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Brown A, Brill J, Amini R, Nurmi C, Li Y. Development of Better Aptamers: Structured Library Approaches, Selection Methods, and Chemical Modifications. Angew Chem Int Ed Engl 2024; 63:e202318665. [PMID: 38253971 DOI: 10.1002/anie.202318665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/22/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
Systematic evolution of ligands by exponential enrichment (SELEX) has been used to discover thousands of aptamers since its development in 1990. Aptamers are short single-stranded oligonucleotides capable of binding to targets with high specificity and selectivity through structural recognition. While aptamers offer advantages over other molecular recognition elements such as their ease of production, smaller size, extended shelf-life, and lower immunogenicity, they have yet to show significant success in real-world applications. By analyzing the importance of structured library designs, reviewing different SELEX methodologies, and the effects of chemical modifications, we provide a comprehensive overview on the production of aptamers for applications in drug delivery systems, therapeutics, diagnostics, and molecular imaging.
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Affiliation(s)
- Alex Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Jake Brill
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Connor Nurmi
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, Ontario, L8S 4 K1, Canada
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2
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Cavett V, Chan AI, Cunningham CN, Paegel BM. Hydrogel-Encapsulated Beads Enable Proximity-Driven Encoded Library Synthesis and Screening. ACS CENTRAL SCIENCE 2023; 9:1603-1610. [PMID: 37637732 PMCID: PMC10451030 DOI: 10.1021/acscentsci.3c00316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Indexed: 08/29/2023]
Abstract
Encoded combinatorial library technologies have dramatically expanded the chemical space for screening but are usually only analyzed by affinity selection binding. It would be highly advantageous to reformat selection outputs to "one-bead-one-compound" solid-phase libraries, unlocking activity-based and cellular screening capabilities. Here, we describe hydrogel-encapsulated magnetic beads that enable such a transformation. Bulk emulsion polymerization of polyacrylamide hydrogel shells around magnetic microbeads yielded uniform particles (7 ± 2 μm diameter) that are compatible with diverse in-gel functionalization (amine, alkyne, oligonucleotides) and transformations associated with DNA-encoded library synthesis (acylation, enzymatic DNA ligation). In a case study of reformatting mRNA display libraries, transcription from DNA-templated magnetic beads encapsulated in gel particles colocalized both RNA synthesis via hybridization with copolymerized complementary DNA and translation via puromycin labeling. Two control epitope templates (V5, HA) were successfully enriched (50- and 99-fold, respectively) from an NNK5 library bead screen via FACS. Proximity-driven library synthesis in concert with magnetic sample manipulation provides a plausible means for reformatting encoded combinatorial libraries at scale.
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Affiliation(s)
- Valerie Cavett
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
| | - Alix I Chan
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Christian N. Cunningham
- Department
of Peptide Therapeutics, Genentech, South San Francisco, California 94080, United States
| | - Brian M. Paegel
- Department
of Pharmaceutical Sciences, University of
California, Irvine, California 92697, United States
- Departments
of Chemistry & Biomedical Engineering, University of California, Irvine, California 92697, United States
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3
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Arnould B, Quillin AL, Heemstra JM. Tracking the Message: Applying Single Molecule Localization Microscopy to Cellular RNA Imaging. Chembiochem 2023; 24:e202300049. [PMID: 36857087 PMCID: PMC10192057 DOI: 10.1002/cbic.202300049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/28/2023] [Accepted: 03/01/2023] [Indexed: 03/02/2023]
Abstract
RNA function is increasingly appreciated to be more complex than merely communicating between DNA sequence and protein structure. RNA localization has emerged as a key contributor to the intricate roles RNA plays in the cell, and the link between dysregulated spatiotemporal localization and disease warrants an exploration beyond sequence and structure. However, the tools needed to visualize RNA with precise resolution are lacking in comparison to methods available for studying proteins. In the past decade, many techniques have been developed for imaging RNA, and in parallel super resolution and single-molecule techniques have enabled imaging of single molecules in cells. Of these methods, single molecule localization microscopy (SMLM) has shown significant promise for probing RNA localization. In this review, we highlight current approaches that allow super resolution imaging of specific RNA transcripts and summarize challenges and future opportunities for developing innovative RNA labeling methods that leverage the power of SMLM.
