Engineering, The University of Hong Kong, Hong Kong (SAR), China
| | - Julian A Tanner
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong (SAR), China
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32
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Control and optical mapping of mechanical transitions in polymer networks and DNA-based soft materials. Curr Opin Colloid Interface Sci 2019. [DOI: 10.1016/j.cocis.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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33
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O'Hara JM, Marashi D, Morton S, Jaeger L, Grabow WW. Optimization of the Split-Spinach Aptamer for Monitoring Nanoparticle Assembly Involving Multiple Contiguous RNAs. NANOMATERIALS 2019; 9:nano9030378. [PMID: 30845655 PMCID: PMC6474029 DOI: 10.3390/nano9030378] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 03/04/2019] [Accepted: 03/04/2019] [Indexed: 12/16/2022]
Abstract
The fact that structural RNA motifs can direct RNAs to fold and self-assemble into predictable pre-defined structures is an attractive quality and driving force for RNA’s use in nanotechnology. RNA’s recognized diversity concerning cellular and synthetically selected functionalities, however, help explain why it continues to draw attention for new nano-applications. Herein, we report the modification of a bifurcated reporter system based on the previously documented Spinach aptamer/DFHBI fluorophore pair that affords the ability to confirm the assembly of contiguous RNA strands within the context of the previously reported multi-stranded RNA nanoring. Exploration of the sequence space associated with the base pairs flanking the aptamer core demonstrate that fluorescent feedback can be optimized to minimize the fluorescence associated with partially-assembled RNA nanorings. Finally, we demonstrate that the aptamer-integrated nanoring is capable of assembling directly from transcribed DNA in one pot.
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Affiliation(s)
- Jack M O'Hara
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA.
| | - Dylan Marashi
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA.
| | - Sean Morton
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA.
| | - Luc Jaeger
- Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9510, USA.
| | - Wade W Grabow
- Department of Chemistry and Biochemistry, Seattle Pacific University, Seattle, WA 918119-1997, USA.
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34
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Abstract
Many proteins can be split into fragments that spontaneously reassemble, without covalent linkage, into a functional protein. For split green fluorescent proteins (GFPs), fragment reassembly leads to a fluorescent readout, which has been widely used to investigate protein-protein interactions. We review the scope and limitations of this approach as well as other diverse applications of split GFPs as versatile sensors, molecular glues, optogenetic tools, and platforms for photophysical studies.
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Affiliation(s)
- Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA; ,
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35
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Ke W, Hong E, Saito RF, Rangel MC, Wang J, Viard M, Richardson M, Khisamutdinov EF, Panigaj M, Dokholyan NV, Chammas R, Dobrovolskaia MA, Afonin KA. RNA-DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET and transcriptional regulation of NF-κB in human cells. Nucleic Acids Res 2019; 47:1350-1361. [PMID: 30517685 PMCID: PMC6379676 DOI: 10.1093/nar/gky1215] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/19/2018] [Accepted: 11/22/2018] [Indexed: 12/17/2022] Open
Abstract
Nucleic acid-based assemblies that interact with each other and further communicate with the cellular machinery in a controlled manner represent a new class of reconfigurable materials that can overcome limitations of traditional biochemical approaches and improve the potential therapeutic utility of nucleic acids. This notion enables the development of novel biocompatible 'smart' devices and biosensors with precisely controlled physicochemical and biological properties. We extend this novel concept by designing RNA-DNA fibers and polygons that are able to cooperate in different human cell lines and that have defined immunostimulatory properties confirmed by ex vivo experiments. The mutual intracellular interaction of constructs results in the release of a large number of different siRNAs while giving a fluorescent response and activating NF-κB decoy DNA oligonucleotides. This work expands the possibilities of nucleic acid technologies by (i) introducing very simple design principles and assembly protocols; (ii) potentially allowing for a simultaneous release of various siRNAs together with functional DNA sequences and (iii) providing controlled rates of reassociation, stabilities in human blood serum, and immunorecognition.
