1
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Song K, Hwang SJ, Jeon Y, Yoon Y. The Biomedical Applications of Biomolecule Integrated Biosensors for Cell Monitoring. Int J Mol Sci 2024; 25:6336. [PMID: 38928042 PMCID: PMC11204277 DOI: 10.3390/ijms25126336] [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: 04/22/2024] [Revised: 06/04/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Cell monitoring is essential for understanding the physiological conditions and cell abnormalities induced by various stimuli, such as stress factors, microbial invasion, and diseases. Currently, various techniques for detecting cell abnormalities and metabolites originating from specific cells are employed to obtain information on cells in terms of human health. Although the states of cells have traditionally been accessed using instrument-based analysis, this has been replaced by various sensor systems equipped with new materials and technologies. Various sensor systems have been developed for monitoring cells by recognizing biological markers such as proteins on cell surfaces, components on plasma membranes, secreted metabolites, and DNA sequences. Sensor systems are classified into subclasses, such as chemical sensors and biosensors, based on the components used to recognize the targets. In this review, we aim to outline the fundamental principles of sensor systems used for monitoring cells, encompassing both biosensors and chemical sensors. Specifically, we focus on biosensing systems in terms of the types of sensing and signal-transducing elements and introduce recent advancements and applications of biosensors. Finally, we address the present challenges in biosensor systems and the prospects that should be considered to enhance biosensor performance. Although this review covers the application of biosensors for monitoring cells, we believe that it can provide valuable insights for researchers and general readers interested in the advancements of biosensing and its further applications in biomedical fields.
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Affiliation(s)
| | | | | | - Youngdae Yoon
- Department of Environmental Health Science, Konkuk University, Seoul 05029, Republic of Korea; (K.S.); (S.-J.H.)
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2
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Scheele R, Weber Y, Nintzel FEH, Herger M, Kaminski TS, Hollfelder F. Ultrahigh Throughput Evolution of Tryptophan Synthase in Droplets via an Aptamer Sensor. ACS Catal 2024; 14:6259-6271. [PMID: 38660603 PMCID: PMC11036396 DOI: 10.1021/acscatal.4c00230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/29/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024]
Abstract
Tryptophan synthase catalyzes the synthesis of a wide array of noncanonical amino acids and is an attractive target for directed evolution. Droplet microfluidics offers an ultrahigh throughput approach to directed evolution (up to 107 experiments per day), enabling the search for biocatalysts in wider regions of sequence space with reagent consumption minimized to the picoliter volume (per library member). While the majority of screening campaigns in this format on record relied on an optically active reaction product, a new assay is needed for tryptophan synthase. Tryptophan is not fluorogenic in the visible light spectrum and thus falls outside the scope of conventional droplet microfluidic readouts, which are incompatible with UV light detection at high throughput. Here, we engineer a tryptophan DNA aptamer into a sensor to quantitatively report on tryptophan production in droplets. The utility of the sensor was validated by identifying five-fold improved tryptophan synthases from ∼100,000 protein variants. More generally, this work establishes the use of DNA-aptamer sensors with a fluorogenic read-out in widening the scope of droplet microfluidic evolution.
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Affiliation(s)
- Remkes
A. Scheele
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | - Yanik Weber
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | | | - Michael Herger
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
| | - Tomasz S. Kaminski
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
- Department
of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
| | - Florian Hollfelder
- Department
of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K.
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3
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Formen JSSK, Hassan DS, Wolf C. Chemometric sensing of stereoisomeric compound mixtures with a redox-responsive optical probe. Chem Sci 2024; 15:1498-1504. [PMID: 38274061 PMCID: PMC10806675 DOI: 10.1039/d3sc05706b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
The analysis of mixtures of chiral compounds is a common task in academic and industrial laboratories typically achieved by laborious and time-consuming physical separation of the individual stereoisomers to allow interference-free quantification, for example using chiral chromatography coupled with UV detection. Current practice thus impedes high-throughput and slows down progress in countless chiral compound development projects. Here we describe a chemometric solution to this problem using a redox-responsive naphthoquinone that enables chromatography-free click chemistry sensing of challenging mixtures. The achiral probe covalently binds amino alcohols within a few minutes at room temperature and generates characteristic UVA and CDA spectra that are intentionally altered via sodium borohydride reduction to provide a second, strikingly different chiroptical data set (UVB and CDB). Chemometric partial least squares processing of the chiroptical outputs then enables spectral deconvolution and accurate determination of individual analyte concentrations. The success of this approach is demonstrated with 35 samples covering considerably varied total analyte amounts and stereoisomeric ratios. All chemicals and machine learning algorithms are readily available and can be immediately adapted by any laboratory.
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Affiliation(s)
| | - Diandra S Hassan
- Department of Chemistry, Georgetown University Washington DC 20057 USA
| | - Christian Wolf
- Department of Chemistry, Georgetown University Washington DC 20057 USA
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4
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Huang PJJ, Liu J. Simultaneous Detection of L-Lactate and D-Glucose Using DNA Aptamers in Human Blood Serum. Angew Chem Int Ed Engl 2023; 62:e202212879. [PMID: 36693796 DOI: 10.1002/anie.202212879] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 01/19/2023] [Accepted: 01/20/2023] [Indexed: 01/26/2023]
Abstract
L-lactate is a key metabolite indicative of physiological states, glycolysis pathways, and various diseases such as sepsis, heart attack, lactate acidosis, and cancer. Detection of lactate has been relying on a few enzymes that need additional oxidants. In this work, DNA aptamers for L-lactate were obtained using a library-immobilization selection method and the highest affinity aptamer reached a Kd of 0.43 mM as determined using isothermal titration calorimetry. The aptamers showed up to 50-fold selectivity for L-lactate over D-lactate and had little responses to other closely related analogs such as pyruvate or 3-hydroxybutyrate. A fluorescent biosensor based on the strand displacement method showed a limit of detection of 0.55 mM L-lactate, and the sensor worked in 90 % serum. Simultaneous detection of L-lactate and D-glucose in the same solution was achieved. This work has broadened the scope of aptamers to simple metabolites and provided a useful probe for continuous and multiplexed monitoring.