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Affiliation(s)
- Benoît Arnould
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Alexandria L Quillin
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Washington University in St. Louis, St. Louis, MO 63130, USA
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4
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Wei X, Ma P, Imran Mahmood K, Zhang Y, Wang Z. Screening of a High-Affinity Aptamer for Aflatoxin M 1 and Development of Its Colorimetric Aptasensor. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:7546-7556. [PMID: 37144950 DOI: 10.1021/acs.jafc.3c01586] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Aflatoxin M1 (AFM1), a secondary metabolite of Aspergillus spp., is highly toxic and widely present in food matrices. Therefore, the detection of AFM1 is of great importance for the protection of food safety. In this study, a five-segment sequence was designed as the initial library. Graphene oxide-SELEX (GO-SELEX) was applied to screen AFM1. After seven rounds of repeated screening, affinity and specificity assays showed that aptamer 9 was the best candidate for AFM1. The dissociation constant (Kd) of aptamer 9 was 109.10 ± 6.02 nM. To verify the efficiency and sensitivity aptamer for the detection of AFM1, a colorimetric sensor based on the aptamer was constructed. The biosensor showed good linearity in the range of AFM1 concentration of 0.5-500.0 ng/mL with a detection limit of 0.50 ng/mL. This colorimetric method was successfully used for the detection of AFM1 in milk powder samples. Its detection recovery was 92.8-105.2%. This study was conducted to provide a reference for the detection of AFM1 in food.
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Affiliation(s)
- Xunjiao Wei
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Pengfei Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Khan Imran Mahmood
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu 610106, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
- Collaborative Innovation Center of Food Safety and Quality Control of Jiangsu Province, Jiangnan University, Wuxi 214122, China
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5
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A review: Construction of aptamer screening methods based on improving the screening rate of key steps. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Crowdsourced RNA design discovers diverse, reversible, efficient, self-contained molecular switches. Proc Natl Acad Sci U S A 2022; 119:e2112979119. [PMID: 35471911 PMCID: PMC9170038 DOI: 10.1073/pnas.2112979119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Internet-based scientific communities promise a means to apply distributed, diverse human intelligence toward previously intractable scientific problems. However, current implementations have not allowed communities to propose experiments to test all emerging hypotheses at scale or to modify hypotheses in response to experiments. We report high-throughput methods for molecular characterization of nucleic acids that enable the large-scale video game–based crowdsourcing of RNA sensor design, followed by high-throughput functional characterization. Iterative design testing of thousands of crowdsourced RNA sensor designs produced near–thermodynamically optimal and reversible RNA switches that act as self-contained molecular sensors and couple five distinct small molecule inputs to three distinct protein binding and fluorogenic outputs. This work suggests a paradigm for widely distributed experimental bioscience.
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7
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Dykstra PB, Kaplan M, Smolke CD. Engineering synthetic RNA devices for cell control. Nat Rev Genet 2022; 23:215-228. [PMID: 34983970 PMCID: PMC9554294 DOI: 10.1038/s41576-021-00436-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 12/16/2022]
Abstract
The versatility of RNA in sensing and interacting with small molecules, proteins and other nucleic acids while encoding genetic instructions for protein translation makes it a powerful substrate for engineering biological systems. RNA devices integrate cellular information sensing, processing and actuation of specific signals into defined functions and have yielded programmable biological systems and novel therapeutics of increasing sophistication. However, challenges centred on expanding the range of analytes that can be sensed and adding new mechanisms of action have hindered the full realization of the field's promise. Here, we describe recent advances that address these limitations and point to a significant maturation of synthetic RNA-based devices.
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Affiliation(s)
- Peter B. Dykstra
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Matias Kaplan
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Christina D. Smolke
- Department of Bioengineering, Stanford University, Stanford, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,
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8
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Fang X, Li W, Gao T, Ain Zahra QU, Luo Z, Pei R. Rapid screening of aptamers for fluorescent targets by integrated digital PCR and flow cytometry. Talanta 2022; 242:123302. [PMID: 35180537 DOI: 10.1016/j.talanta.2022.123302] [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: 12/21/2021] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
Abstract
In this paper, we report the development of a new strategy termed integrated digital PCR-fluorescence activated sorting based SELEX (IFS-SELEX) that enables rapid screening of aptamers against fluorescent targets. Initially, this strategy employs an integrated digital PCR system to amplify each sequence of a preliminarily enriched library, which is obtained by a traditional SELEX method, on the surface of polystyrene beads. Then, the as-prepared beads are incubated with the fluorescent target and then subjected to fluorescence-activated sorting. Since only those sequences with high binding affinity for the target are collected and sequenced, unnecessary analysis of ineligible sequences is avoided by this method, and the aptamer selection process is thereby greatly streamlined. As a proof-of-concept, we applied this strategy for the screening of aptamers against two fluorescent targets, i.e., ciprofloxacin (CFX) and thioflavin T (ThT), and successfully obtained corresponding sequences with low dissociation constants. The binding affinities of aptamers for ThT were well associated with the sorting regions defined in the fluorescence channel of the flow cytometry process. The experimental results demonstrated that the as-designed IFS-SELEX method can serve as a universal platform for rapid, facile, and efficient aptamer selection against various fluorescent targets.