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Affiliation(s)
- Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Enping Hong
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Renata F Saito
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Maria Cristina Rangel
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Jian Wang
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Mathias Viard
- Basic Science Program, Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Melina Richardson
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | | | - Martin Panigaj
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, Slovak Republic
| | - Nikolay V Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033, USA
| | - Roger Chammas
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- Centro de Investigação Translacional em Oncologia (LIM24), Departamento de Radiologia e Oncologia, Faculdade de Medicina da Universidade de São Paulo and Instituto do Câncer do Estado de São Paulo, São Paulo, SP, Brazil
| | - Marina A Dobrovolskaia
- Nanotechnology Characterization Lab., Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21702, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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36
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Rossetti M, Del Grosso E, Ranallo S, Mariottini D, Idili A, Bertucci A, Porchetta A. Programmable RNA-based systems for sensing and diagnostic applications. Anal Bioanal Chem 2019; 411:4293-4302. [PMID: 30734852 DOI: 10.1007/s00216-019-01622-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/08/2019] [Accepted: 01/16/2019] [Indexed: 11/28/2022]
Abstract
The emerging field of RNA nanotechnology harnesses the versatility of RNA molecules to generate nature-inspired systems with programmable structure and functionality. Such methodology has therefore gained appeal in the fields of biosensing and diagnostics, where specific molecular recognition and advanced input/output processing are demanded. The use of RNA modules and components allows for achieving diversity in structure and function, for processing information with molecular precision, and for programming dynamic operations on the grounds of predictable non-covalent interactions. When RNA nanotechnology meets bioanalytical chemistry, sensing of target molecules can be performed by harnessing programmable interactions of RNA modules, advanced field-ready biosensors can be manufactured by interfacing RNA-based devices with supporting portable platforms, and RNA sensors can be engineered to be genetically encoded allowing for real-time imaging of biomolecules in living cells. In this article, we report recent advances in RNA-based sensing technologies and discuss current trends in RNA nanotechnology-enabled biomedical diagnostics. In particular, we describe programmable sensors that leverage modular designs comprising dynamic aptamer-based units, synthetic RNA nanodevices able to perform target-responsive regulation of gene expression, and paper-based sensors incorporating artificial RNA networks. Graphical Abstract ᅟ.
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Affiliation(s)
- Marianna Rossetti
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Simona Ranallo
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Davide Mariottini
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Andrea Idili
- Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Alessandro Bertucci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy. .,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
| | - Alessandro Porchetta
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, 00133, Rome, Italy.
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37
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Chandler M, Lyalina T, Halman J, Rackley L, Lee L, Dang D, Ke W, Sajja S, Woods S, Acharya S, Baumgarten E, Christopher J, Elshalia E, Hrebien G, Kublank K, Saleh S, Stallings B, Tafere M, Striplin C, Afonin KA. Broccoli Fluorets: Split Aptamers as a User-Friendly Fluorescent Toolkit for Dynamic RNA Nanotechnology. Molecules 2018; 23:E3178. [PMID: 30513826 PMCID: PMC6321606 DOI: 10.3390/molecules23123178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/29/2018] [Accepted: 11/29/2018] [Indexed: 02/06/2023] Open
Abstract
RNA aptamers selected to bind fluorophores and activate their fluorescence offer a simple and modular way to visualize native RNAs in cells. Split aptamers which are inactive until the halves are brought within close proximity can become useful for visualizing the dynamic actions of RNA assemblies and their interactions in real time with low background noise and eliminated necessity for covalently attached dyes. Here, we design and test several sets of F30 Broccoli aptamer splits, that we call fluorets, to compare their relative fluorescence and physicochemical stabilities. We show that the splits can be simply assembled either through one-pot thermal annealing or co-transcriptionally, thus allowing for direct tracking of transcription reactions via the fluorescent response. We suggest a set of rules that enable for the construction of responsive biomaterials that readily change their fluorescent behavior when various stimuli such as the presence of divalent ions, exposure to various nucleases, or changes in temperature are applied. We also show that the strand displacement approach can be used to program the controllable fluorescent responses in isothermal conditions. Overall, this work lays a foundation for the future development of dynamic systems for molecular computing which can be used to monitor real-time processes in cells and construct biocompatible logic gates.
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Affiliation(s)
- Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Tatiana Lyalina
- Laboratory of Solution Chemistry of Advanced Materials and Technologies, ITMO University, Lomonosova St. 9, 191002 St. Petersburg, Russia.
