1
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Olave B. DNA nanotechnology in ionic liquids and deep eutectic solvents. Crit Rev Biotechnol 2024; 44:941-961. [PMID: 37518062 DOI: 10.1080/07388551.2023.2229950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 08/01/2023]
Abstract
Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.
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Affiliation(s)
- Beñat Olave
- University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
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2
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Li Z, Duan S, Liu B. Freezing Functional Nucleic Acids: From Molecular Reactions to Surface Immobilization. Chembiochem 2024:e202400416. [PMID: 38979890 DOI: 10.1002/cbic.202400416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 07/10/2024]
Abstract
Biochemical reactions are typically slowed down by decreasing temperature. However, accelerated reaction kinetics have been observed for a long time. More recent examples have highlighted the unique role of freezing in fabricating supermaterials, degrading environmental contaminants, and accelerating bioreactions. Functional nucleic acids are DNA or RNA oligonucleotides with versatile properties, including target recognition, catalysis, and molecular co4mputing. In this review, we discuss the current observations and understanding of freezing-facilitated reactions involving functional nucleic acids. Molecular reactions such as ligation/conjugation, cleavage, and hybridization are discussed. Moreover, freezing-induced DNA-nanoparticle conjugations are introduced. Then, we describe our effect in immobilizing DNA on bulk surfaces. Finally, we address some critical questions and research opportunities in the field.
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Affiliation(s)
- Zhenglian Li
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Siyi Duan
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Biwu Liu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
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3
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Wang J, Chang Y, Liu M. Proximity-Dependent Activation of Split DNAzyme Kinase. Chembiochem 2024:e202400368. [PMID: 38954271 DOI: 10.1002/cbic.202400368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/15/2024] [Accepted: 07/02/2024] [Indexed: 07/04/2024]
Abstract
Binary (also known as split) nucleic acid enzymes have emerged as novel tools in biosensors. We report a new split strategy to split the DNAzyme kinase into two independent and non-functional fragments, denoted Dk1sub and Dk1enz. In the presence of the specific target, their free ends are brought sufficiently close to interact with each other without the formation of Watson-Crick base pairings between Dk1sub and Dk1enz, thus allowing the DNA phosphorylation reaction. We term this approach proximity-dependent activation of split DNAzyme kinase (ProxSDK). The utility of ProxSDK is demonstrated by engineering a biosensing system that is capable of measuring specific DNA-protein interactions. We envision that the approach described herein will find useful applications in biosensing, imaging, and clinical diagnosis.
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Affiliation(s)
- Jiayi Wang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian POCT Laboratory, Dalian University of Technology, Dalian, 116024, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian POCT Laboratory, Dalian University of Technology, Dalian, 116024, China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian POCT Laboratory, Dalian University of Technology, Dalian, 116024, China
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4
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Chang T, Li G, Chang D, Amini R, Zhu X, Zhao T, Gu J, Li Z, Li Y. An RNA-Cleaving DNAzyme That Requires an Organic Solvent to Function. Angew Chem Int Ed Engl 2023; 62:e202310941. [PMID: 37648674 DOI: 10.1002/anie.202310941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Engineering functional nucleic acids that are active under unusual conditions will not only reveal their hidden abilities but also lay the groundwork for pursuing them for unique applications. Although many DNAzymes have been derived to catalyze diverse chemical reactions in aqueous solutions, no prior study has been set up to purposely derive DNAzymes that require an organic solvent to function. Herein, we utilized in vitro selection to isolate RNA-cleaving DNAzymes from a random-sequence DNA pool that were "compelled" to accept 35 % dimethyl sulfoxide (DMSO) as a cosolvent, via counter selection in a purely aqueous solution followed by positive selection in the same solution containing 35 % DMSO. This experiment led to the discovery of a new DNAzyme that requires 35 % DMSO for its catalytic activity and exhibits drastically reduced activity without DMSO. This DNAzyme also requires divalent metal ions for catalysis, and its activity is enhanced by monovalent ions. A minimized, more efficient DNAzyme was also derived. This work demonstrates that highly functional, organic solvent-dependent DNAzymes can be isolated from random-sequence DNA libraries via forced in vitro selection, thus expanding the capability and potential utility of catalytic DNA.