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Affiliation(s)
- Xiaona Fang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China; CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Wenjing Li
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China; CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Tian Gao
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China; CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China
| | - Qurat Ul Ain Zahra
- Biomedical Imaging Center, University of Science and Technology of China, Hefei, Anhui, 230026, China; The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Zhaofeng Luo
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310022, China.
| | - Renjun Pei
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, 230026, China; CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, China.
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9
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Yao H, Niu YB, Hu YP, Sun XW, Zhang QP, Zhang YM, Wei TB, Lin Q. Metal-ion-mediated synergistic coordination: construction of AIE-metallogel sensor arrays for anions and amino acids. NEW J CHEM 2022. [DOI: 10.1039/d2nj02992h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metallogel-based six membered sensor arrays show applications in multi-analyte detection and fluorescence encryption.
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Affiliation(s)
- Hong Yao
- Key laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
| | - Yan-Bing Niu
- Key laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
| | - Yin-Ping Hu
- Key laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
| | - Xiao-Wen Sun
- Key laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
| | - Qin-Peng Zhang
- Key laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
| | - You-Ming Zhang
- Key laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
- Deputy Director-General of Gansu Natural Energy Research Institute, Renmin Road 23, Lanzhou, Gansu, 730070, P. R. China
| | - Tai-Bao Wei
- Key laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
| | - Qi Lin
- Key laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
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10
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Fluorescent functional nucleic acid: Principles, properties and applications in bioanalyzing. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116292] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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11
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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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12
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Swetha P, Fan Z, Wang F, Jiang JH. Genetically encoded light-up RNA aptamers and their applications for imaging and biosensing. J Mater Chem B 2021; 8:3382-3392. [PMID: 31984401 DOI: 10.1039/c9tb02668a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Intracellular small ligands and biomacromolecules are playing crucial roles not only as executors but also as regulators. It is essential to develop tools to investigate their dynamics to interrogate their functions and reflect the cellular status. Light-up RNA aptamers are RNA sequences that can bind with their cognate nonfluorescent fluorogens and greatly activate their fluorescence. The emergence of genetically encoded light-up RNA aptamers has provided fascinating tools for studying intracellular small ligands and biomacromolecules owing to their high fluorescence activation degree and facile programmability. Here we review the burgeoning field of light-up RNA aptamers. We first briefly introduce light-up RNA aptamers with a focus on the photophysical properties of the fluorogens. Then design strategies of genetically encoded light-up RNA aptamer based sensors including turn-on, signal amplification and ratiometric rationales are emphasized.
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Affiliation(s)
- Puchakayala Swetha
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hu-nan University, Changsha, 410082, P. R. China.
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13
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Saito S. SELEX-based DNA Aptamer Selection: A Perspective from the Advancement of Separation Techniques. ANAL SCI 2021; 37:17-26. [PMID: 33132238 DOI: 10.2116/analsci.20sar18] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
DNA aptamers, which are short, single-stranded DNA sequences that selectively bind to target substances (proteins, cells, small molecules, metal ions), can be acquired by means of the systematic evolution of ligands by exponential enrichment (SELEX) methodology. In the SELEX procedure, one of the keys for the effective acquisition of high-affinity and functional aptamer sequences is the separation stage to isolate target-bound DNA from unbound DNA in a randomized DNA library. In this review, various remarkable advancements in separation techniques for SELEX-based aptamer selection developed in this decade, are described and discussed, including CE-, microfluidic chip-, solid phase-, and FACS-based SELEX along with other methods.
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Affiliation(s)
- Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo Sakura, Saitama, 338-8570, Japan.
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14
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Kong J, Wang Y, Qi W, Huang M, Su R, He Z. Green fluorescent protein inspired fluorophores. Adv Colloid Interface Sci 2020; 285:102286. [PMID: 33164780 DOI: 10.1016/j.cis.2020.102286] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 10/11/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022]
Abstract
Green fluorescence proteins (GFP) are appealing to a variety of biomedical and biotechnology applications, such as protein fusion, subcellular localizations, cell visualization, protein-protein interaction, and genetically encoded sensors. To mimic the fluorescence of GFP, various compounds, such as GFP chromophores analogs, hydrogen bond-rich proteins, and aromatic peptidyl nanostructures that preclude free rotation of the aryl-alkene bond, have been developed to adapt them for a fantastic range of applications. Herein, we firstly summarize the structure and luminescent mechanism of GFP. Based on this, the design strategy, fluorescent properties, and the advanced applications of GFP-inspired fluorophores are then carefully discussed. The diverse advantages of bioinspired fluorophores, such as biocompatibility, structural simplicity, and capacity to form a variety of functional nanostructures, endow them potential candidates as the next-generation bio-organic optical materials.