| | - Justin Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Lauren Rackley
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Lauren Lee
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Dylan Dang
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Sameer Sajja
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Steven Woods
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Shrija Acharya
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Elijah Baumgarten
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Jonathan Christopher
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Emman Elshalia
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Gabriel Hrebien
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kinzey Kublank
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Saja Saleh
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Bailey Stallings
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Michael Tafere
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Caryn Striplin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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38
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Wang S, Majumder S, Emery NJ, Liu AP. Simultaneous monitoring of transcription and translation in mammalian cell-free expression in bulk and in cell-sized droplets. Synth Biol (Oxf) 2018; 3:ysy005. [PMID: 30003145 PMCID: PMC6034425 DOI: 10.1093/synbio/ysy005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/24/2018] [Accepted: 04/17/2018] [Indexed: 12/17/2022] Open
Abstract
Transcription and translation are two critical processes during eukaryotic gene expression that regulate cellular activities. The development of mammalian cell-free expression (CFE) systems provides a platform for studying these two critical processes in vitro for bottom-up synthetic biology applications such as construction of an artificial cell. Moreover, real-time monitoring of the dynamics of synthesized mRNA and protein is key to characterize and optimize gene circuits before implementing in living cells or in artificial cells. However, there are few tools for measurement of mRNA and protein dynamics in mammalian CFE systems. Here, we developed a locked nucleic acid (LNA) probe for monitoring transcription in a HeLa-based CFE system in real-time. By using this LNA probe in conjunction with a fluorescent reporter protein, we were able to simultaneously monitor mRNA and protein dynamics in bulk reactions and cell-sized single-emulsion droplets. We found rapid production of mRNA transcripts that decreased over time as protein production ensued in bulk reactions. Our results also showed that transcription in cell-sized droplets has different dynamics compared to the transcription in bulk reactions. The use of this LNA probe in conjunction with fluorescent proteins in HeLa-based mammalian CFE system provides a versatile in vitro platform for studying mRNA dynamics for bottom-up synthetic biology applications.
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Affiliation(s)
- Shue Wang
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Sagardip Majumder
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas J Emery
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.,Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA.,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, USA.,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA.,Biophysics Program, University of Michigan, Ann Arbor, MI, USA
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39
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Torelli E, Kozyra JW, Gu JY, Stimming U, Piantanida L, Voïtchovsky K, Krasnogor N. Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon. Sci Rep 2018; 8:6989. [PMID: 29725066 PMCID: PMC5934368 DOI: 10.1038/s41598-018-25270-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/12/2018] [Indexed: 12/27/2022] Open
Abstract
RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter. This RNA scaffold and the complementary staples fold in a physiologically compatible isothermal condition. In order to monitor the folding, we designed a new split Broccoli aptamer system. The aptamer is divided into two nonfunctional sequences each of which is integrated into the 5' or 3' end of two staple strands complementary to the RNA scaffold. Using fluorescence measurements and in-gel imaging, we demonstrate that once RNA origami assembly occurs, the split aptamer sequences are brought into close proximity forming the aptamer and turning on the fluorescence. This light-up 'bio-orthogonal' RNA origami provides a prototype that can have potential for in vivo origami applications.
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Affiliation(s)
- Emanuela Torelli
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom.
| | - Jerzy Wieslaw Kozyra
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom
| | - Jing-Ying Gu
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Ulrich Stimming
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Luca Piantanida
- Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom
| | - Kislon Voïtchovsky
- Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom.
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40
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Bouhedda F, Autour A, Ryckelynck M. Light-Up RNA Aptamers and Their Cognate Fluorogens: From Their Development to Their Applications. Int J Mol Sci 2017; 19:ijms19010044. [PMID: 29295531 PMCID: PMC5795994 DOI: 10.3390/ijms19010044] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 12/31/2022] Open
Abstract
An RNA-based fluorogenic module consists of a light-up RNA aptamer able to specifically interact with a fluorogen to form a fluorescent complex. Over the past decade, significant efforts have been devoted to the development of such modules, which now cover the whole visible spectrum, as well as to their engineering to serve in a wide range of applications. In this review, we summarize the different strategies used to develop each partner (the fluorogen and the light-up RNA aptamer) prior to giving an overview of their applications that range from live-cell RNA imaging to the set-up of high-throughput drug screening pipelines. We then conclude with a critical discussion on the current limitations of these modules and how combining in vitro selection with screening approaches may help develop even better molecules.