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Affiliation(s)
- Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1, Canada
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5
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Yu CH, Sczepanski JT. The influence of chirality on the behavior of oligonucleotides inside cells: revealing the potent cytotoxicity of G-rich l-RNA. Chem Sci 2023; 14:1145-1154. [PMID: 36756313 PMCID: PMC9891384 DOI: 10.1039/d2sc05511b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/30/2022] [Indexed: 12/31/2022] Open
Abstract
Due to their intrinsic nuclease resistance, mirror image l-oligonucleotides are being increasingly employed in the development of biomedical research tools and therapeutics. Yet, the influence of chirality on the behavior of oligonucleotides in living systems, and specifically, the extent to which l-oligonucleotides interact with endogenous biomacromolecules and the resulting consequences remain unknown. In this study, we characterized the intracellular behavior of l-oligonucleotides for the first time, revealing important chirality-dependent effects on oligonucleotide cytotoxicity. We show that exogenously delivered l-oligonucleotides have the potential to be highly cytotoxic, which is dependent on backbone chemistry, sequence, and structure. Notably, for the sequences tested, we found that single-stranded G-rich l-RNAs are more cytotoxic than their d-DNA/RNA counterparts, exhibiting low nanomolar EC50 values. Importantly, RNA-seq analysis of differentially expressed genes suggests that G-rich l-RNAs stimulate an innate immune response and pro-inflammatory cytokine production. These data not only challenge the general perception that mirror image l-oligonucleotides are nontoxic and nonimmunogenic, but also reveal previously unrecognized therapeutic opportunities. Moreover, by establishing sequence/structure toxicity relationships, this work will guide how future l-oligonucleotide-based biotechnologies are designed and applied.
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Affiliation(s)
- Chen-Hsu Yu
- Department of Chemistry, Texas A&M University College Station Texas 77843 USA
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6
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DNA-Immobilized Special Conformation Recognition of L-Penicillamine Using a Chiral Molecular Imprinting Technique. Polymers (Basel) 2022; 14:polym14194133. [PMID: 36236082 PMCID: PMC9571851 DOI: 10.3390/polym14194133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/08/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022] Open
Abstract
A new chiral molecularly imprinted polymer (MIP) sensor with dual recognition ability was developed for the highly selective separation of enantiomers with toxic side effects in drugs. The sensor contains double-stranded deoxyribonucleic acid (dsDNA) as the element that immobilizes the chiral molecular conformation: the dsDNA enables the imprinted cavities to match the three-dimensional structure and functional groups from the chiral molecule. By embedding the spatial orientation of dsDNA in MIPs, one can accurately capture and immobilize the molecular conformation, eliminating the influence of interfering analogues. Herein, L-penicillamine (L-Pen) was selected as the chiral template molecule and embedded into dsDNA to form dsDNA-L-Pen complex, which was then embedded into the MIPs by electropolymerization. After elution, the stereo-selective imprinted cavities were obtained. The ATATATATATAT-TATATATATATA base sequence showed a high affinity for the embedded L-Pen, which endowed the imprinted cavities with a larger number of sites and improved the selectivity toward Pen enantiomers. Under the optimal working conditions, the current response of the MIP/dsDNA sensor exhibited a positive linear relationship with the logarithm of the L-Pen concentration in the range of 3.0 × 10-16 to 3.0 × 10-13 mol/L, and the detection limit was 2.48 × 10-16 mol/L. After the introduction of dsDNA into the MIP, the selectivity of the sensor toward D-Pen increased by 6.4 times, and the sensor was successfully applied in the analysis of L-Pen in penicillamine tablets.
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7
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Wagen CC, McMinn SE, Kwan EE, Jacobsen EN. Screening for generality in asymmetric catalysis. Nature 2022; 610:680-686. [PMID: 36049504 PMCID: PMC9645431 DOI: 10.1038/s41586-022-05263-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022]
Abstract
Research in the field of asymmetric catalysis over the past half century has resulted in landmark advances, enabling the efficient synthesis of chiral building blocks, pharmaceuticals and natural products1-3. A small number of asymmetric catalytic reactions have been identified that display high selectivity across a broad scope of substrates; not coincidentally, these are the reactions that have the greatest impact on how enantioenriched compounds are synthesized4-8. We postulate that substrate generality in asymmetric catalysis is rare not simply because it is intrinsically difficult to achieve, but also because of the way chiral catalysts are identified and optimized9. Typical discovery campaigns rely on a single model substrate, and thus select for high performance in a narrow region of chemical space. Here we put forth a practical approach for using multiple model substrates to select simultaneously for both enantioselectivity and generality in asymmetric catalytic reactions from the outset10,11. Multisubstrate screening is achieved by conducting high-throughput chiral analyses by supercritical fluid chromatography-mass spectrometry with pooled samples. When applied to Pictet-Spengler reactions, the multisubstrate screening approach revealed a promising and unexpected lead for the general enantioselective catalysis of this important transformation, which even displayed high enantioselectivity for substrate combinations outside of the screening set.
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Affiliation(s)
- Corin C Wagen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | | | - Eugene E Kwan
- Process Research and Development, Merck & Co. Inc, Boston, MA, USA.
| | - Eric N Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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8
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Zheng H, GhavamiNejad A, GhavamiNejad P, Samarikhalaj M, Giacca A, Poudineh M. Hydrogel Microneedle-Assisted Assay Integrating Aptamer Probes and Fluorescence Detection for Reagentless Biomarker Quantification. ACS Sens 2022; 7:2387-2399. [PMID: 35866892 DOI: 10.1021/acssensors.2c01033] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Analyzing interstitial fluid (ISF) via microneedle (MN) devices enables patient health monitoring in a minimally invasive manner and in point-of-care settings. However, most MN-based diagnostic approaches require complicated fabrication processes and postprocessing of the extracted ISF or are limited to detection of electrochemically active biomarkers. Here, we show on-needle measurement of target analytes by integrating hydrogel microneedles with aptamer probes as the recognition elements. Fluorescently tagged aptamer probes are chemically attached to the hydrogel matrix using a simple and novel approach, while a cross-linked patch is formed. For reagentless detection, we employ a strand displacement strategy where fluorophore-conjugated aptamers are hybridized with a DNA competitor strand conjugated to a quencher molecule. The assay is utilized for rapid (2 min) measurement of glucose, adenosine triphosphate, l-tyrosinamide, and thrombin ex vivo. Furthermore, the system enables specific and sensitive quantification of rising and falling concentrations of glucose in an animal model of diabetes to track hypoglycemia, euglycemia, and hyperglycemia conditions. Our assay can be applied for rapid measurement of a diverse range of biomarkers, proteins, or small molecules, introducing a generalizable platform for biomolecule quantification, and has the potential to improve the quality of life of patients who are in need of close monitoring of biomarkers of health and disease.