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15
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Endoh T, Sugimoto N. Signaling Aptamer Optimization through Selection Using RNA-Capturing Microsphere Particles. Anal Chem 2020; 92:7955-7963. [PMID: 32363852 DOI: 10.1021/acs.analchem.0c01338] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An RNA signaling aptamer is composed of two units: a sensing aptamer that binds the input target molecule and a working aptamer that binds the output target molecule to result in a detectable signal. A conformational change of the signaling aptamer that induces an allosteric interaction with the output target molecule in response to the input target molecule depends on a junction region, which connects the two aptamer units. Efficient and effective optimization of the junction region remains a technical challenge. In this study, we demonstrate a simple strategy for optimizing the junction region through functional RNA selection using RNA-capturing microsphere particles. From approximately 0.2 million sequence variants, a signaling aptamer that enabled intracellular detection of S-adenosyl methionine with a high signal-to-noise ratio, which is approximately 2-fold higher relative fluorescence increment compared to the previously reported signaling aptamer, was obtained after single round of selection. The technology demonstrated here can be used to select RNA sequences that carry out specific functions in response to particular stimuli.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan.,Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan
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16
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RNA-based fluorescent biosensors for live cell imaging of small molecules and RNAs. Curr Opin Biotechnol 2020; 63:157-166. [PMID: 32086101 DOI: 10.1016/j.copbio.2020.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/23/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022]
Abstract
Genetically encodable fluorescent biosensors provide spatiotemporal information on their target analytes in a label-free manner, which has enabled the study of cell biology and signaling in living cells. Over the past three decades, fueled by the development of a wide palette of fluorescent proteins, protein-based fluorescent biosensors against a broad array of targets have been developed. Recently, with the development of fluorogenic RNA aptamer-dye pairs that function in live cells, RNA-based fluorescent (RBF) biosensors have emerged as a complementary class of biosensors. Here we review the current state-of-the-art for fluorogenic RNA aptamers and RBF biosensors for imaging small molecules and RNAs, and highlight some emerging opportunities.
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17
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Gao T, Luo Y, Li W, Cao Y, Pei R. Progress in the isolation of aptamers to light-up the dyes and the applications. Analyst 2020; 145:701-718. [DOI: 10.1039/c9an01825e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The progress in the selection of aptamers to light-up the dyes and the related applications are reviewed.
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Affiliation(s)
- Tian Gao
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Yu Luo
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Yanwei Cao
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface
- Suzhou Institute of Nano-Tech and Nano-Bionics
- Chinese Academy of Sciences
- Suzhou
- China
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18
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A dimerization-based fluorogenic dye-aptamer module for RNA imaging in live cells. Nat Chem Biol 2019; 16:69-76. [PMID: 31636432 PMCID: PMC6920041 DOI: 10.1038/s41589-019-0381-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 08/22/2019] [Indexed: 01/19/2023]
Abstract
Live-cell imaging of RNA has remained a challenge because of the lack of naturally fluorescent RNAs. Recently developed RNA aptamers that can light-up small fluorogenic dyes could overcome this limitation, but they still suffer from poor brightness and photostability. Here, we propose a concept of cell-permeable fluorogenic dimer of sulforhodamine B dyes (Gemini-561) and corresponding dimerized aptamer (o-Coral) that can drastically enhance performance of the current RNA imaging method. The unprecedented brightness and photostability together with high affinity of this complex allowed, for the first time, direct fluorescence imaging in live mammalian cells of RNA polymerase-III transcription products as well as messenger RNAs labelled with a single copy of the aptamer, i.e. without tag multimerization. The developed fluorogenic module enables fast and sensitive detection of RNA inside live cells, while the proposed design concept opens the route to new generation of ultrabright RNA probes.