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Affiliation(s)
- Farah Bouhedda
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
| | - Alexis Autour
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
| | - Michael Ryckelynck
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
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41
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Wang Z, Luo Y, Xie X, Hu X, Song H, Zhao Y, Shi J, Wang L, Glinsky G, Chen N, Lal R, Fan C. In Situ Spatial Complementation of Aptamer-Mediated Recognition Enables Live-Cell Imaging of Native RNA Transcripts in Real Time. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707795] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Zejun Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
| | - Yao Luo
- School of Life Sciences; Sichuan University; Chengdu 610064 China
| | - Xiaodong Xie
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
| | - Xingjie Hu
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
| | - Haiyun Song
- Shanghai Institutes for Biological Sciences; Chinese Academy of Sciences; Shanghai 200031 China
| | - Yun Zhao
- School of Life Sciences; Sichuan University; Chengdu 610064 China
| | - Jiye Shi
- UCB Pharma; 208 Bath Road Slough SL1 3WE UK
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
| | - Gennadi Glinsky
- University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Nan Chen
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
| | - Ratnesh Lal
- University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center; Shanghai Institute of Applied Physics; Chinese Academy of Sciences; University of Chinese Academy of Sciences; Shanghai 201800 China
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42
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Wang Z, Luo Y, Xie X, Hu X, Song H, Zhao Y, Shi J, Wang L, Glinsky G, Chen N, Lal R, Fan C. In Situ Spatial Complementation of Aptamer-Mediated Recognition Enables Live-Cell Imaging of Native RNA Transcripts in Real Time. Angew Chem Int Ed Engl 2017; 57:972-976. [PMID: 28991414 DOI: 10.1002/anie.201707795] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/18/2017] [Indexed: 12/18/2022]
Abstract
Direct cellular imaging of the localization and dynamics of biomolecules helps to understand their function and reveals novel mechanisms at the single-cell resolution. In contrast to routine fluorescent-protein-based protein imaging, technology for RNA imaging remains less well explored because of the lack of enabling technology. Herein, we report the development of an aptamer-initiated fluorescence complementation (AiFC) method for RNA imaging by engineering a green fluorescence protein (GFP)-mimicking turn-on RNA aptamer, Broccoli, into two split fragments that could tandemly bind to target mRNA. When genetically encoded in cells, endogenous mRNA molecules recruited Split-Broccoli and brought the two fragments into spatial proximity, which formed a fluorophore-binding site in situ and turned on fluorescence. Significantly, we demonstrated the use of AiFC for high-contrast and real-time imaging of endogenous RNA molecules in living mammalian cells. We envision wide application and practical utility of this enabling technology to in vivo single-cell visualization and mechanistic analysis of macromolecular interactions.
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Affiliation(s)
- Zejun Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Yao Luo
- School of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Xiaodong Xie
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Xingjie Hu
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Haiyun Song
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yun Zhao
- School of Life Sciences, Sichuan University, Chengdu, 610064, China
| | - Jiye Shi
- UCB Pharma, 208 Bath Road, Slough, SL1 3WE, UK
| | - Lihua Wang
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Gennadi Glinsky
- University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nan Chen
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Ratnesh Lal
- University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
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43
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Bertucci A, Porchetta A, Ricci F. Antibody-Templated Assembly of an RNA Mimic of Green Fluorescent Protein. Anal Chem 2017; 90:1049-1053. [PMID: 29131585 DOI: 10.1021/acs.analchem.7b02102] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
One of the most intriguing ways through which nature achieves regulation of biological pathways encompasses the coordination of noncovalent interactions that bring biomolecules to be colocalized in a designated restricted space. Inspired by this mechanism, we have explored the possibility of using antibodies as bivalent biomolecular substrates for the templated assembly of a functional RNA structure. We have developed a biosupramolecular complementation assay by assembling a fluorescent Spinach aptamer, which is a synthetic RNA mimic of the Green Fluorescent Protein, from its split segments. We have employed two antigen-tagged RNA strands that, upon binding to the target antibody, are colocalized in a confined space and can reassemble into the native Spinach conformation, yielding a measurable fluorescence emission as a function of the templating antibody concentration. We have demonstrated the generality of our approach using two different antigen/antibody systems and found that both platforms show high binding affinity, specificity for the target antibody, and enough selectivity to work in crude cellular extracts. This study highlights the potential of biosupramolecular RNA engineering for the development of innovative biomimetic tools for nanobiotechnology and bioanalytical assays.
