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Jiang Y, Huang S, Ma H, Weng J, Du X, Lin Z, Kim J, You W, Zhang H, Wang D, Kim JS, Sun H. RNA-Activatable Near-Infrared Photosensitizer for Cancer Therapy. J Am Chem Soc 2024. [PMID: 39215718 DOI: 10.1021/jacs.4c09470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Photodynamic therapy (PDT) has recently come to the forefront as an exceptionally powerful and promising method for the treatment of cancer. Existing photosensitizers are predominantly engineered to target diverse biomolecules, including proteins, DNA, lipids, and carbohydrates, and have proven to greatly enhance the efficacy or specificity of PDT. However, it is noteworthy that there exists a conspicuous scarcity of photosensitizers specifically designed to target RNAs. Recognizing the crucial and multifaceted roles played by RNAs in various cellular processes and disease states, we have ventured into the development of a novel RNA-targeting photosensitizer, named Se-718, designed specifically for PDT-based cancer therapy. Se-718 has been engineered to exhibit a high molar absorption coefficient in the NIR region, which is crucial for effective PDT. More importantly, Se-718 has demonstrated a distinct RNA-targeting capability, as evidenced through rigorous testing in both circular dichroism and fluorescence experiments. Furthermore, Se-718 has been shown to display both type I and type II photodynamic properties. This unique characteristic enables the efficient killing of cancer cells under a wide range of oxygen conditions, both normoxic (21% O2) and hypoxic (2% O2). The IC50 of Se-718 can be as low as 100 nM, and its light-to-dark toxicity ratio is an impressive 215 times higher, outperforming most photosensitizers currently available. Moreover, in vivo studies conducted with tumor-bearing mice have demonstrated the excellent antitumor effects and high safety profile of Se-718. Considering the outstanding PDT efficacy of Se-718, we are optimistic that the development of RNA-targeting photosensitizers may provide an innovative and highly effective option for cancer therapeutics in the near future.
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Affiliation(s)
- Yin Jiang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Shumei Huang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon ,Hong Kong999077, China
| | - Haiying Ma
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangdong510000, China
| | - Jintao Weng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaomeng Du
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Zhenxin Lin
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Jaewon Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Wenhui You
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Huatang Zhang
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
- Guangdong Laboratory of Chemistry and Fine Chemical Industry Jieyang Center, Jieyang ,Guangdong522000,China
| | - Dongqing Wang
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon ,Hong Kong999077, China
| | - Jong Seung Kim
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Hongyan Sun
- Department of Chemistry and COSDAF (Centre of Super-Diamond and Advanced Films), City University of Hong Kong, 83 Tat Chee Avenue, Kowloon ,Hong Kong999077, China
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2
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Xi Q, Wang SY, Deng XB, Zhang CH. Catalytic Hairpin Assembly-Based Self-Ratiometric Gel Electrophoresis Detection Platform for Reliable Nucleic Acid Analysis. BIOSENSORS 2024; 14:232. [PMID: 38785706 PMCID: PMC11118829 DOI: 10.3390/bios14050232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024]
Abstract
The development of gel electrophoresis-based biodetection assays for point-of-care analysis are highly demanding. In this work, we proposed a ratiometric gel electrophoresis-based biosensing platform by employing catalytic hairpin assembly (CHA) process functions as both the signal output and the signal amplification module. Two types of nucleic acids, DNA and miRNA, are chosen for demonstration. The proposed strategy indeed provides a new paradigm for the design of a portable detection platform and may hold great potential for sensitive diagnoses.
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Affiliation(s)
- Qiang Xi
- Hunan Prevention and Treatment Institute for Occupational Diseases, Affiliated Prevention and Treatment Institute for Occupational Diseases of University of South China, Changsha 410007, China; (Q.X.); (S.-Y.W.)
| | - Si-Yi Wang
- Hunan Prevention and Treatment Institute for Occupational Diseases, Affiliated Prevention and Treatment Institute for Occupational Diseases of University of South China, Changsha 410007, China; (Q.X.); (S.-Y.W.)
| | - Xiao-Bing Deng
- Hunan Prevention and Treatment Institute for Occupational Diseases, Affiliated Prevention and Treatment Institute for Occupational Diseases of University of South China, Changsha 410007, China; (Q.X.); (S.-Y.W.)
| | - Chong-Hua Zhang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, China
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3
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Brannetti S, Gentile S, Chamorro-Garcia A, Barbero L, Del Grosso E, Ricci F. Decorated DNA-Based Scaffolds as Lateral Flow Biosensors. Angew Chem Int Ed Engl 2023; 62:e202313243. [PMID: 37804080 DOI: 10.1002/anie.202313243] [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: 09/06/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/08/2023]
Abstract
Here we develop Lateral Flow Assays (LFAs) that employ as functional elements DNA-based structures decorated with reporter tags and recognition elements. We have rationally re-engineered tile-based DNA tubular structures that can act as scaffolds and can be decorated with recognition elements of different nature (i.e. antigens, aptamers or proteins) and with orthogonal fluorescent dyes. As a proof-of-principle we have developed sandwich and competitive multiplex lateral flow platforms for the detection of several targets, ranging from small molecules (digoxigenin, Dig and dinitrophenol, DNP), to antibodies (Anti-Dig, Anti-DNP and Anti-MUC1/EGFR bispecific antibodies) and proteins (thrombin). Coupling the advantages of functional DNA-based scaffolds together with the simplicity of LFAs, our approach offers the opportunity to detect a wide range of targets with nanomolar sensitivity and high specificity.