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Affiliation(s)
- Hanjia Zheng
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Amin GhavamiNejad
- Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Peyman GhavamiNejad
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Melisa Samarikhalaj
- Departments of Physiology and Medicine, Institute of Medical Science and Banting and Best Diabetes Centre, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Adria Giacca
- Departments of Physiology and Medicine, Institute of Medical Science and Banting and Best Diabetes Centre, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Mahla Poudineh
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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9
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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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10
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Wang S, Xie S, Zeng H, Du H, Zhang J, Wan X. Self-Reporting Activated Ester-Amine Reaction for Enantioselective Multi-Channel Visual Detection of Chiral Amines. Angew Chem Int Ed Engl 2022; 61:e202202268. [PMID: 35285991 DOI: 10.1002/anie.202202268] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Indexed: 01/04/2023]
Abstract
Chiral recognition is of importance not only in living systems but also in estimating the optical purity of enantiomeric drugs and fabricating advanced materials. Herein we report a novel self-reporting activated ester-amine reaction that can provide multi-channel visual detection of organic amines. It relies on the reaction extent dependent cis-transoid to cis-cisoid helical transition of the polyphenylacetylene backbone and the thus triggered fluorescence. Owing to the high selectivity, this visual process can recognize structurally diverse achiral amines and quantitatively check the impurity content. It also shows an outstanding enantioselectivity towards various chiral amines and can be applied to determine enantiomeric composition. The multiple responses in absorption, circular dichroism, photoluminescence, and circularly polarized luminescence make the helical transition of the polymer backbone a potential detection mode for high-throughput screening of chiral chemicals.
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Affiliation(s)
- Sheng Wang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Siyu Xie
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Hua Zeng
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Hongxu Du
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jie Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Xinhua Wan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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11
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Liu F, Li N, Shang Y, Wang Y, Liu Q, Ma Z, Jiang Q, Ding B. A DNA‐Based Plasmonic Nanodevice for Cascade Signal Amplification. Angew Chem Int Ed Engl 2022; 61:e202114706. [DOI: 10.1002/anie.202114706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Fengsong Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Na Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Yingxu Shang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
| | - Yiming Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Qing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
| | - Zhentao Ma
- He'nan Institute of Advanced Technology School of Materials Science and Engineering Zhengzhou University Zhengzhou 450001 China
| | - Qiao Jiang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication National Center for Nanoscience and Technology Beijing 100190 China
- University of Chinese Academy of Sciences Beijing 100049 China
- He'nan Institute of Advanced Technology School of Materials Science and Engineering Zhengzhou University Zhengzhou 450001 China
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12
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Tian J, Jiang YX, Yu XQ, Yu SS. Rapid chiral assay of amino compounds using diethyl squarate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 272:120871. [PMID: 35151169 DOI: 10.1016/j.saa.2022.120871] [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: 10/07/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The versatility and importance of chiral compounds make it urgent to develop fast and efficient methods to detect the absolute configuration, enantiomeric excess(ee), and concentration of chiral compounds. In this study, we demonstrate that commercially available diethyl squarate can rapidly react with various types of chiral amino compounds and exhibit characteristic ultraviolet (UV) and circular dichroism (CD) signals. The UV and CD signals can determine the total concentration of the two enantiomers and ee value of the sample, respectively. The probe showed a broad substrate scope, applicable to 39 tested chiral amino compounds, including chiral amino acids, amino alcohols, and amines. Additionally, the probe accurately detected 10 samples of phenylalanine, phenylglycinol, and phenethylamine with the error range less than 8%, demonstrating the practicability of this method.
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Affiliation(s)
- Jun Tian
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry Sichuan University, 29, Wangjiang Road, Chengdu, Sichuan Province 610064, China
| | - Yi-Xuan Jiang
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry Sichuan University, 29, Wangjiang Road, Chengdu, Sichuan Province 610064, China
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry Sichuan University, 29, Wangjiang Road, Chengdu, Sichuan Province 610064, China.
| | - Shan-Shan Yu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry Sichuan University, 29, Wangjiang Road, Chengdu, Sichuan Province 610064, China.
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13
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Wang S, Xie S, Zeng H, Du H, Zhang J, Wan X. Self‐Reporting Activated Ester‐Amine Reaction for Enantioselective Multi‐Channel Visual Detection of Chiral Amines. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Sheng Wang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
| | - Siyu Xie
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
| | - Hua Zeng
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
| | - Hongxu Du
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
| | - Jie Zhang
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
| | - Xinhua Wan
- Beijing National Laboratory for Molecular Sciences Key Laboratory of Polymer Chemistry and Physics of Ministry of Education, College of Chemistry and Molecular Engineering Peking University Beijing 100871 China
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14
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Liu F, Li N, Shang Y, Wang Y, Liu Q, Ma Z, Jiang Q, Ding B. A DNA‐based plasmonic nanodevice for cascade signal amplification. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fengsong Liu
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Na Li
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Yingxu Shang
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Yiming Wang
- National Center for Nanoscience and Technology CAS Key Labortory of Nanosystem and Hierarchical Fabrication CHINA
| | - Qing Liu
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Zhentao Ma
- Zhengzhou University School of Materials Science and Engineering CHINA
| | - Qiao Jiang
- National Center for Nanoscience and Technology CAS Key Laboratory of Nanosystem and Hierarchical Fabrication CHINA
| | - Baoquan Ding
- National Center for Nanoscience and Technology, China CAS Key Laboratory of Nanosystem and Hierarchical Fabrication No. 11, BeiYiTiao, ZhongGuanCun 100190 Beijing CHINA
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15
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Chen Y, Nagao R, Murayama K, Asanuma H. Orthogonal Amplification Circuits Composed of Acyclic Nucleic Acids Enable RNA Detection. J Am Chem Soc 2022; 144:5887-5892. [PMID: 35258290 DOI: 10.1021/jacs.1c12659] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Construction of complex DNA circuits is difficult due to unintended hybridization and degradation by enzymes under biological conditions. We herein report a hybridization chain reaction (HCR) circuit composed of left-handed acyclic d-threoninol nucleic acid (d-aTNA), which is orthogonal to right-handed DNA and RNA. Because of its high thermal stability, use of an aTNA hairpin with a short 7 base-pair stem ensured clear ON-OFF control of the HCR circuit. The aTNA circuit was stable against nucleases. A circuit based on right-handed acyclic l-threoninol nucleic acid (l-aTNA) was also designed, and high orthogonality between d- and l-aTNA HCRs was confirmed by activation of each aTNA HCR via a corresponding input strand. A dual OR logic gate was successfully established using serinol nucleic acid (SNA), which could initiate both d- and l-aTNA circuits. The d-aTNA HCR was used for an RNA-dependent signal amplification system via the SNA interface. The design resulted in 80% yield of the cascade reaction in 3000 s without a significant leak. This work represents the first example of use of heterochiral HCR circuits for detection of RNA molecules. The method has potential for direct visualization of RNA in vivo and the FISH method.