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19
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Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Carlson PD, Shi X, Costantino DA, Herschlag D, Lucks JB, Jewett MC, Kieft JS, Das R. Computational design of three-dimensional RNA structure and function. NATURE NANOTECHNOLOGY 2019; 14:866-873. [PMID: 31427748 PMCID: PMC7324284 DOI: 10.1038/s41565-019-0517-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 06/24/2019] [Indexed: 05/30/2023]
Abstract
RNA nanotechnology seeks to create nanoscale machines by repurposing natural RNA modules. The field is slowed by the current need for human intuition during three-dimensional structural design. Here, we demonstrate that three distinct problems in RNA nanotechnology can be reduced to a pathfinding problem and automatically solved through an algorithm called RNAMake. First, RNAMake discovers highly stable single-chain solutions to the classic problem of aligning a tetraloop and its sequence-distal receptor, with experimental validation from chemical mapping, gel electrophoresis, solution X-ray scattering and crystallography with 2.55 Å resolution. Second, RNAMake automatically generates structured tethers that integrate 16S and 23S ribosomal RNAs into single-chain ribosomal RNAs that remain uncleaved by ribonucleases and assemble onto messenger RNA. Third, RNAMake enables the automated stabilization of small-molecule binding RNAs, with designed tertiary contacts that improve the binding affinity of the ATP aptamer and improve the fluorescence and stability of the Spinach RNA in cell extracts and in living Escherichia coli cells.
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Affiliation(s)
- Joseph D Yesselman
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Eiler
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Erik D Carlson
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Michael R Gotrik
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Anne E d'Aquino
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Alexandra N Ooms
- Department of Cancer Genetics & Genomics, Stanford University School of Medicine, Stanford, CA, USA
| | - Wipapat Kladwang
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul D Carlson
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA
| | - Xuesong Shi
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - David A Costantino
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
- Department of Chemistry, Stanford University School of Medicine, Stanford, CA, USA
- Stanford ChEM-H (Chemistry, Engineering, and Medicine for Human Health), Stanford University, Stanford, CA, USA
| | - Julius B Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Jeffrey S Kieft
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | - Rhiju Das
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Physics, Stanford University, Stanford, CA, USA.
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20
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Wei TB, Zhang QP, Fan YQ, Mao PP, Wang J, Guan XW, Zhang YM, Yao H, Lin Q. A novel supramolecular AIE π-gel for fluorescence detection and separation of metal ions from aqueous solution. SOFT MATTER 2019; 15:6530-6535. [PMID: 31348474 DOI: 10.1039/c9sm01270b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A novel supramolecular aggregation induced emission (AIE) π-gel (ONT) was constructed by using a functionalized trimesic amide (TCP) molecule assembled with a bis-pyridine functionalized naphthalene diimide (ND) molecule using a non-covalent interaction. The ONT showed strong AIE at 468 nm. Furthermore, the ONT could detect and adsorb ferric (Fe3+) or cupric (Cu2+) ions from water. Meanwhile, a thin film based on supramolecular AIE π-gel ONT was prepared, which could be used as a fluorescent security display material for detecting Fe3+ or Cu2+. Thus, the AIE π-gel ONT shows potential for practical applications in efficient multi-analyte detection and separation and as a fluorescent display material.
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Affiliation(s)
- Tai-Bao Wei
- Key Laboratory of Polymer Materials of Gansu Province, Research Center of Gansu Military and Civilian Integration Advanced Structural Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Qin-Peng Zhang
- Key Laboratory of Polymer Materials of Gansu Province, Research Center of Gansu Military and Civilian Integration Advanced Structural Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Yan-Qing Fan
- Key Laboratory of Polymer Materials of Gansu Province, Research Center of Gansu Military and Civilian Integration Advanced Structural Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Peng-Peng Mao
- Key Laboratory of Polymer Materials of Gansu Province, Research Center of Gansu Military and Civilian Integration Advanced Structural Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Jiao Wang
- Key Laboratory of Polymer Materials of Gansu Province, Research Center of Gansu Military and Civilian Integration Advanced Structural Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Xiao-Wen Guan
- Key Laboratory of Polymer Materials of Gansu Province, Research Center of Gansu Military and Civilian Integration Advanced Structural Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - You-Ming Zhang
- Key Laboratory of Polymer Materials of Gansu Province, Research Center of Gansu Military and Civilian Integration Advanced Structural Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Hong Yao
- Key Laboratory of Polymer Materials of Gansu Province, Research Center of Gansu Military and Civilian Integration Advanced Structural Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
| | - Qi Lin
- Key Laboratory of Polymer Materials of Gansu Province, Research Center of Gansu Military and Civilian Integration Advanced Structural Materials, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou 730070, China.