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Affiliation(s)
- Simone Brannetti
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Serena Gentile
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Alejandro Chamorro-Garcia
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Luca Barbero
- RBM-Merck an affiliate of Merck KGaA, Via Ribes 1, 10010, Turin, Italy
| | - Erica Del Grosso
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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4
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Liu W, Han Y, Liu M, Chen L, Xu J. Effect of defects on optical and electronic properties of graphene quantum dots: a density functional theory study. RSC Adv 2023; 13:16232-16240. [PMID: 37266493 PMCID: PMC10230513 DOI: 10.1039/d3ra02564k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023] Open
Abstract
The effects of different types of defects (vacancy, Stone-Wales defects, and heteroatom doping) and varying defect concentrations (single and double defects) on the structure, electronic, and optical properties of graphene quantum dots (GQDs) are systematically investigated using time-dependent density functional theory (TD-DFT). The results reveal that most defects induce noticeable structural distortions, with increasing deformation at higher defect concentrations. Compared to pristine GQD model C96 (with a maximum absorption peak at 592 nm), the absorption spectra of 6 defective C96 exhibit blue shifts ranging from 554 to 591 nm, while 12 defective C96 lead to red shifts (598-668 nm). The HOMO-LUMO gaps vary from 0.62 to 2.04 eV (2.10 eV for pristine C96). Quantitative analysis of the absorption spectra and molecular orbital energy levels demonstrate that the electronic and optical properties of defective C96 strongly depend on the types, concentrations, and locations of defects. NTO analysis illustrates that higher electron localization exists in defective C96, which is attributed to the disruption of the original π-conjugation caused by structural distortions and different orbital hybridizations. These findings offer a comprehensive insight into the impact of defects on GQDs and provide valuable guidance for exploiting the unique features of GQDs to expand new applications in various fields.
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Affiliation(s)
- Wei Liu
- Department of Optical Engineering, College of Optical, Mechanical and Electrical Engineering, Zhejiang A&F University Hangzhou Zhejiang 311300 P. R. China
| | - Yaning Han
- Department of Optical Engineering, College of Optical, Mechanical and Electrical Engineering, Zhejiang A&F University Hangzhou Zhejiang 311300 P. R. China
| | - Min Liu
- Department of Optical Engineering, College of Optical, Mechanical and Electrical Engineering, Zhejiang A&F University Hangzhou Zhejiang 311300 P. R. China
| | - Liang Chen
- School of Physical Science and Technology, Ningbo University Ningbo Zhejiang 315211 P. R. China
- Department of Optical Engineering, College of Optical, Mechanical and Electrical Engineering, Zhejiang A&F University Hangzhou Zhejiang 311300 P. R. China
| | - Jing Xu
- Department of Optical Engineering, College of Optical, Mechanical and Electrical Engineering, Zhejiang A&F University Hangzhou Zhejiang 311300 P. R. China
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5
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Zhang P, Ouyang Y, Zhuo Y, Chai Y, Yuan R. Recent Advances in DNA Nanostructures Applied in Sensing Interfaces and Cellular Imaging. Anal Chem 2023; 95:407-419. [PMID: 36625113 DOI: 10.1021/acs.analchem.2c04540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Pu Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yu Ouyang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China.,Institute of Chemistry, Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yaqin Chai
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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6
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Guo S, Sun Y, Li Z. Lysosome Imaging Based on Fluorescent Carbon Dots. Methods Mol Biol 2023; 2566:37-43. [PMID: 36152240 DOI: 10.1007/978-1-0716-2675-7_3] [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] [Indexed: 06/16/2023]
Abstract
Lysosomes play key roles in different cellular processes such as autophagy, phagocytosis, and apoptosis. Lysosomal dysfunction is related to many diseases. Fluorescence lysosome staining strategy is valuable for the researches on the lysosome involvement in different pathological diagnosis. Here we describe fluorescence lysosome staining methods with carbon dots for the identification of lysosomes in living and fixed cells.
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Affiliation(s)
- Shuo Guo
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou University, Zhengzhou, China
| | - Yuanqiang Sun
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou University, Zhengzhou, China
| | - Zhaohui Li
- College of Chemistry, Institute of Analytical Chemistry for Life Science, Zhengzhou University, Zhengzhou, China.
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7
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Xie L, Zheng R, Hu H, Li L. Determination of hypochlorite and bisulfite in water by bifunctional colorimetric sensor based on octupolar conjugated merocyanine dyes. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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8
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Wang W, Shen Y, Wang F, Liu Y, Liu X. Bio-inspired dynamic biomolecule assembling for fine regulation of protein activity. Chem Commun (Camb) 2021; 57:11205-11208. [PMID: 34622901 DOI: 10.1039/d1cc03926a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A versatile approach for the fine control of DNA-based hierarchical assembly via dual stimuli and two assembly strategies is developed. Moreover, with a reasonable design of functional thrombin aptamer structures on the formed DNA nanoassembly, it can achieve precise regulation of thrombin activity.
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Affiliation(s)
- Wenxiao Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China. .,College of Chemistry and Chemical Engineering, Linyi University, Linyi, 276000, P. R. China
| | - Yu Shen
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China.
| | - Fuan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China.
| | - Ying Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China.
| | - Xiaoqing Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China.
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9
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Huo S, Zhou Y, Liao Z, Zhao P, Zou M, Göstl R, Herrmann A. Reversible regulation of metallo-base-pair interactions for DNA dehybridization by ultrasound. Chem Commun (Camb) 2021; 57:7438-7440. [PMID: 34232244 DOI: 10.1039/d1cc02402g] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mechanical force applied by ultrasound in solution leads to the dissociation of DNA metallo-base-pair interactions when these motifs are functionalized with oligodeoxynucleotide sequences of sufficient length. The annealing and force-induced denaturing process is followed by the attachment of distance-sensitive fluorescent probes and is found to be reversible.