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Affiliation(s)
- Tianjun Chang
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Guangping Li
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Ryan Amini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Xiaoni Zhu
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Tongqian Zhao
- School of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Zhongping Li
- Institute of Environmental Science, Shanxi University, Taiyuan, 030006, China
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
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5
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Zhou Q, Zhang G, Wu Y, Zhang Q, Liu Y, Chang Y, Liu M. In Vitro Selection of M 2+-Independent, Fast-Responding Acidic Deoxyribozymes for Bacterial Detection. J Am Chem Soc 2023; 145:21370-21377. [PMID: 37683187 DOI: 10.1021/jacs.3c06155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
We report on the first efforts to isolate acidic RNA-cleaving DNAzymes (aRCDs) from a random-sequence DNA pool by in vitro selection that are activated by a microbe Escherichia coli (E. coli), at pH 5.3. Importantly, these E. coli-responsive aRCDs only require monovalent metal ions as cofactors for cleaving a fluorogenic chimeric DNA/RNA substrate. Such characteristics can be used to efficiently protect RCDs from both intrinsic chemical instability and external enzymatic degradation. One remarkable DNAzyme, aRCD-EC1, is specific for E. coli, and its target is likely a protein. Furthermore, truncated aRCD-EC1 had significantly improved catalytic activity with an observed rate constant (kobs) of 1.18 min-1, making it the fastest bacteria-responding RCD reported to date. Clinical evaluation of this aRCD-based fluorescent assay using 40 patient urine samples demonstrated a diagnostic sensitivity of 100% and a specificity of 100% at a total analysis time of 50 min without a bacterial culture. This work can expand the repertoire of DNAzymes that are active under nonphysiological conditions, thus facilitating the development of diverse DNAzyme-based biosensors in clinical diagnosis.
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Affiliation(s)
- Qinbin Zhou
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
| | - Guangxiao Zhang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
| | - Yunping Wu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
| | - Qiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yi Liu
- Department of Neurology, Dalian Municipal Central Hospital Affiliated Hospital of Dalian Medical University, Dalian 116033, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
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Huang R, Shu B. Editorial: Enzyme-based theranostics. Front Bioeng Biotechnol 2023; 11:1280647. [PMID: 37711447 PMCID: PMC10497944 DOI: 10.3389/fbioe.2023.1280647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/16/2023] Open
Affiliation(s)
- Ru Huang
- State Key Laboratory of Digital Medical Engineering, School of Biomedical Engineering, Hainan University, Haikou, China
- Key Laboratory of Biomedical Engineering of Hainan Province, One Health Institute, Hainan University, Haikou, China
| | - Bowen Shu
- Dermatology Hospital, Southern Medical University, Guangzhou, China
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7
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Cao X, Chen C, Zhu Q. Biosensors based on functional nucleic acids and isothermal amplification techniques. Talanta 2023; 253:123977. [PMID: 36201957 DOI: 10.1016/j.talanta.2022.123977] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 12/13/2022]
Abstract
In the past few years, with the in-depth research of functional nucleic acids and isothermal amplification techniques, their applications in the field of biosensing have attracted great interest. Since functional nucleic acids have excellent flexibility and convenience in their structural design, they have significant advantages as recognition elements in biosensing. At the same time, isothermal amplification techniques have higher amplification efficiency, so the combination of functional nucleic acids and isothermal amplification techniques can greatly promote the widespread application of biosensors. For the purpose of further improving the performance of biosensors, this review introduces several widely used functional nucleic acids and isothermal amplification techniques, as well as their classification, basic principles, application characteristics, and summarizes their important applications in the field of biosensing. We hope to provide some references for the design and construction of new tactics to enhance the detection sensitivity and detection range of biosensing.
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Affiliation(s)
- Xiuen Cao
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, 410013, Hunan, China.