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Affiliation(s)
- Alessandro Bertucci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133, Rome, Italy
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44
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Alam KK, Tawiah KD, Lichte MF, Porciani D, Burke DH. A Fluorescent Split Aptamer for Visualizing RNA-RNA Assembly In Vivo. ACS Synth Biol 2017; 6:1710-1721. [PMID: 28548488 PMCID: PMC5603824 DOI: 10.1021/acssynbio.7b00059] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
RNA–RNA
assembly governs key biological processes and is
a powerful tool for engineering synthetic genetic circuits. Characterizing
RNA assembly in living cells often involves monitoring fluorescent
reporter proteins, which are at best indirect measures of underlying
RNA–RNA hybridization events and are subject to additional
temporal and load constraints associated with translation and activation
of reporter proteins. In contrast, RNA aptamers that sequester small
molecule dyes and activate their fluorescence are increasingly utilized
in genetically encoded strategies to report on RNA-level events. Split-aptamer
systems have been rationally designed to generate signal upon hybridization
of two or more discrete RNA transcripts, but none directly function
when expressed in vivo. We reasoned that the improved
physiological properties of the Broccoli aptamer enable construction
of a split-aptamer system that could function in living cells. Here
we present the Split-Broccoli system, in which self-assembly is nucleated
by a thermostable, three-way junction RNA architecture and fluorescence
activation requires both strands. Functional assembly of the system
approximately follows second-order kinetics in vitro and improves when cotranscribed, rather than when assembled from
purified components. Split-Broccoli fluorescence
is digital in vivo and retains functional modularity
when fused to RNAs that regulate circuit function through RNA–RNA
hybridization, as demonstrated with an RNA Toehold switch. Split-Broccoli represents the first functional split-aptamer
system to operate in vivo. It offers a genetically
encoded and nondestructive platform to monitor and exploit RNA–RNA
hybridization, whether as an all-RNA, stand-alone AND gate or as a
tool for monitoring assembly of RNA–RNA hybrids.
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Affiliation(s)
- Khalid K. Alam
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Kwaku D. Tawiah
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Matthew F. Lichte
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - David Porciani
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri 65212, United States
| | - Donald H. Burke
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri 65212, United States
- Department
of Bioengineering, University of Missouri, Columbia, Missouri 65211, United States
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45
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Alexander SC, Devaraj NK. Developing a Fluorescent Toolbox To Shed Light on the Mysteries of RNA. Biochemistry 2017; 56:5185-5193. [PMID: 28671838 DOI: 10.1021/acs.biochem.7b00510] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Technologies that detect and image RNA have illuminated the complex roles played by RNA, redefining the traditional and superficial role first outlined by the central dogma of biology. Because there is such a wide diversity of RNA structure arising from an assortment of functions within biology, a toolbox of approaches have emerged for investigation of this important class of biomolecules. These methods are necessary to detect and elucidate the localization and dynamics of specific RNAs and in doing so unlock our understanding of how RNA dysregulation leads to disease. Current methods for detecting and imaging RNA include in situ hybridization techniques, fluorescent aptamers, RNA binding proteins fused to fluorescent reporters, and covalent labeling strategies. Because of the inherent diversity of these methods, each approach comes with a set of strengths and limitations that leave room for future improvement. This perspective seeks to highlight the most recent advances and remaining challenges for the wide-ranging toolbox of technologies that illuminate RNA's contribution to cellular complexity.
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Affiliation(s)
- Seth C Alexander
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
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46
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van Gijtenbeek LA, Kok J. Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Front Microbiol 2017; 8:1161. [PMID: 28690601 PMCID: PMC5479882 DOI: 10.3389/fmicb.2017.01161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
To be able to visualize the abundance and spatiotemporal features of RNAs in bacterial cells would permit obtaining a pivotal understanding of many mechanisms underlying bacterial cell biology. The first methods that allowed observing single mRNA molecules in individual cells were introduced by Bertrand et al. (1998) and Femino et al. (1998). Since then, a plethora of techniques to image RNA molecules with the aid of fluorescence microscopy has emerged. Many of these approaches are useful for the large eukaryotic cells but their adaptation to study RNA, specifically mRNA molecules, in bacterial cells progressed relatively slow. Here, an overview will be given of fluorescent techniques that can be used to reveal specific RNA molecules inside fixed and living single bacterial cells. It includes a critical evaluation of their caveats as well as potential solutions.
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Affiliation(s)
- Lieke A van Gijtenbeek
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
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47
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Xia Y, Zhang R, Wang Z, Tian J, Chen X. Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes. Chem Soc Rev 2017; 46:2824-2843. [PMID: 28345687 PMCID: PMC5472208 DOI: 10.1039/c6cs00675b] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.
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Affiliation(s)
- Yuqiong Xia
- Engineering Research Center of Molecular-imaging and Neuro-imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China.