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Affiliation(s)
- Shuaidong Huo
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Science, Xiamen University, 361102 Xiamen, China and DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany. and Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Yu Zhou
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany. and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Zhihuan Liao
- Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Science, Xiamen University, 361102 Xiamen, China
| | - Pengkun Zhao
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany. and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Miancheng Zou
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany. and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Robert Göstl
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany.
| | - Andreas Herrmann
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany. and Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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10
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Lu S, Shen J, Fan C, Li Q, Yang X. DNA Assembly-Based Stimuli-Responsive Systems. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100328. [PMID: 34258165 PMCID: PMC8261508 DOI: 10.1002/advs.202100328] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/05/2021] [Indexed: 05/06/2023]
Abstract
Stimuli-responsive designs with exogenous stimuli enable remote and reversible control of DNA nanostructures, which break many limitations of static nanostructures and inspired development of dynamic DNA nanotechnology. Moreover, the introduction of various types of organic molecules, polymers, chemical bonds, and chemical reactions with stimuli-responsive properties development has greatly expand the application scope of dynamic DNA nanotechnology. Here, DNA assembly-based stimuli-responsive systems are reviewed, with the focus on response units and mechanisms that depend on different exogenous stimuli (DNA strand, pH, light, temperature, electricity, metal ions, etc.), and their applications in fields of nanofabrication (DNA architectures, hybrid architectures, nanomachines, and constitutional dynamic networks) and biomedical research (biosensing, bioimaging, therapeutics, and theranostics) are discussed. Finally, the opportunities and challenges for DNA assembly-based stimuli-responsive systems are overviewed and discussed.
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Affiliation(s)
- Shasha Lu
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jianlei Shen
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Chunhai Fan
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
- Institute of Molecular MedicineShanghai Key Laboratory for Nucleic Acid Chemistry and NanomedicineDepartment of UrologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qian Li
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Xiurong Yang
- School of Chemistry and Chemical EngineeringFrontiers Science Center for Transformative MoleculesInstitute of Translational MedicineShanghai Jiao Tong UniversityShanghai200240China
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11
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Yu SY, Ruan YF, Liu YL, Han DM, Zhou H, Zhao WW, Jiang D, Xu JJ, Chen HY. Photocontrolled Nanopipette Biosensor for ATP Gradient Electroanalysis of Single Living Cells. ACS Sens 2021; 6:1529-1535. [PMID: 33847485 DOI: 10.1021/acssensors.1c00463] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Emerging nanopipette tools have demonstrated substantial potential for advanced single-cell analysis, which plays vital roles from fundamental cellular biology to biomedical diagnostics. Highly recyclable nanopipettes with easy and quick regeneration are of special interest for precise and multiple measurements. However, existing recycle strategies are generally plagued by operational complexity and limited efficiency. Light, acting in a noncontact way, should be the ideal external stimulus to address this issue. Herein, we present the photocontrolled nanopipette capable of probing cellular adenosine triphosphate (ATP) gradient at single-cell level with good sensitivity, selectivity, and reversibility, which stems from the use of ATP-specific azobenzene (Azo)-incorporated DNA aptamer strands (AIDAS) and thereby the sensible transduction of variable nanopore size by the ionic currents passing through the aperture. Photoisomerized conformational change of the AIDAS by alternative UV/vis light stimulation ensures its noninvasive regeneration and repeated detection. Inducement and inhibition of the cellular ATP could also be probed by this nanosensor.
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Affiliation(s)
- Si-Yuan Yu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Yi-Fan Ruan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Yi-Li Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - De-Man Han
- Engineering Research Center of Recycling & Comprehensive Utilization of Pharmaceutical and Chemical Waste of Zhejiang Province, Taizhou University, Jiaojiang 318000, China
| | - Hong Zhou
- Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Dechen Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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12
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Kachwala MJ, Smith CW, Nandu N, Yigit MV. Reprogrammable Gel Electrophoresis Detection Assay Using CRISPR-Cas12a and Hybridization Chain Reaction. Anal Chem 2021; 93:1934-1938. [PMID: 33404234 DOI: 10.1021/acs.analchem.0c04949] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hybridization chain reaction (HCR) is a DNA-based target-induced cascade reaction. Due to its unique enzyme-free amplification feature, HCR is often employed for sensing applications. Much like DNA nanostructures that have been designed to respond to a specific stimulus, HCR employs nucleic acids that reconfigure and assemble in the presence of a specific trigger. Despite its standalone capabilities, HCR is highly modular; therefore, it can be advanced and repurposed when coupled with latest discoveries. To this effect, we have developed a gel electrophoresis-based detection approach which combines the signal amplification feature of HCR with the programmability and sensitivity of the CRISPR-Cas12a system. By incorporating CRISPR-Cas12a, we have achieved greater sensitivity and reversed the signal output from TURN OFF to TURN ON. CRISPR-Cas12a also enabled us to rapidly reprogram the assay for the detection of both ssDNA and dsDNA target sequences by replacing a single reaction component in the detection kit. Detection of conserved, both ssDNA and dsDNA, regions of tobacco curly shoot virus (TCSV) and hepatitis B virus (HepBV) genomes is demonstrated with this methodology. This low-cost gel electrophoresis assay can detect as little as 1.5 fmol of the target without any additional target amplification steps and is about 100-fold more sensitive than HCR-alone approach.