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Affiliation(s)
- Yanglingzhi Chen
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Ryuya Nagao
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
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16
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Wolf C, Hassan DS, Kariapper FS, Lynch CC. Accelerated Asymmetric Reaction Screening with Optical Assays. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/a-1754-2271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
AbstractAsymmetric reaction development often involves optimization of several mutually dependent parameters that affect the product yield and enantiomeric excess. Widely available high-throughput experimentation equipment and optical sensing assays can drastically streamline comprehensive optimization efforts and speed up the discovery process at reduced cost, workload, and waste production. A variety of chiroptical assays that utilize fluorescence, UV, and circular dichroism measurements to determine reaction yields and ee values are now available, enabling the screening of numerous small-scale reaction samples in parallel with multi-well plate technology. Many of these optical methods considerably shorten work-up protocols typically required for traditional asymmetric reaction analysis and some can be directly applied to crude mixtures thus eliminating cumbersome separation and purification steps altogether.1 Introduction2 Fluorescence Assays3 UV Sensing Methods4 Sensing with Circular Dichroism Probes5 Hybrid Approaches6 Optical Analysis with Intrinsically CD-Active Reaction Products7 Conclusion
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17
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Yu CH, Kabza AM, Sczepanski JT. Assembly of long L-RNA by native RNA ligation. Chem Commun (Camb) 2021; 57:10508-10511. [PMID: 34550128 DOI: 10.1039/d1cc04296c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Due to their intrinsic nuclease resistance, L-oligonucleotides are being increasingly utilized in the development of molecular tools and sensors. Yet, it remains challenging to synthesize long L-oligonucleotides, potential limiting future applications. Herein, we report straightforward and versitile approach to assemble long L-RNAs from two or more shorter fragments using T4 RNA ligase 1. We show that this approach is compatible with the assembly of several classes of functional L-RNA, which we highlight by generating a 124 nt L-RNA biosensor that functions in serum.
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Affiliation(s)
- Chen-Hsu Yu
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
| | - Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, TX, USA.
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18
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Sanford AA, Rangel AE, Feagin TA, Lowery RG, Argueta-Gonzalez HS, Heemstra JM. RE-SELEX: restriction enzyme-based evolution of structure-switching aptamer biosensors. Chem Sci 2021; 12:11692-11702. [PMID: 34659704 PMCID: PMC8442683 DOI: 10.1039/d1sc02715h] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/23/2021] [Indexed: 11/21/2022] Open
Abstract
Aptamers are widely employed as recognition elements in small molecule biosensors due to their ability to recognize small molecule targets with high affinity and selectivity. Structure-switching aptamers are particularly promising for biosensing applications because target-induced conformational change can be directly linked to a functional output. However, traditional evolution methods do not select for the significant conformational change needed to create structure-switching biosensors. Modified selection methods have been described to select for structure-switching architectures, but these remain limited by the need for immobilization. Herein we describe the first homogenous, structure-switching aptamer selection that directly reports on biosensor capacity for the target. We exploit the activity of restriction enzymes to isolate aptamer candidates that undergo target-induced displacement of a short complementary strand. As an initial demonstration of the utility of this approach, we performed selection against kanamycin A. Four enriched candidate sequences were successfully characterized as structure-switching biosensors for detection of kanamycin A. Optimization of biosensor conditions afforded facile detection of kanamycin A (90 μM to 10 mM) with high selectivity over three other aminoglycosides. This research demonstrates a general method to directly select for structure-switching biosensors and can be applied to a broad range of small-molecule targets.
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Affiliation(s)
- Aimee A Sanford
- Department of Chemistry, Emory University Atlanta Georgia 30322 USA
| | - Alexandra E Rangel
- Department of Chemistry, Center for Cell and Genome Science, University of Utah Salt Lake City Utah 84112 USA
| | - Trevor A Feagin
- Department of Chemistry, Center for Cell and Genome Science, University of Utah Salt Lake City Utah 84112 USA
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19
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Through the looking glass: milestones on the road towards mirroring life. Trends Biochem Sci 2021; 46:931-943. [PMID: 34294544 DOI: 10.1016/j.tibs.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/05/2021] [Accepted: 06/18/2021] [Indexed: 12/24/2022]
Abstract
Naturally occurring DNA, RNA, and proteins predominantly exist in only one enantiomeric form (homochirality). Advances in biotechnology and chemical synthesis allow the production of the respective alternate enantiomeric form, enabling access to mirror-image versions of these natural biopolymers. Exploiting the unique properties of such mirror molecules has already led to many applications, such as biostable and nonimmunogenic therapeutics or sensors. However, a 'roadblock' for unlocking the mirror world is the lack of biological systems capable of synthesizing critical building blocks including mirror oligonucleotides and oligopeptides to reducing cost and improve purity. Here, we provide an overview of the current progress, applications, and challenges of the molecular mirror world by identifying milestones towards mirroring life.