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21
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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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22
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Huang M, Song J, Huang P, Chen X, Wang W, Zhu Z, Song Y, Yang C. Molecular Crowding Evolution for Enabling Discovery of Enthalpy-Driven Aptamers for Robust Biomedical Applications. Anal Chem 2019; 91:10879-10886. [PMID: 31347355 DOI: 10.1021/acs.analchem.9b02697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An enthalpy-driven ligand is an ideal probe for practical applications because of the formation of abundant specific bonds between the ligand and target, compared to an entropy-driven ligand with a similar Gibbs free energy change. However, there has been a lack of direct discovery strategy for identifying enthalpy-driven ligands. In this work, a molecular crowding SELEX (systematic evolution of ligands by exponential enrichment) strategy for discovering enthalpy-driven aptamers was developed to improve the affinity and selectivity of aptamers in complex samples. Three aptamer sequences were successfully evolved against a tumor biomarker protein, and all proved to be enthalpy-driven by thermodynamics analysis, establishing the feasibility of molecular crowding SELEX for effective discovery of enthalpy-driven aptamers. Further comparison of aptamers evolved from conventional SELEX in buffer and molecular crowding SELEX (SYL-H2C) revealed much higher affinity of SYL-H2C. With its improved thermodynamic properties, the enthalpy-driven SYL-H2C aptamer was able to detect circulating tumor cells in real cancer patient blood samples with excellent detection accuracy (10/10). The proposed molecular crowding screening strategy offers a promising direction for discovering robust binding probes for a great variety of biomedical applications.
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Affiliation(s)
- Mengjiao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Peifeng Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Xiaofeng Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China.,Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China.,Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
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23
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Endoh T, Ohyama T, Sugimoto N. RNA-Capturing Microsphere Particles (R-CAMPs) for Optimization of Functional Aptamers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1805062. [PMID: 30773785 DOI: 10.1002/smll.201805062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/23/2019] [Indexed: 06/09/2023]
Abstract
RNA aptamers are useful building blocks for constructing functional nucleic acid-based nanoarchitectures. The abilities of aptamers to recognize specific ligands have also been utilized for various biotechnological applications. Solution conditions, which can differ depending on the application, impact the affinity of the aptamers, and thus it is important to optimize the aptamers for the solution conditions to be employed. To simplify the aptamer optimization process, an efficient method that enables re-selection of an aptamer from a partially randomized library is developed. The process relies on RNA-capturing microsphere particles (R-CAMPs): each particle displays different clones of identical DNA and RNA sequences. Using a fluorescence-activated cell sorter, the R-CAMPs that are linked to functional aptamers are sorted. It is demonstrated that after a single round of reselection, several functional aptamers, including the wild-type, are selected from a library of 16 384 sequences. The selection using R-CAMPs is further performed under the solution containing high concentration of ethylene glycol, suggesting applicability in various conditions to optimize an aptamer for a particular application. As any type of RNA clone can be displayed on the microspheres, the technology demonstrated here will be useful for the selection of RNAs based on diverse functions.
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Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Tatsuya Ohyama
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
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24
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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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25
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2019; 58:1266-1279. [PMID: 30102012 PMCID: PMC6391945 DOI: 10.1002/anie.201806482] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 12/16/2022]
Abstract
The cellular functions of RNA are not limited to their role as blueprints for protein synthesis. In particular, noncoding RNA, such as, snRNAs, lncRNAs, miRNAs, play important roles. With increasing numbers of RNAs being identified, it is well known that the transcriptome outnumbers the proteome by far. This emphasizes the great importance of functional RNA characterization and the need to further develop tools for these investigations, many of which are still in their infancy. Fluorescent light-up aptamers (FLAPs) are RNA sequences that can bind nontoxic, cell-permeable small-molecule fluorogens and enhance their fluorescence over many orders of magnitude upon binding. FLAPs can be encoded on the DNA level using standard molecular biology tools and are subsequently transcribed into RNA by the cellular machinery, so that they can be used as fluorescent RNA tags (FLAP-tags). In this Minireview, we give a brief overview of the fluorogens that have been developed and their binding RNA aptamers, with a special focus on published crystal structures. A summary of current and future cellular FLAP applications with an emphasis on the study of RNA-RNA and RNA-protein interactions using split-FLAP and Förster resonance energy transfer (FRET) systems is given.
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Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical SciencesVU University AmsterdamDe Boelelaan 11081081HZAmsterdamThe Netherlands
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26
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Steinmetzger C, Palanisamy N, Gore KR, Höbartner C. A Multicolor Large Stokes Shift Fluorogen-Activating RNA Aptamer with Cationic Chromophores. Chemistry 2019; 25:1931-1935. [PMID: 30485561 DOI: 10.1002/chem.201805882] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Indexed: 12/31/2022]
Abstract
Large Stokes shift (LSS) fluorescent proteins (FPs) exploit excited state proton transfer pathways to enable fluorescence emission from the phenolate intermediate of their internal 4-hydroxybenzylidene imidazolone (HBI) chromophore. An RNA aptamer named Chili mimics LSS FPs by inducing highly Stokes-shifted emission from several new green and red HBI analogues that are non-fluorescent when free in solution. The ligands are bound by the RNA in their protonated phenol form and feature a cationic aromatic side chain for increased RNA affinity and reduced magnesium dependence. In combination with oxidative functionalization at the C2 position of the imidazolone, this strategy yielded DMHBO+ , which binds to the Chili aptamer with a low-nanomolar KD . Because of its highly red-shifted fluorescence emission at 592 nm, the Chili-DMHBO+ complex is an ideal fluorescence donor for Förster resonance energy transfer (FRET) to the rhodamine dye Atto 590 and will therefore find applications in FRET-based analytical RNA systems.