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Affiliation(s)
- Mahera J Kachwala
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Christopher W Smith
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Nidhi Nandu
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mehmet V Yigit
- Department of Chemistry, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States.,The RNA Institute, University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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13
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Hossain MN, Ahmad S, Kraatz H. Consecutive Silver(I) Ion Incorporation into Oligonucleotides containing Cytosine‐Cytosine Mispairs. Chempluschem 2020; 86:224-231. [DOI: 10.1002/cplu.202000607] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/25/2020] [Indexed: 12/18/2022]
Affiliation(s)
- M. Nur Hossain
- Department of Physical and Environmental Sciences University of Toronto Scarborough 11265 Military Trail Toronto M1 C 1 A4 Canada
| | - Syed Ahmad
- Department of Physical and Environmental Sciences University of Toronto Scarborough 11265 Military Trail Toronto M1 C 1 A4 Canada
- Department of Chemistry University of Toronto 80 St. George Street Toronto M5S 3H6 Canada
| | - Heinz‐Bernhard Kraatz
- Department of Physical and Environmental Sciences University of Toronto Scarborough 11265 Military Trail Toronto M1 C 1 A4 Canada
- Department of Chemistry University of Toronto 80 St. George Street Toronto M5S 3H6 Canada
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Abstract
In recent years, a diverse set of mechanisms have been developed that allow DNA strands with specific sequences to sense information in their environment and to control material assembly, disassembly, and reconfiguration. These sequences could serve as the inputs and outputs for DNA computing circuits, enabling DNA circuits to act as chemical information processors to program complex behavior in chemical and material systems. This review describes processes that can be sensed and controlled within such a paradigm. Specifically, there are interfaces that can release strands of DNA in response to chemical signals, wavelengths of light, pH, or electrical signals, as well as DNA strands that can direct the self-assembly and dynamic reconfiguration of DNA nanostructures, regulate particle assemblies, control encapsulation, and manipulate materials including DNA crystals, hydrogels, and vesicles. These interfaces have the potential to enable chemical circuits to exert algorithmic control over responsive materials, which may ultimately lead to the development of materials that grow, heal, and interact dynamically with their environments.
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Affiliation(s)
- Dominic Scalise
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rebecca Schulman
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA.,Department of Computer Science, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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15
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16
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He J, Li J, Han Q, Si C, Niu G, Li M, Wang J, Niu J. Photoactive Metal-Organic Framework for the Reduction of Aryl Halides by the Synergistic Effect of Consecutive Photoinduced Electron-Transfer and Hydrogen-Atom-Transfer Processes. ACS APPLIED MATERIALS & INTERFACES 2020; 12:2199-2206. [PMID: 31859478 DOI: 10.1021/acsami.9b13538] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Consecutive photoinduced electron transfer (ConPET) has advantages on overcoming the current energetic limitation of visible-light photoredox catalysis for utilizing the energies of two photons in one catalytic cycle. A heterogeneous approach for radical chain reduction of various aryl bromides and chlorides without adding any cocatalyst is introduced by incorporating polyoxometalates (POMs) and amine catalysts into a naphthalenediimide (NDI)-based polymer. CoW-DPNDI-PYI exhibits high activity in the photocatalytic reduction of aryl halides by the synergistic effects of ConPET and hydrogen-atom-transfer (HAT) processes and an enzyme-mimicking CO2 cycloaddition reaction. The ConPET process with N,N'-bis(4-pyridylmethyl)naphthalenediimide (DPNDI) facilitates effective solar energy conversion. POMs and amine catalysts, as efficient HAT catalysts and electron donors, improve the generation of the ConPET process. The success of this work demonstrates the great application of the synergistic effects of ConPET and HAT processes in heterogeneous photocatalysis C-H arylation.
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Affiliation(s)
- Jiachen He
- Key Laboratory of Polyoxometalate Chemistry of Henan Province, School of Chemistry and Chemical Engineering , Henan University , Kaifeng 475004 , P. R. China
| | - Jie Li
- Key Laboratory of Polyoxometalate Chemistry of Henan Province, School of Chemistry and Chemical Engineering , Henan University , Kaifeng 475004 , P. R. China
| | - Qiuxia Han
- Key Laboratory of Polyoxometalate Chemistry of Henan Province, School of Chemistry and Chemical Engineering , Henan University , Kaifeng 475004 , P. R. China
| | - Chen Si
- Key Laboratory of Polyoxometalate Chemistry of Henan Province, School of Chemistry and Chemical Engineering , Henan University , Kaifeng 475004 , P. R. China
| | - Guiqin Niu
- Key Laboratory of Polyoxometalate Chemistry of Henan Province, School of Chemistry and Chemical Engineering , Henan University , Kaifeng 475004 , P. R. China
| | - Mingxue Li
- Key Laboratory of Polyoxometalate Chemistry of Henan Province, School of Chemistry and Chemical Engineering , Henan University , Kaifeng 475004 , P. R. China
| | - Jingping Wang
- Key Laboratory of Polyoxometalate Chemistry of Henan Province, School of Chemistry and Chemical Engineering , Henan University , Kaifeng 475004 , P. R. China
| | - Jingyang Niu
- Key Laboratory of Polyoxometalate Chemistry of Henan Province, School of Chemistry and Chemical Engineering , Henan University , Kaifeng 475004 , P. R. China
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17
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Wang J, Song Q, Guo X, Cui X, Tan L, Dong L. Precise Cross-Dimensional Regulation of the Structure of a Photoreversible DNA Nanoswitch. Anal Chem 2019; 91:14530-14537. [PMID: 31617350 DOI: 10.1021/acs.analchem.9b03547] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, an accurately and digitally regulated allosteric nanoswitch based on the conformational control of two DNA hairpins was developed. By switching between UV irradiation and blue light conditions, the second molecular beacon (H#2) would bind/separate with a repression sequence (RES) via the introduced PTG molecules (a photosensitive azobenzene derivative), resulting in the target aptamer sequence in the first molecular beacon (H#1) not being able/being able to hold the stem-loop configuration, hence losing/regaining the ability to bind with the target. Importantly, we successfully monitor conformation changes of the nanoswitch by an elegant mathematical model for connecting Ki (the dissociation constant between RES and H#2) with Kd (the overall equilibrium constant of the nanoswitch binding the target), hence realizing "observing" DNA structure across dimensions from "structural visualization" to digitization and, accurately, digitally regulating DNA structure from digitization to "structural visualization".