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20
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Nelson E, Formen JSSK, Wolf C. Rapid organocatalytic chirality analysis of amines, amino acids, alcohols, amino alcohols and diols with achiral iso(thio)cyanate probes. Chem Sci 2021; 12:8784-8790. [PMID: 34257878 PMCID: PMC8246279 DOI: 10.1039/d1sc02061g] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 05/24/2021] [Indexed: 12/03/2022] Open
Abstract
The widespread occurrence and significance of chiral compounds does not only require new methods for their enantioselective synthesis but also efficient tools that allow rapid determination of the absolute configuration, enantiomeric composition and overall concentration of nonracemic mixtures. Although chiral analysis is a frequently encountered challenge in the chemical, environmental, materials and health sciences it is typically addressed with slow and laborious chromatographic or NMR spectroscopic techniques. We now show with almost 40 analytes representing 5 different compound classes, including mono-alcohols which are particularly challenging sensing targets, that this task can be solved very quickly by chiroptical sensing with a single, readily available arylisocyanate probe. The probe reacts smoothly and irreversibly with amino and alcohol groups when an organocatalyst is used at room temperature toward urea or carbamate products exhibiting characteristic UV and CD signals above 300 nm. The UV signal induction is not enantioselective and correlated to the total concentration of both enantiomers, the concomitant generation of a CD band allows determination of the enantiomeric composition from the same sample, and the sense of the induced Cotton effect reveals the absolute configuration by comparison with a reference. This approach eliminates complications that can arise when enantiomerically impure NMR derivatizing agents are used and it outperforms time-consuming HPLC protocols. The generation of distinct UV and CD signals at high wavelengths overcomes issues with insufficient resolution of overlapping signals often encountered with chiral NMR solvating agents that rely on weak binding forces. The broad solvent compatibility is another noteworthy and important characteristic of this assay. It addresses frequently encountered problems with insufficient solubility of polar analytes, for example pharmaceuticals, in standard mobile phase mixtures required for chiral HPLC analysis. We anticipate that the broad application spectrum, ruggedness and practicality of organocatalytic chiroptical sensing with aryliso(thio)cyanate probes together with the availability of automated CD multi-well plate readers carry exceptional promise to accelerate chiral compound development projects at reduced cost and with less waste production. Organocatalysis with a simple arylisocyanate probe enables accelerated optical concentration and enantiomeric ratio determination of a large variety of chiral compounds based on straightforward UV/CD analysis.![]()
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Affiliation(s)
- Eryn Nelson
- Department of Chemistry, Georgetown University Washington DC 20057 USA
| | | | - C Wolf
- Department of Chemistry, Georgetown University Washington DC 20057 USA
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21
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Huang X, Wang X, Quan M, Yao H, Ke H, Jiang W. Biomimetic Recognition and Optical Sensing of Carboxylic Acids in Water by Using a Buried Salt Bridge and the Hydrophobic Effect. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012467] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xuan Huang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Xiaoping Wang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Mao Quan
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Huan Yao
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Hua Ke
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Wei Jiang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
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22
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Huang X, Wang X, Quan M, Yao H, Ke H, Jiang W. Biomimetic Recognition and Optical Sensing of Carboxylic Acids in Water by Using a Buried Salt Bridge and the Hydrophobic Effect. Angew Chem Int Ed Engl 2020; 60:1929-1935. [DOI: 10.1002/anie.202012467] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/21/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Xuan Huang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Xiaoping Wang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Mao Quan
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Huan Yao
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Hua Ke
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Wei Jiang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology (SUSTech) Xueyuan Blvd 1088 Shenzhen 518055 China
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23
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Thanzeel FY, Balaraman K, Wolf C. Quantitative Chirality and Concentration Sensing of Alcohols, Diols, Hydroxy Acids, Amines and Amino Alcohols using Chlorophosphite Sensors in a Relay Assay. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005324] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- F. Yushra Thanzeel
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
| | - Kaluvu Balaraman
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
| | - Christian Wolf
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
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24
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Huang Y, Cheng Z, Han R, Gao X, Qian L, Wen Y, Zhang X, Liu G. Target-induced molecular-switch on triple-helix DNA-functionalized carbon nanotubes for simultaneous visual detection of nucleic acids and proteins. Chem Commun (Camb) 2020; 56:13657-13660. [PMID: 33064111 DOI: 10.1039/d0cc05986b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report an easy and efficient approach based on a target-induced molecular-switch on triple-helix DNA (THD)-functionalized carbon nanotubes (CNTs) for the simultaneous visual detection of nucleic acids and proteins with a lateral flow nucleic acid biosensor. The assay had the capability to detect a minimum of 25 pM target DNA and 0.25 nM thrombin simultaneously within 20 min.
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Affiliation(s)
- Yan Huang
- Research Center for Biomedical and Health Science, Anhui Science and Technology University, Fengyang 233100, P. R. China.
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25
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Wang L, Quan M, Yang T, Chen Z, Jiang W. A Green and Wide‐Scope Approach for Chiroptical Sensing of Organic Molecules through Biomimetic Recognition in Water. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202011566] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Li‐Li Wang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Mao Quan
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Ti‐Long Yang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Zhao Chen
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Wei Jiang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
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26
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Wang L, Quan M, Yang T, Chen Z, Jiang W. A Green and Wide‐Scope Approach for Chiroptical Sensing of Organic Molecules through Biomimetic Recognition in Water. Angew Chem Int Ed Engl 2020; 59:23817-23824. [DOI: 10.1002/anie.202011566] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Li‐Li Wang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Mao Quan
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Ti‐Long Yang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Zhao Chen
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
| | - Wei Jiang
- Shenzhen Grubbs Institute Guangdong Provincial Key Laboratory of Catalysis Department of Chemistry Southern University of Science and Technology Xueyuan Blvd 1088 Shenzhen 518055 China
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27
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Thanzeel FY, Balaraman K, Wolf C. Quantitative Chirality and Concentration Sensing of Alcohols, Diols, Hydroxy Acids, Amines and Amino Alcohols using Chlorophosphite Sensors in a Relay Assay. Angew Chem Int Ed Engl 2020; 59:21382-21386. [PMID: 32762103 DOI: 10.1002/anie.202005324] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 08/03/2020] [Indexed: 11/08/2022]
Abstract
Analytical methods that allow simultaneous determination of the concentration and enantiomeric composition of small sample amounts and are also compatible with high-throughput multi-well plate technology have received increasing attention in recent years. We now introduce a new class of broadly useful small-molecule probes and a relay sensing strategy that together accomplish these tasks with five classes of compounds including the challenging group of mono-alcohols-a scope that stands out among previously reported UV, fluorescence, and CD assays. Several chlorophosphite probes and aniline indicators have been evaluated and used for on-the-fly CD/UV sensing following a continuous workflow. The wide application range of the readily available sensors is highlighted with almost 30 alcohols, diols, hydroxy acids, amines and amino alcohols, and the accuracy of the stereochemical analysis is showcased with samples covering a wide range of concentrations and enantiomeric ratios.