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Affiliation(s)
- Christian Steinmetzger
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Navaneethan Palanisamy
- International Max Planck Research School Molecular Biology, University of Göttingen, Germany.,Present address: BIOSS Center for Biological Signaling Studies, University of Freiburg, Germany
| | - Kiran R Gore
- Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany.,Present address: Department of Chemistry, University of Mumbai, India
| | - Claudia Höbartner
- Institute of Organic Chemistry, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.,International Max Planck Research School Molecular Biology, University of Göttingen, Germany.,Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), Göttingen, Germany
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27
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Gordon CKL, Eisenstein M, Soh HT. Direct Selection Strategy for Isolating Aptamers with pH-Sensitive Binding Activity. ACS Sens 2018; 3:2574-2580. [PMID: 30520292 PMCID: PMC6312627 DOI: 10.1021/acssensors.8b00945] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
An
aptamer reagent that can switch its binding affinity in a pH-responsive
manner would be highly valuable for many biomedical applications including
imaging and drug delivery. Unfortunately, the discovery of such aptamers
is difficult and only a few have been reported to date. Here we report
the first experimental strategy for generating pH-responsive aptamers
through direct selection. As an exemplar, we report streptavidin-binding
aptamers that retain nanomolar affinity at pH 7.4 but exhibit a ∼100-fold
decrease in affinity at pH 5.2. These aptamers were generated by incorporating
a known streptavidin-binding DNA motif into an aptamer library and
performing FACS-based screening at multiple pH conditions. Upon structural
analysis, we found that one aptamer’s affinity-switching behavior
is driven by a noncanonical G-A base-pair that controls its folding
in a highly pH-dependent manner. We believe our strategy could be
readily extended to other aptamer-target systems because it does not
require a priori structural knowledge of the aptamer or the target.
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Affiliation(s)
| | | | - Hyongsok Tom Soh
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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28
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Kumar S, Jain S, Dilbaghi N, Ahluwalia AS, Hassan AA, Kim KH. Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications. Trends Biochem Sci 2018; 44:190-213. [PMID: 30559045 DOI: 10.1016/j.tibs.2018.11.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/01/2018] [Accepted: 11/01/2018] [Indexed: 02/07/2023]
Abstract
DNAzymes have been widely explored owing to their excellent catalytic activity in a broad range of applications, notably in sensing and biomedical devices. These newly discovered applications have built high hopes for designing novel catalytic DNAzymes. However, the selection of efficient DNAzymes is a challenging process but one that is of crucial importance. Initially, systemic evolution of ligands by exponential enrichment (SELEX) was a labor-intensive and time-consuming process, but recent advances have accelerated the automated generation of DNAzyme molecules. This review summarizes recent advances in SELEX that improve the affinity and specificity of DNAzymes. The thriving generation of new DNAzymes is expected to open the door to several healthcare applications. Therefore, a significant portion of this review is dedicated to various biological applications of DNAzymes, such as sensing, therapeutics, and nanodevices. In addition, discussion is further extended to the barriers encountered for the real-life application of these DNAzymes to provide a foundation for future research.
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Affiliation(s)
- Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India; Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA.
| | - Shikha Jain
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana, 125001, India
| | | | - Ashraf Aly Hassan
- Department of Civil Engineering, College of Engineering, University of Nebraska at Lincoln, PO Box 886105, Lincoln, NE 68588-6105, USA
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Republic of Korea.