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Affiliation(s)
- Jing Wang
- College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China.,School of Chemistry and Chemical Engineering , Chongqing University , Chongqing 400044 , China.,Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education , Chongqing University , Chongqing 40004 , China
| | - Qitao Song
- College of Chemistry and Molecular Engineering , Peking University , Beijing 100871 , China.,Peking-Tsinghua Center for Life Sciences , Peking University , 100871 Beijing , China
| | - Xiaogang Guo
- College of Chemistry and Chemical Engineering , Yangtze Normal. University , Chongqing 408100 , China
| | - Xun Cui
- School of Materials Science and Engineering , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Luxi Tan
- School of Chemistry and Chemical Engineering , Chongqing University , Chongqing 400044 , China.,Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education , Chongqing University , Chongqing 40004 , China
| | - Lichun Dong
- School of Chemistry and Chemical Engineering , Chongqing University , Chongqing 400044 , China.,Key Laboratory of Low-grade Energy Utilization Technologies & Systems of the Ministry of Education , Chongqing University , Chongqing 40004 , China
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18
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Wang Y, Tang J, Zhang S, Xu H, Ding T. Light-controlled nanoswitches: from fabrication to photoelectric switching. NANOSCALE 2019; 11:18496-18500. [PMID: 31577320 DOI: 10.1039/c9nr07493g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Plasmon-assisted optical growth significantly improves the controllability of polymerization on the nanoscale, which greatly facilitates the fabrication of nanodevices and their integration. Traditional approaches for nanodevices strongly rely on nanofabrication techniques, which involve complicated multi-steps and expensive instrumentation. Here, we build photoelectric nanoswitches by precisely implanting photoelectric active polymers, polypyrrole, into metallic bowtie nanogaps via charge transfer induced oxidative polymerization, which show conductivity up to 4 μS m-1 with an optical switching response time of ∼50 ms. We further demonstrate their photoelectric switchability with different laser powers, wavelengths and amounts of polypyrrole in the gaps. This plasmon-assisted optical growth strategy not only provides a facile and accurate means to control the polymerization process, but also greatly expedites the fabrication of nanodevices and their integration.
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Affiliation(s)
- Yunxia Wang
- Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education of China, School of Physics and Technology, Wuhan University, Wuhan, 430072 China.
| | - Jibo Tang
- Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education of China, School of Physics and Technology, Wuhan University, Wuhan, 430072 China. and The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Shunping Zhang
- Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education of China, School of Physics and Technology, Wuhan University, Wuhan, 430072 China.
| | - Hongxing Xu
- Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education of China, School of Physics and Technology, Wuhan University, Wuhan, 430072 China.
| | - Tao Ding
- Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education of China, School of Physics and Technology, Wuhan University, Wuhan, 430072 China.
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19
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Fang X, Zheng Y, Duan Y, Liu Y, Zhong W. Recent Advances in Design of Fluorescence-Based Assays for High-Throughput Screening. Anal Chem 2019; 91:482-504. [PMID: 30481456 PMCID: PMC7262998 DOI: 10.1021/acs.analchem.8b05303] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiaoni Fang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yongzan Zheng
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yaokai Duan
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yang Liu
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
| | - Wenwan Zhong
- Department of Chemistry, University of California, Riverside, California 92521, United States
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521, United States
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20
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Dunn KE, Trefzer MA, Johnson S, Tyrrell AM. Towards a Bioelectronic Computer: A Theoretical Study of a Multi-Layer Biomolecular Computing System That Can Process Electronic Inputs. Int J Mol Sci 2018; 19:E2620. [PMID: 30181468 PMCID: PMC6164260 DOI: 10.3390/ijms19092620] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/21/2018] [Accepted: 09/03/2018] [Indexed: 01/06/2023] Open
Abstract
DNA molecular machines have great potential for use in computing systems. Since Adleman originally introduced the concept of DNA computing through his use of DNA strands to solve a Hamiltonian path problem, a range of DNA-based computing elements have been developed, including logic gates, neural networks, finite state machines (FSMs) and non-deterministic universal Turing machines. DNA molecular machines can be controlled using electrical signals and the state of DNA nanodevices can be measured using electrochemical means. However, to the best of our knowledge there has as yet been no demonstration of a fully integrated biomolecular computing system that has multiple levels of information processing capacity, can accept electronic inputs and is capable of independent operation. Here we address the question of how such a system could work. We present simulation results showing that such an integrated hybrid system could convert electrical impulses into biomolecular signals, perform logical operations and take a decision, storing its history. We also illustrate theoretically how the system might be able to control an autonomous robot navigating through a maze. Our results suggest that a system of the proposed type is technically possible but for practical applications significant advances would be required to increase its speed.
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Affiliation(s)
- Katherine E Dunn
- Department of Electronic Engineering, University of York, Heslington, York YO10 5DD, UK.
| | - Martin A Trefzer
- Department of Electronic Engineering, University of York, Heslington, York YO10 5DD, UK.
| | - Steven Johnson
- Department of Electronic Engineering, University of York, Heslington, York YO10 5DD, UK.
| | - Andy M Tyrrell
- Department of Electronic Engineering, University of York, Heslington, York YO10 5DD, UK.
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21
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Ora A, Järvihaavisto E, Zhang H, Auvinen H, Santos HA, Kostiainen MA, Linko V. Cellular delivery of enzyme-loaded DNA origami. Chem Commun (Camb) 2018; 52:14161-14164. [PMID: 27869278 DOI: 10.1039/c6cc08197e] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In this communication, we show that active enzymes can be delivered into HEK293 cells in vitro when they are attached to tubular DNA origami nanostructures. We use bioluminescent enzymes as a cargo and monitor their activity from a cell lysate. The results show that the enzymes stay intact and retain their activity in the transfection process. The method is highly modular, which makes it a compelling candidate for a great variety of delivery applications.