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Affiliation(s)
- F Yushra Thanzeel
- Department of Chemistry, Georgetown University, 37th and O Streets, Washington, DC, 20057, USA
| | - Kaluvu Balaraman
- Department of Chemistry, Georgetown University, 37th and O Streets, Washington, DC, 20057, USA
| | - Christian Wolf
- Department of Chemistry, Georgetown University, 37th and O Streets, Washington, DC, 20057, USA
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28
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Lackey HH, Peterson EM, Harris JM, Heemstra JM. Probing the Mechanism of Structure-Switching Aptamer Assembly by Super-Resolution Localization of Individual DNA Molecules. Anal Chem 2020; 92:6909-6917. [PMID: 32297506 DOI: 10.1021/acs.analchem.9b05563] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Oligonucleotide aptamers can be converted into structure-switching biosensors by incorporating a short, typically labeled oligonucleotide that is complementary to the analyte-binding region. Binding of a target analyte can disrupt the hybridization equilibrium between the aptamer and the labeled-complementary oligo producing a concentration-dependent signal for target-analyte sensing. Despite its importance in the performance of a biosensor, the mechanism of analyte-response of most structure-switching aptamers is not well understood. In this work, we employ single-molecule fluorescence imaging to investigate the competitive kinetics of association of a labeled complementary oligonucleotide and a target analyte, l-tyrosinamide (L-Tym), interacting with an L-Tym-binding aptamer. The complementary readout strand is fluorescently labeled, allowing us to measure its hybridization kinetics with individual aptamers immobilized on a surface and located with super-resolution techniques; the small-molecule L-Tym analyte is not labeled in order to avoid having an attached dye molecule impact its interactions with the aptamer. We measure the association kinetics of unlabeled L-Tym by detecting its influence on the hybridization of the labeled complementary strand. We find that L-Tym slows the association rate of the complementary strand with the aptamer but does not impact its dissociation rate, suggesting an SN1-like mechanism where the complementary strand must dissociate before L-Tym can bind. The competitive model revealed a slow association rate between L-Tym and the aptamer, producing a long-lived L-Tym-aptamer complex that blocks hybridization with the labeled complementary strand. These results provide insight about the kinetics and mechanism of analyte recognition in this structure-switching aptamer, and the methodology provides a general means of measuring the rates of unlabeled-analyte binding kinetics in aptamer-based biosensors.
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Affiliation(s)
- Hershel H Lackey
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Eric M Peterson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jennifer M Heemstra
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, United States.,Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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29
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Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
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Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
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30
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Chiral recognition and enantiomer excess determination based on emission wavelength change of AIEgen rotor. Nat Commun 2020; 11:161. [PMID: 31919426 PMCID: PMC6952378 DOI: 10.1038/s41467-019-13955-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 12/03/2019] [Indexed: 11/09/2022] Open
Abstract
Chiral recognition, such as enantioselective interactions of enzyme with chiral agents, is one of the most important issues in the natural world. But artificial chiral receptors are much less efficient than natural ones. For tackling the chiral recognition and enantiomer excess (ee) analysis, up until now all the fluorescent receptors have been developed based on fluorescence intensity changes. Here we report that the chiral recognition of a large number of chiral carboxylic acids, including chiral agrochemicals 2,4-D, is carried out based on fluorescent colour changes rather than intensity changes of AIEgen rotors. Moreover, the fluorescence wavelength of the AIEgen rotor linearly changes with ee of the carboxylic acid, enabling the ee to be accurately measured with average absolute errors (AAE) of less than 2.8%. Theoretical calculation demonstrates that the wavelength change is ascribed to the rotation of the AIEgen rotor upon interaction with different enantiomers. Artificial receptors for chiral recognition are important in enantiomer excess analysis but current artificial detectors are based on fluorescence intensity changes only. Here the authors propose a different detection mechanism based on change of the fluorescence emission wavelength of an AIEgen rotor.
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31
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Oukacine F, Ravelet C, Peyrin E. Enantiomeric sensing and separation by nucleic acids. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115733] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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32
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Ligand Design for Asymmetric Catalysis: Combining Mechanistic and Chemoinformatics Approaches. TOP ORGANOMETAL CHEM 2020. [DOI: 10.1007/3418_2020_47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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33
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De los Santos ZA, MacAvaney S, Russell K, Wolf C. Tandem Use of Optical Sensing and Machine Learning for the Determination of Absolute Configuration, Enantiomeric and Diastereomeric Ratios, and Concentration of Chiral Samples. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201912904] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | - Sean MacAvaney
- Department of Computer Science Georgetown University Washington DC 20057 USA
| | - Katina Russell
- Department of Computer Science Georgetown University Washington DC 20057 USA
| | - Christian Wolf
- Department of Chemistry Georgetown University Washington DC 20057 USA
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34
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De Los Santos ZA, MacAvaney S, Russell K, Wolf C. Tandem Use of Optical Sensing and Machine Learning for the Determination of Absolute Configuration, Enantiomeric and Diastereomeric Ratios, and Concentration of Chiral Samples. Angew Chem Int Ed Engl 2019; 59:2440-2448. [PMID: 31714669 DOI: 10.1002/anie.201912904] [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: 10/09/2019] [Revised: 11/04/2019] [Indexed: 12/17/2022]
Abstract
We have developed an optical method for accurate concentration, er, and dr analysis of amino alcohols based on a simple mix-and-measure workflow that is fully adaptable to multiwell plate technology and microscale analysis. The conversion of the four aminoindanol stereoisomers with salicylaldehyde to the corresponding Schiff base allows analysis of the dr based on a change in the UV maximum at 420 nm that is very different for the homo- and heterochiral diastereomers and of the concentration of the sample using a hypsochromic shift of another absorption band around 340 nm that is independent of the analyte stereochemistry. Subsequent in situ formation of CuII assemblies in the absence and presence of base enables quantification of the er values for each diastereomeric pair by CD analysis. Applying a linear programming method and a parameter sweep algorithm, we determined the concentration and relative amounts of each of the four stereoisomers in 20 samples of vastly different stereoisomeric compositions with an averaged absolute percent error of 1.7 %.