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48
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Halman JR, Satterwhite E, Roark B, Chandler M, Viard M, Ivanina A, Bindewald E, Kasprzak WK, Panigaj M, Bui MN, Lu JS, Miller J, Khisamutdinov EF, Shapiro BA, Dobrovolskaia MA, Afonin KA. Functionally-interdependent shape-switching nanoparticles with controllable properties. Nucleic Acids Res 2017; 45:2210-2220. [PMID: 28108656 PMCID: PMC5389727 DOI: 10.1093/nar/gkx008] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/22/2016] [Accepted: 01/03/2017] [Indexed: 12/18/2022] Open
Abstract
We introduce a new concept that utilizes cognate nucleic acid nanoparticles which are fully complementary and functionally-interdependent to each other. In the described approach, the physical interaction between sets of designed nanoparticles initiates a rapid isothermal shape change which triggers the activation of multiple functionalities and biological pathways including transcription, energy transfer, functional aptamers and RNA interference. The individual nanoparticles are not active and have controllable kinetics of re-association and fine-tunable chemical and thermodynamic stabilities. Computational algorithms were developed to accurately predict melting temperatures of nanoparticles of various compositions and trace the process of their re-association in silico. Additionally, tunable immunostimulatory properties of described nanoparticles suggest that the particles that do not induce pro-inflammatory cytokines and high levels of interferons can be used as scaffolds to carry therapeutic oligonucleotides, while particles with strong interferon and mild pro-inflammatory cytokine induction may qualify as vaccine adjuvants. The presented concept provides a simple, cost-effective and straightforward model for the development of combinatorial regulation of biological processes in nucleic acid nanotechnology.
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Affiliation(s)
- Justin R. Halman
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Emily Satterwhite
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Brandon Roark
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Morgan Chandler
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Mathias Viard
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
- Basic Science Program, Leidos Biomedical Research, Inc., RNA Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Anna Ivanina
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Eckart Bindewald
- Basic Science Program, Leidos Biomedical Research, Inc., RNA Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Wojciech K. Kasprzak
- Basic Science Program, Leidos Biomedical Research, Inc., RNA Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Martin Panigaj
- Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Safarik University in Kosice, Kosice, 041 54, Slovak Republic
| | - My N. Bui
- Department of Chemistry, Ball State University, Muncie, IN 47306, USA
| | - Jacob S. Lu
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Johann Miller
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | | | - Bruce A. Shapiro
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Marina A. Dobrovolskaia
- Nanotechnology Characterization Lab, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Kirill A. Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
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49
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Kantin GP, Krasavin MY. Microwave-promoted reaction of N-(alk-1-enyl)chloroacetamides with sodium azide unexpectedly yields 1H-imidazol-5(4H)-ones. MENDELEEV COMMUNICATIONS 2017. [DOI: 10.1016/j.mencom.2017.01.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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50
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Martins AN, Ke W, Jawahar V, Striplin M, Striplin C, Freed EO, Afonin KA. Intracellular Reassociation of RNA-DNA Hybrids that Activates RNAi in HIV-Infected Cells. Methods Mol Biol 2017; 1632:269-283. [PMID: 28730446 PMCID: PMC6941940 DOI: 10.1007/978-1-4939-7138-1_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Human immunodeficiency virus Type 1 (HIV-1) is the major cause of acquired immune deficiency syndrome (AIDS). In 2014, it was estimated that 1.2 million people died from AIDS-related illnesses. RNA interference-based therapy to block HIV replication is a field that, as of now, is without any FDA-approved drugs available for clinical use. In this chapter we describe a protocol for testing and utilizing a new approach that relies on reassociation of RNA-DNA hybrids activating RNAi and blocking HIV replication in human cells.
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Affiliation(s)
- Angelica N Martins
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC, 28223, USA
| | - Weina Ke
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University Blvd., Charlotte, NC, 28223, USA
| | - Vaishnavi Jawahar
- Department of Biological Sciences, University of North Carolina at Charlotte, 9201 University City Boulevard, Charlotte, NC, 28223, USA
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University Blvd., Charlotte, NC, 28223, USA
| | - Morriah Striplin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University Blvd., Charlotte, NC, 28223, USA
| | - Caryn Striplin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University Blvd., Charlotte, NC, 28223, USA
| | - Eric O Freed
- HIV Dynamics and Replication Program, NCI, Frederick, MD, 21702, USA
| | - Kirill A Afonin
- Nanoscale Science Program, Department of Chemistry, University of North Carolina at Charlotte, 9201 University Blvd., Charlotte, NC, 28223, USA.
- The Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
- Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA.
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