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Affiliation(s)
- Ari Ora
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Erika Järvihaavisto
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Hongbo Zhang
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00790 Helsinki, Finland
| | - Henni Auvinen
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Hélder A Santos
- Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, FI-00790 Helsinki, Finland
| | - Mauri A Kostiainen
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
| | - Veikko Linko
- Biohybrid Materials, Department of Biotechnology and Chemical Technology, Aalto University, P. O. Box 16100, FI-00076 Aalto, Finland.
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22
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Bertucci A, Guo J, Oppmann N, Glab A, Ricci F, Caruso F, Cavalieri F. Probing transcription factor binding activity and downstream gene silencing in living cells with a DNA nanoswitch. NANOSCALE 2018; 10:2034-2044. [PMID: 29323382 DOI: 10.1039/c7nr07814e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Transcription factor DNA binding activity is of pivotal importance in living systems because of its primary involvement in the regulation of genetic machinery. The analysis of transient expression levels of transcription factors in response to a certain cell status is a powerful means for investigating cellular dynamics at the biomolecular level. Herein, a DNA-based molecular switch that enables probing of transcription factor DNA binding activity is directly used in living cells. We demonstrate that the DNA nanoswitch allows for dynamic fluorescence imaging of NF-κB and quantification of downstream gene silencing in real time. The present strategy is based on a functional DNA nanodevice that transduces, through a binding-induced conformational change, the recognition of a specific transcription factor into a fluorescent signal. In addition, stochastic optical resolution microscopy, a super-resolution microscopy technique, is used to track the internalization and intracellular trafficking of the DNA nanodevice with high spatial resolution. Overall, it has been shown that a rationally designed DNA nanodevice can be used to achieve rapid, simple, and cost-effective real-time determination of transcription factor binding activity and downstream gene silencing.
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Affiliation(s)
- Alessandro Bertucci
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, and the Department of Chemical and Biomolecular Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia.
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23
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Kamal A, She Z, Sharma R, Kraatz HB. A study of the interactions of Hg(II) with T-T mispair containing hairpin loops. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.05.058] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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24
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Zhang P, Lin Z, Zhuo Y, Yuan R, Chai Y. Dual microRNAs-Fueled DNA Nanogears: A Case of Regenerated Strategy for Multiple Electrochemiluminescence Detection of microRNAs with Single Luminophore. Anal Chem 2017; 89:1338-1345. [DOI: 10.1021/acs.analchem.6b04402] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Pu Zhang
- Key Laboratory
of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Zongfan Lin
- Key Laboratory
of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ying Zhuo
- Key Laboratory
of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Ruo Yuan
- Key Laboratory
of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yaqin Chai
- Key Laboratory
of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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25
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Zhu X, Chen X, Ban F, Cao Y, Zhao J, Chen G, Li G. The design of a mechanical wave-like DNA nanomachine for the fabrication of a programmable and multifunctional molecular device. Chem Commun (Camb) 2017; 53:10504-10507. [DOI: 10.1039/c7cc05174c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A DNA nanomachine is designed for switching just like a mechanical wave upon binding with an input.
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Affiliation(s)
- Xiaoli Zhu
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Xiaoxia Chen
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Fangfang Ban
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Ya Cao
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Jing Zhao
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
| | - Genxi Li
- Center for Molecular Recognition and Biosensing
- School of Life Sciences
- Shanghai University
- Shanghai 200444
- China
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26
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Peng P, Shi L, Wang H, Li T. A DNA nanoswitch-controlled reversible nanosensor. Nucleic Acids Res 2016; 45:541-546. [PMID: 27899631 PMCID: PMC5314764 DOI: 10.1093/nar/gkw1146] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 10/14/2016] [Accepted: 11/02/2016] [Indexed: 02/07/2023] Open
Abstract
We present a conceptually new reversible nanosensor regulated by a DNA nanoswitch. This system is not only responsive to external stimuli (e.g. ATP) but also can be reversibly switched between ‘OFF’ and ‘ON’ states via toehold mediated strand displacement reactions. It functions like a molecular net woven by DNA to capture or release the target molecules. As a proof-of-principle experiment, ATP is here chosen as the model to demonstrate our new strategy, which holds great promise for applications such as switchable DNA nanomachines and nanocarriers for drug delivery.
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Affiliation(s)
- Pai Peng
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Lili Shi
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Huihui Wang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Tao Li
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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27
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Rossetti M, Ranallo S, Idili A, Palleschi G, Porchetta A, Ricci F. Allosteric DNA nanoswitches for controlled release of a molecular cargo triggered by biological inputs. Chem Sci 2016; 8:914-920. [PMID: 28572901 PMCID: PMC5452262 DOI: 10.1039/c6sc03404g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/03/2016] [Indexed: 12/14/2022] Open
Abstract
A rationally designed new class of DNA-based nanoswitches allosterically regulated by specific biological targets, antibodies and transcription factors, can load and release a molecular cargo in a controlled fashion.
Here we demonstrate the rational design of a new class of DNA-based nanoswitches which are allosterically regulated by specific biological targets, antibodies and transcription factors, and are able to load and release a molecular cargo (i.e. doxorubicin) in a controlled fashion. In our first model system we rationally designed a stem-loop DNA-nanoswitch that adopts two mutually exclusive conformations: a “Load” conformation containing a doxorubicin-intercalating domain and a “Release” conformation containing a duplex portion recognized by a specific transcription-factor (here Tata Binding Protein). The binding of the transcription factor pushes this conformational equilibrium towards the “Release” state thus leading to doxorubicin release from the nanoswitch. In our second model system we designed a similar stem-loop DNA-nanoswitch for which conformational change and subsequent doxorubicin release can be triggered by a specific antibody. Our approach augments the current tool kit of smart drug release mechanisms regulated by different biological inputs.