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Affiliation(s)
| | - Sean MacAvaney
- Department of Computer Science, Georgetown University, Washington, DC, 20057, USA
| | - Katina Russell
- Department of Computer Science, Georgetown University, Washington, DC, 20057, USA
| | - Christian Wolf
- Department of Chemistry, Georgetown University, Washington, DC, 20057, USA
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35
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Dai Y, Furst A, Liu CC. Strand Displacement Strategies for Biosensor Applications. Trends Biotechnol 2019; 37:1367-1382. [DOI: 10.1016/j.tibtech.2019.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/18/2022]
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36
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Chovelon B, Fiore E, Faure P, Peyrin E, Ravelet C. Kissing interactions for the design of a multicolour fluorescence anisotropy chiral aptasensor. Talanta 2019; 205:120098. [DOI: 10.1016/j.talanta.2019.06.098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/23/2019] [Accepted: 06/27/2019] [Indexed: 01/03/2023]
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37
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Thanzeel FY, Balaraman K, Wolf C. Streamlined Asymmetric Reaction Development: A Case Study with Isatins. Chemistry 2019; 25:11020-11025. [DOI: 10.1002/chem.201902688] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/08/2019] [Indexed: 12/31/2022]
Affiliation(s)
- F. Yushra Thanzeel
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
| | - Kaluvu Balaraman
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
| | - Christian Wolf
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
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38
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Young BE, Kundu N, Sczepanski JT. Mirror-Image Oligonucleotides: History and Emerging Applications. Chemistry 2019; 25:7981-7990. [PMID: 30913332 PMCID: PMC6615976 DOI: 10.1002/chem.201900149] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Indexed: 01/13/2023]
Abstract
As chiral molecules, naturally occurring d-oligonucleotides have enantiomers, l-DNA and l-RNA, which are comprised of l-(deoxy)ribose sugars. These mirror-image oligonucleotides have the same physical and chemical properties as that of their native d-counterparts, yet are highly orthogonal to the stereospecific environment of biology. Consequently, l-oligonucleotides are resistant to nuclease degradation and many of the off-target interactions that plague traditional d-oligonucleotide-based technologies; thus making them ideal for biomedical applications. Despite a flurry of interest during the early 1990s, the inability of d- and l-oligonucleotides to form contiguous Watson-Crick base pairs with each other has ultimately led to the perception that l-oligonucleotides have only limited utility. Recently, however, scientists have begun to uncover novel strategies to harness the bio-orthogonality of l-oligonucleotides, while overcoming (and even exploiting) their inability to Watson-Crick base pair with the natural polymer. Herein, a brief history of l-oligonucleotide research is presented and emerging l-oligonucleotide-based technologies, as well as their applications in research and therapy, are presented.
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Affiliation(s)
- Brian E. Young
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Jonathan T. Sczepanski
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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39
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De los Santos ZA, Yusin G, Wolf C. Enantioselective sensing of carboxylic acids with a bis(urea)oligo(phenylene)ethynylene foldamer. Tetrahedron 2019. [DOI: 10.1016/j.tet.2019.01.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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40
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De los Santos ZA, Lynch CC, Wolf C. Optische Chiralitätssensorik mit ligandenfreien, weit verbreiteten Cobaltsalzen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811761] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zeus A. De los Santos
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
| | - Ciarán C. Lynch
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
| | - Christian Wolf
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
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41
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De los Santos ZA, Lynch CC, Wolf C. Optical Chirality Sensing with an Auxiliary‐Free Earth‐Abundant Cobalt Probe. Angew Chem Int Ed Engl 2018; 58:1198-1202. [DOI: 10.1002/anie.201811761] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 11/20/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Zeus A. De los Santos
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
| | - Ciarán C. Lynch
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
| | - Christian Wolf
- Department of Chemistry Georgetown University 37th and O Streets Washington DC 20057 USA
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42
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Click chemistry enables quantitative chiroptical sensing of chiral compounds in protic media and complex mixtures. Nat Commun 2018; 9:5323. [PMID: 30552322 PMCID: PMC6294054 DOI: 10.1038/s41467-018-07695-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/16/2018] [Indexed: 12/31/2022] Open
Abstract
Click reactions have become powerful synthetic tools with unique applications in the health and materials sciences. Despite the progress with optical sensors that exploit the principles of dynamic covalent chemistry, metal coordination or supramolecular assemblies, quantitative analysis of complex mixtures remains challenging. Herein, we report the use of a readily available coumarin conjugate acceptor for chiroptical click chirality sensing of the absolute configuration, concentration and enantiomeric excess of several compound classes. This method has several attractive features, including wide scope, fast substrate fixation without by-product formation or complicate equilibria often encountered in reversible substrate binding, excellent solvent compatibility, and tolerance of air and water. The ruggedness and practicality of this approach are demonstrated by comprehensive analysis of nonracemic monoamine samples and crude asymmetric imine hydrogenation mixtures without work-up. Click chemosensing addresses increasingly important time efficiency, cost, labor and chemical sustainability aspects and streamlines asymmetric reaction development at the mg scale.
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43
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Zhao C, Song H, Scott P, Zhao A, Tateishi-Karimata H, Sugimoto N, Ren J, Qu X. Mirror-Image Dependence: Targeting Enantiomeric G-Quadruplex DNA Using Triplex Metallohelices. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809207] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
| | - Hualong Song
- Department of Chemistry; University of Warwick; Gibbet Hill Road Coventry CV4 7AL UK
| | - Peter Scott
- Department of Chemistry; University of Warwick; Gibbet Hill Road Coventry CV4 7AL UK
| | - Andong Zhao
- University of Chinese Academy of Sciences; Beijing 100039 P. R. China
| | | | | | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization; Changchun Institute of Applied Chemistry; Chinese Academy of Sciences; Changchun Jilin 130022 P. R. China
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44
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Zhao C, Song H, Scott P, Zhao A, Tateishi-Karimata H, Sugimoto N, Ren J, Qu X. Mirror-Image Dependence: Targeting Enantiomeric G-Quadruplex DNA Using Triplex Metallohelices. Angew Chem Int Ed Engl 2018; 57:15723-15727. [PMID: 30311333 DOI: 10.1002/anie.201809207] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 09/21/2018] [Indexed: 12/22/2022]
Abstract
Natural d-DNA and l-DNA are mirror-image counterparts. However, because of the inherent flexibility and conformation diversity of DNA, it is still not clear how enantiomeric compounds recognize d-DNA and l-DNA. Herein, taking G-quadruplex (G4) DNA as an example that has diverse conformations and distinct biofunctions, the binding of ten pairs of iron triplex metallohelices to d- and l-G4 DNA were evaluated. The Δ-enantiomer binds to d-DNA and the Λ-enantiomer binds to l-DNA, exhibiting almost the same stabilization effect and binding affinity. The binding affinity of the Δ-metallohelix with d-G4 is nearly 70-fold higher than that of Λ-metallohelix binding d-G4. Δ-Metallohelix binding to d-G4 follows a two-step binding process driven by a favorable enthalpy contribution to compensate for the associated unfavorable entropy.