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An RNA-cleaving threose nucleic acid enzyme capable of single point mutation discrimination. Nat Chem 2022; 14:350-359. [PMID: 34916596 DOI: 10.1038/s41557-021-00847-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 10/25/2021] [Indexed: 01/19/2023]
Abstract
Threose nucleic acid has been considered a potential evolutionary progenitor of RNA because of its chemical simplicity, base pairing properties and capacity for higher-order functions such as folding and specific ligand binding. Here we report the in vitro selection of RNA-cleaving threose nucleic acid enzymes. One such enzyme, Tz1, catalyses a site-specific RNA-cleavage reaction with an observed pseudo first-order rate constant (kobs) of 0.016 min-1. The catalytic activity of Tz1 is maximal at 8 mM Mg2+ and remains relatively constant from pH 5.3 to 9.0. Tz1 preferentially cleaves a mutant epidermal growth factor receptor RNA substrate with a single point substitution, while leaving the wild-type intact. We demonstrate that Tz1 mediates selective gene silencing of the mutant epidermal growth factor receptor in eukaryotic cells. The identification of catalytic threose nucleic acids provides further experimental support for threose nucleic acid as an ancestral genetic and functional material. The demonstration of Tz1 mediating selective knockdown of intracellular RNA suggests that functional threose nucleic acids could be developed for future biomedical applications.
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Ma L, Huang Z, Liu J. Selection of a self-cleaving ribozyme activated in a chemically and thermally denaturing environment. Chem Commun (Camb) 2021; 57:7641-7644. [PMID: 34250983 DOI: 10.1039/d1cc03102c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A new self-cleaving ribozyme was obtained from in vitro selection, displaying site-specific cleavage activity under denaturing conditions, such as high temperatures up to 95 °C, and denaturing solvents (20 M formamide). Adding salt such as Mg2+ also inhibited its activity. The conserved ribozyme sequence was found in the genome of several extremophiles, suggesting its potential biological relevance. This study provides an example of a ribozyme working under exotic conditions, which may expand the application of ribozymes in non-biological environments.
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Affiliation(s)
- Lingzi Ma
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.
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Kaddour H, Lucchi H, Hervé G, Vergne J, Maurel MC. Kinetic Study of the Avocado Sunblotch Viroid Self-Cleavage Reaction Reveals Compensatory Effects between High-Pressure and High-Temperature: Implications for Origins of Life on Earth. BIOLOGY 2021; 10:720. [PMID: 34439952 PMCID: PMC8389264 DOI: 10.3390/biology10080720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/23/2021] [Accepted: 07/25/2021] [Indexed: 11/17/2022]
Abstract
A high pressure apparatus allowing one to study enzyme kinetics under pressure was used to study the self-cleavage activity of the avocado sunblotch viroid. The kinetics of this reaction were determined under pressure over a range up to 300 MPa (1-3000 bar). It appears that the initial rate of this reaction decreases when pressure increases, revealing a positive ΔV≠ of activation, which correlates with the domain closure accompanying the reaction and the decrease of the surface of the viroid exposed to the solvent. Although, as expected, temperature increases the rate of the reaction whose energy of activation was determined, it appeared that it does not significantly influence the ΔV≠ of activation and that pressure does not influence the energy of activation. These results provide information about the structural aspects or this self-cleavage reaction, which is involved in the process of maturation of this viroid. The behavior of ASBVd results from the involvement of the hammerhead ribozyme present at its catalytic domain, indeed a structural motif is very widespread in the ancient and current RNA world.
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Affiliation(s)
- Hussein Kaddour
- Department of pharmacology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA;
| | - Honorine Lucchi
- Société PYMABS, 5 rue Henri Auguste Desbyeres, 91000 Évry-Courcouronnes, France;
| | - Guy Hervé
- Laboratoire BIOSIPE, Institut de biologie Paris-Seine, Sorbonne Université, 7 quai Saint-Bernard, 75005 Paris, France;
| | - Jacques Vergne
- Institut de Systématique, Evolution, Biodiversité, (ISYEB), Sorbonne Université, Museum National d’Histoire Naturelle, CNRS, EPHE, F 75005 Paris, France;
| | - Marie-Christine Maurel
- Institut de Systématique, Evolution, Biodiversité, (ISYEB), Sorbonne Université, Museum National d’Histoire Naturelle, CNRS, EPHE, F 75005 Paris, France;
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