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Affiliation(s)
- Marianna Rossetti
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Simona Ranallo
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Andrea Idili
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Giuseppe Palleschi
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Alessandro Porchetta
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
| | - Francesco Ricci
- Chemistry Department , University of Rome Tor Vergata , Via della Ricerca Scientifica , Rome 00133 , Italy . ;
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28
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Jeong H, Ranallo S, Rossetti M, Heo J, Shin J, Park K, Ricci F, Hong J. Electronic Activation of a DNA Nanodevice Using a Multilayer Nanofilm. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:5572-5578. [PMID: 27577954 DOI: 10.1002/smll.201601273] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/20/2016] [Indexed: 06/06/2023]
Abstract
A method to control activation of a DNA nanodevice by supplying a complementary DNA (cDNA) strand from an electro-responsive nanoplatform is reported. To develop functional nanoplatform, hexalayer nanofilm is precisely designed by layer-by-layer assembly technique based on electrostatic interaction with four kinds of materials: Hydrolyzed poly(β-amino ester) can help cDNA release from the film. A cDNA is used as a key building block to activate DNA nanodevice. Reduced graphene oxides (rGOs) and the conductive polymer provide conductivity. In particular, rGOs efficiently incorporate a cDNA in the film via several interactions and act as a barrier. Depending on the types of applied electronic stimuli (reductive and oxidative potentials), a cDNA released from the electrode can quantitatively control the activation of DNA nanodevice. From this report, a new system is successfully demonstrated to precisely control DNA release on demand. By applying more advanced form of DNA-based nanodevices into multilayer system, the electro-responsive nanoplatform will expand the availability of DNA nanotechnology allowing its improved application in areas such as diagnosis, biosensing, bioimaging, and drug delivery.
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Affiliation(s)
- Hyejoong Jeong
- Laboratory of Functional Nano Films, School of Chemical Engineering and Material Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Simona Ranallo
- Chemistry Department, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - Marianna Rossetti
- Chemistry Department, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy
| | - Jiwoong Heo
- Laboratory of Functional Nano Films, School of Chemical Engineering and Material Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jooseok Shin
- Laboratory of Organic Materials, School of Chemical Engineering and Material Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Kwangyong Park
- Laboratory of Organic Materials, School of Chemical Engineering and Material Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Francesco Ricci
- Chemistry Department, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, 00133, Italy.
| | - Jinkee Hong
- Laboratory of Functional Nano Films, School of Chemical Engineering and Material Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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29
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Kim E, Liu Y, Ben-Yoav H, Winkler TE, Yan K, Shi X, Shen J, Kelly DL, Ghodssi R, Bentley WE, Payne GF. Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels. Adv Healthc Mater 2016; 5:2595-2616. [PMID: 27616350 PMCID: PMC5485850 DOI: 10.1002/adhm.201600516] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/26/2016] [Indexed: 12/14/2022]
Abstract
The Information Age transformed our lives but it has had surprisingly little impact on the way chemical information (e.g., from our biological world) is acquired, analyzed and communicated. Sensor systems are poised to change this situation by providing rapid access to chemical information. This access will be enabled by technological advances from various fields: biology enables the synthesis, design and discovery of molecular recognition elements as well as the generation of cell-based signal processors; physics and chemistry are providing nano-components that facilitate the transmission and transduction of signals rich with chemical information; microfabrication is yielding sensors capable of receiving these signals through various modalities; and signal processing analysis enhances the extraction of chemical information. The authors contend that integral to the development of functional sensor systems will be materials that (i) enable the integrative and hierarchical assembly of various sensing components (for chemical recognition and signal transduction) and (ii) facilitate meaningful communication across modalities. It is suggested that stimuli-responsive self-assembling biopolymers can perform such integrative functions, and redox provides modality-spanning communication capabilities. Recent progress toward the development of electrochemical sensors to manage schizophrenia is used to illustrate the opportunities and challenges for enlisting sensors for chemical information processing.
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Affiliation(s)
- Eunkyoung Kim
- Institute for Biosystems and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Yi Liu
- Institute for Biosystems and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Hadar Ben-Yoav
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Thomas E Winkler
- Institute for Systems Research, University of Maryland, College Park, MD, 20742, USA
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, 20742, USA
| | - Kun Yan
- School of Resource and Environmental Science, Hubei Biomass-Resource Chemistry Environmental Biotechnology Key Laboratory, Wuhan University, Wuhan, 430079, China
| | - Xiaowen Shi
- School of Resource and Environmental Science, Hubei Biomass-Resource Chemistry Environmental Biotechnology Key Laboratory, Wuhan University, Wuhan, 430079, China
| | - Jana Shen
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD, 21201, USA
| | - Deanna L Kelly
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, MD, 21228, USA
| | - Reza Ghodssi
- Institute for Systems Research, University of Maryland, College Park, MD, 20742, USA
- Department of Electrical and Computer Engineering, University of Maryland, College Park, MD, 20742, USA
| | - William E Bentley
- Institute for Biosystems and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Gregory F Payne
- Institute for Biosystems and Biotechnology Research, University of Maryland, College Park, MD, 20742, USA.
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA.