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Affiliation(s)
- Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Hualong Song
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Peter Scott
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Andong Zhao
- University of Chinese Academy of Sciences, Beijing, 100039, P. R. China
| | | | | | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
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45
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Tan Z, Heemstra JM. High-Throughput Measurement of Small-Molecule Enantiopurity by Using Flow Cytometry. Chembiochem 2018; 19:1853-1857. [PMID: 30126025 DOI: 10.1002/cbic.201800341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Indexed: 12/18/2022]
Abstract
Fluorescence-activated cell sorting (FACS) offers a powerful approach to high-throughput library screening in directed evolution experiments. However, FACS is rarely used in the evolution of stereoselective enzymes, due to the difficulty of designing fluorescence-based assays for measuring enantiopurity. Here, we describe a new FACS-based enantiopurity analysis approach that overcomes these limitations by using enantiomeric DNA biosensors labeled with orthogonal fluorophores. By co-encapsulating the biosensors with a mixture of target enantiomers in microfluidic droplets, we could demonstrate the use of FACS to differentiate between droplets having various levels of target enantiopurity. We envision the utility of this method for high-throughput screening of enantiopurity in the directed evolution of stereoselective enzymes, thereby facilitating the discovery of new asymmetric biocatalysts for the synthesis of pharmaceuticals and other high-value chemicals.
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Affiliation(s)
- Zhesen Tan
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA.,Department of Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
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46
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Herrera BT, Pilicer SL, Anslyn EV, Joyce LA, Wolf C. Optical Analysis of Reaction Yield and Enantiomeric Excess: A New Paradigm Ready for Prime Time. J Am Chem Soc 2018; 140:10385-10401. [PMID: 30059621 DOI: 10.1021/jacs.8b06607] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This Perspective highlights the advances of optical methods for asymmetric reaction discovery. Optical analysis allows for the determination of absolute configuration, enantiomeric excess and reaction yield that is amenable to high-throughput experimentation. Thus, the synthetic organic community is encouraged to incorporate the methods discussed to expedite the development of high-yielding, enantioselective transformations.
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Affiliation(s)
- Brenden T Herrera
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Samantha L Pilicer
- Department of Chemistry , Georgetown University , Washington, D.C. 20057 , United States
| | - Eric V Anslyn
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Leo A Joyce
- Department of Process Research & Development , Merck & Co., Inc. , Rahway , New Jersey 07065 , United States
| | - Christian Wolf
- Department of Chemistry , Georgetown University , Washington, D.C. 20057 , United States
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47
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De los Santos ZA, Joyce LA, Sherer EC, Welch CJ, Wolf C. Optical Chirality Sensing with a Stereodynamic Aluminum Biphenolate Probe. J Org Chem 2018; 84:4639-4645. [DOI: 10.1021/acs.joc.8b01301] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Leo A. Joyce
- Department of Process and Analytical Chemistry, Merck Research Laboratories, Rahway, New Jersey 07065, United States
| | - Edward C. Sherer
- Department of Process and Analytical Chemistry, Merck Research Laboratories, Rahway, New Jersey 07065, United States
| | | | - Christian Wolf
- Department of Chemistry, Georgetown University, Washington, DC 20057, United States
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48
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Lu S, Wang S, Zhao J, Sun J, Yang X. A pH-controlled bidirectionally pure DNA hydrogel: reversible self-assembly and fluorescence monitoring. Chem Commun (Camb) 2018; 54:4621-4624. [PMID: 29671425 DOI: 10.1039/c8cc01603h] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A concept for a pure DNA hydrogel has been demonstrated in which triplex structures act as the core components and are assisted by single strands and artfully designed Y-shaped structures. Typically, the triplex structure which is based on protonated cytosine-guanine-cytosine (C-G·C+) is formed at pH 5.0 and disassembles at pH 7.0, whereas the thymine-adenine-thymine (T-A·T)-based triplex structure is formed at pH 7.0 and disassembles at pH 10.0. Therefore, such triplex DNA structure-based pure DNA hydrogels provide pH-controlled reversible self-assembly of DNA structures with a transition between gel and liquid states. More significantly, the introduction of both a fluorophore (FAM) and a quencher (BHQ1) to the hydrogels provides an innovative method for monitoring the self-assembly and disassembly processes through a fluorescence technology.
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Affiliation(s)
- Shasha Lu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China.
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49
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Practical Application of Aptamer-Based Biosensors in Detection of Low Molecular Weight Pollutants in Water Sources. Molecules 2018; 23:molecules23020344. [PMID: 29414854 PMCID: PMC6017897 DOI: 10.3390/molecules23020344] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 01/08/2023] Open
Abstract
Water pollution has become one of the leading causes of human health problems. Low molecular weight pollutants, even at trace concentrations in water sources, have aroused global attention due to their toxicity after long-time exposure. There is an increased demand for appropriate methods to detect these pollutants in aquatic systems. Aptamers, single-stranded DNA or RNA, have high affinity and specificity to each of their target molecule, similar to antigen-antibody interaction. Aptamers can be selected using a method called Systematic Evolution of Ligands by EXponential enrichment (SELEX). Recent years we have witnessed great progress in developing aptamer selection and aptamer-based sensors for low molecular weight pollutants in water sources, such as tap water, seawater, lake water, river water, as well as wastewater and its effluents. This review provides an overview of aptamer-based methods as a novel approach for detecting low molecular weight pollutants in water sources.
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50
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Ni C, Zha D, Ye H, Hai Y, Zhou Y, Anslyn EV, You L. Dynamic Covalent Chemistry within Biphenyl Scaffolds: Reversible Covalent Bonding, Control of Selectivity, and Chirality Sensing with a Single System. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201711602] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Cailing Ni
- State Key Laboratory of Structural Chemistry; Fujian Institute of Research on the Structure of Matter; Chinese Academy of Sciences; Fuzhou 350002 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Daijun Zha
- State Key Laboratory of Structural Chemistry; Fujian Institute of Research on the Structure of Matter; Chinese Academy of Sciences; Fuzhou 350002 China
| | - Hebo Ye
- State Key Laboratory of Structural Chemistry; Fujian Institute of Research on the Structure of Matter; Chinese Academy of Sciences; Fuzhou 350002 China
- University of Chinese Academy of Sciences; Beijing 100049 China
| | - Yu Hai
- State Key Laboratory of Structural Chemistry; Fujian Institute of Research on the Structure of Matter; Chinese Academy of Sciences; Fuzhou 350002 China
| | - Yuntao Zhou
- State Key Laboratory of Structural Chemistry; Fujian Institute of Research on the Structure of Matter; Chinese Academy of Sciences; Fuzhou 350002 China
| | - Eric V. Anslyn
- Department of Chemistry; The University of Texas at Austin; Austin TX 78712 USA
| | - Lei You
- State Key Laboratory of Structural Chemistry; Fujian Institute of Research on the Structure of Matter; Chinese Academy of Sciences; Fuzhou 350002 China
- University of Chinese Academy of Sciences; Beijing 100049 China
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