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29
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Neubacher S, Hennig S. RNA Structure and Cellular Applications of Fluorescent Light-Up Aptamers. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806482] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Saskia Neubacher
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Sven Hennig
- Department of Chemistry & Pharmaceutical Sciences; VU University Amsterdam; De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
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30
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Qu H, Wang L, Liu J, Zheng L. Direct Screening for Cytometric Bead Assays for Adenosine Triphosphate. ACS Sens 2018; 3:2071-2078. [PMID: 30084633 DOI: 10.1021/acssensors.8b00224] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cytometric bead assays have caught much attention because of their many exceptional advantages. Unfortunately, the immobilization of existing molecular recognition elements including monoclonal antibodies and aptamers onto solid particles may lead to the functional failure of the molecular recognition elements since they are generally obtained in free state. Herein we develop a powerful screening approach for direct and rapid discovery of aptamer based cytometric bead assays (AB-CBAs) by individually measuring the functional activity of every aptamer particles in a library and sorting them at rates of up to 108 particles per hour. The strategy is based on the transformation of molecular libraries into pools of monoclonal aptamer particles so that one individual particle displays ∼105 copies of an identical aptamer sequence. Our library design incorporates a two-color fluorescent reporter system in which changes in aptamer structure generate an optical readout, such that we can use fluorescence-activated cell sorting to rapidly and selectively separate the individual aptamer particles that exhibit large fluorescent signal change upon target binding. For demonstration, we isolated AB-CBA aptamer particles with high signaling performance for ATP after just 3 rounds of screening. We believe that the rapid and direct screening features of this strategy make it an excellent platform for generating AB-CBAs for for a wide range of important analytes.
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Affiliation(s)
- Hao Qu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Lu Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jian Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Lei Zheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
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31
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Poly-Target Selection Identifies Broad-Spectrum RNA Aptamers. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:605-619. [PMID: 30472639 PMCID: PMC6251793 DOI: 10.1016/j.omtn.2018.10.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/18/2022]
Abstract
Aptamer selections often yield distinct subpopulations, each with unique phenotypes that can be leveraged for specialized applications. Although most selections aim to attain ever higher specificity, we sought to identify aptamers that recognize increasingly divergent primate lentiviral reverse transcriptases (RTs). We hypothesized that aptamer subpopulations in libraries pre-enriched against a single RT may exhibit broad-spectrum binding and inhibition, and we devised a multiplexed poly-target selection to elicit those phenotypes against a panel of primate lentiviral RTs. High-throughput sequencing and coenrichment/codepletion analysis of parallel and duplicate selection trajectories rapidly narrowed the list of candidate aptamers by orders of magnitude and identified dozens of priority candidates for further screening. Biochemical characterization validated a novel aptamer motif and several rare and unobserved variants of previously known motifs that inhibited recombinant RTs to varying degrees. These broad-spectrum aptamers also suppressed replication of viral constructs carrying phylogenetically diverse RTs. The poly-target selection and coenrichment/codepletion approach described herein is a generalizable strategy for identifying cross-reactivity among related targets from combinatorial libraries.
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Salveson PJ, Haerianardakani S, Thuy-Boun A, Yoo S, Kreutzer AG, Demeler B, Nowick JS. Repurposing Triphenylmethane Dyes to Bind to Trimers Derived from Aβ. J Am Chem Soc 2018; 140:11745-11754. [PMID: 30125493 DOI: 10.1021/jacs.8b06568] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Soluble oligomers of the β-amyloid peptide, Aβ, are associated with the progression of Alzheimer's disease. Although many small molecules bind to these assemblies, the details of how these molecules interact with Aβ oligomers remain unknown. This paper reports that crystal violet, and other C3 symmetric triphenylmethane dyes, bind to C3 symmetric trimers derived from Aβ17-36. Binding changes the color of the dyes from purple to blue, and causes them to fluoresce red when irradiated with green light. Job plot and analytical ultracentrifugation experiments reveal that two trimers complex with one dye molecule. Studies with several triphenylmethane dyes reveal that three N, N-dialkylamino substituents are required for complexation. Several mutant trimers, in which Phe19, Phe20, and Ile31 were mutated to cyclohexylalanine, valine, and cyclohexylglycine, were prepared to probe the triphenylmethane dye binding site. Size exclusion chromatography, SDS-PAGE, and X-ray crystallographic studies demonstrate that these mutations do not impact the structure or assembly of the triangular trimer. Fluorescence spectroscopy and analytical ultracentrifugation experiments reveal that the dye packs against an aromatic surface formed by the Phe20 side chains and is clasped by the Ile31 side chains. Docking and molecular modeling provide a working model of the complex in which the triphenylmethane dye is sandwiched between two triangular trimers. Collectively, these findings demonstrate that the X-ray crystallographic structures of triangular trimers derived from Aβ can be used to guide the discovery of ligands that bind to soluble oligomers derived from Aβ.
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Affiliation(s)
- Patrick J Salveson
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Sepehr Haerianardakani
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Alexander Thuy-Boun
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Stan Yoo
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Adam G Kreutzer
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
| | - Borries Demeler
- Department of Biochemistry , University of Texas Health Science Center , San Antonio , Texas 78229-3900 , United States
| | - James S Nowick
- Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States
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