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della Sala F, Chen JLY, Ranallo S, Badocco D, Pastore P, Ricci F, Prins LJ. Reversible Electrochemical Modulation of a Catalytic Nanosystem. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Flavio della Sala
- Department of Chemical Sciences; University of Padova; Via Marzolo 1 35131 Padova Italy
| | - Jack L.-Y. Chen
- Department of Chemical Sciences; University of Padova; Via Marzolo 1 35131 Padova Italy
| | - Simona Ranallo
- Chemistry Department; University of Rome Tor Vergata; Via della Ricerca Scientifica 00133 Rome Italy
| | - Denis Badocco
- Department of Chemical Sciences; University of Padova; Via Marzolo 1 35131 Padova Italy
| | - Paolo Pastore
- Department of Chemical Sciences; University of Padova; Via Marzolo 1 35131 Padova Italy
| | - Francesco Ricci
- Chemistry Department; University of Rome Tor Vergata; Via della Ricerca Scientifica 00133 Rome Italy
| | - Leonard J. Prins
- Department of Chemical Sciences; University of Padova; Via Marzolo 1 35131 Padova Italy
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Della Sala F, Chen JLY, Ranallo S, Badocco D, Pastore P, Ricci F, Prins LJ. Reversible Electrochemical Modulation of a Catalytic Nanosystem. Angew Chem Int Ed Engl 2016; 55:10737-40. [PMID: 27468981 DOI: 10.1002/anie.201605309] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Indexed: 12/21/2022]
Abstract
A catalytic system based on monolayer-functionalized gold nanoparticles (Au NPs) that can be electrochemically modulated and reversibly activated is reported. The catalytic activity relies on the presence of metal ions (Cd(2+) and Cu(2+) ), which can be complexed by the nanoparticle-bound monolayer. This activates the system towards the catalytic cleavage of 2-hydroxypropyl-p-nitrophenyl phosphate (HPNPP), which can be monitored by UV/Vis spectroscopy. It is shown that Cu(2+) metal ions can be delivered to the system by applying an oxidative potential to an electrode on which Cu(0) was deposited. By exploiting the different affinity of Cd(2+) and Cu(2+) ions for the monolayer, it was also possible to upregulate the catalytic activity after releasing Cu(2+) from an electrode into a solution containing Cd(2+) . Finally, it is shown that the activity of this supramolecular nanosystem can be reversibly switched on or off by oxidizing/reducing Cu/Cu(2+) ions under controlled conditions.
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Affiliation(s)
- Flavio Della Sala
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Jack L-Y Chen
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Simona Ranallo
- Chemistry Department, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Denis Badocco
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Paolo Pastore
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy
| | - Francesco Ricci
- Chemistry Department, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy.
| | - Leonard J Prins
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131, Padova, Italy.
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Liu Z, Liu Y, Kim E, Bentley WE, Payne GF. Electrochemical Probing through a Redox Capacitor To Acquire Chemical Information on Biothiols. Anal Chem 2016; 88:7213-21. [PMID: 27385047 PMCID: PMC4962791 DOI: 10.1021/acs.analchem.6b01394] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
The
acquisition of chemical information is a critical need for
medical diagnostics, food/environmental monitoring, and national security.
Here, we report an electrochemical information processing approach
that integrates (i) complex electrical inputs/outputs, (ii) mediators
to transduce the electrical I/O into redox signals that can actively
probe the chemical environment, and (iii) a redox capacitor that manipulates
signals for information extraction. We demonstrate the capabilities
of this chemical information processing strategy using biothiols because
of the emerging importance of these molecules in medicine and because
their distinct chemical properties allow evaluation of hypothesis-driven
information probing. We show that input sequences can be tailored
to probe for chemical information both qualitatively (step inputs
probe for thiol-specific signatures) and quantitatively. Specifically,
we observed picomolar limits of detection and linear responses to
concentrations over 5 orders of magnitude (1 pM–0.1 μM).
This approach allows the capabilities of signal processing to be extended
for rapid, robust, and on-site analysis of chemical information.
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Affiliation(s)
- Zhengchun Liu
- Department of Biomedical Engineering, School of Geosciences and Info-Physics, Central South University , Changsha 410083, People's Republic of China.,Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Yi Liu
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Eunkyoung Kim
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - William E Bentley
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research and Fischell Department of Bioengineering, University of Maryland , College Park, Maryland 20742, United States
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Dunn KE, Trefzer MA, Johnson S, Tyrrell AM. Assessing the potential of surface-immobilized molecular logic machines for integration with solid state technology. Biosystems 2016; 146:3-9. [PMID: 27208444 DOI: 10.1016/j.biosystems.2016.05.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/12/2016] [Accepted: 05/12/2016] [Indexed: 01/22/2023]
Abstract
Molecular computation with DNA has great potential for low power, highly parallel information processing in a biological or biochemical context. However, significant challenges remain for the field of DNA computation. New technology is needed to allow multiplexed label-free readout and to enable regulation of molecular state without addition of new DNA strands. These capabilities could be provided by hybrid bioelectronic systems in which biomolecular computing is integrated with conventional electronics through immobilization of DNA machines on the surface of electronic circuitry. Here we present a quantitative experimental analysis of a surface-immobilized OR gate made from DNA and driven by strand displacement. The purpose of our work is to examine the performance of a simple representative surface-immobilized DNA logic machine, to provide valuable information for future work on hybrid bioelectronic systems involving DNA devices. We used a quartz crystal microbalance to examine a DNA monolayer containing approximately 5×10(11)gatescm(-2), with an inter-gate separation of approximately 14nm, and we found that the ensemble of gates took approximately 6min to switch. The gates could be switched repeatedly, but the switching efficiency was significantly degraded on the second and subsequent cycles when the binding site for the input was near to the surface. Otherwise, the switching efficiency could be 80% or better, and the power dissipated by the ensemble of gates during switching was approximately 0.1nWcm(-2), which is orders of magnitude less than the power dissipated during switching of an equivalent array of transistors. We propose an architecture for hybrid DNA-electronic systems in which information can be stored and processed, either in series or in parallel, by a combination of molecular machines and conventional electronics. In this architecture, information can flow freely and in both directions between the solution-phase and the underlying electronics via surface-immobilized DNA machines that provide the interface between the molecular and electronic domains.
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Affiliation(s)
- Katherine E Dunn
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK.
| | - Martin A Trefzer
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK
| | - Steven Johnson
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK
| | - Andy M Tyrrell
- Department of Electronics, University of York, Heslington, York YO10 5DD, UK
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