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Singh D, Gupta GD, Gupta N, Verma P, Dey A, Kaur S, Kumar A, Raj N. A Critical Appraisal of Functionalized 2-Dimensional Carbon-Based Nanomaterials for Drug Delivery Applications. RECENT PATENTS ON NANOTECHNOLOGY 2024; 18:479-493. [PMID: 37702173 DOI: 10.2174/1872210518666230911150337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 06/12/2023] [Accepted: 07/17/2023] [Indexed: 09/14/2023]
Abstract
The development of an efficient and innovative drug delivery system is essential to improve the pharmacological parameters of the medicinal compound or drug. The technique or manner used to improve the pharmacological parameters plays a crucial role in the delivery system. In the current scenario, various drug delivery systems are available where nanotechnology has firmly established itself in the field of drug delivery. One of the most prevalent elements is carbon with its allotropic modifications such as graphene-based nanomaterials, carbon nanotubes, carbon dots, and carbon fullerenes, these nanomaterials offer notable physiochemical and biochemical properties for the delivery applications due to their smaller size, surface area, and ability to interact with the cells or tissues. The exceptional physicochemical properties of carbon-based 2D nanomaterials, such as graphene and carbon nanotubes, make them attractive candidates for drug delivery systems. These nanomaterials offer a large surface area, high drug loading capacity, and tunable surface chemistry, enabling efficient encapsulation, controlled release, and targeted delivery of therapeutic agents. These properties of the nanomaterials can be exploited for drug delivery applications, like assisting the target delivery of drugs and aiding combination molecular imaging. This review emphasizes on the recent patents on 2D carbon-based nanomaterial and their role in drug delivery systems. Carbon-based 2D nanomaterials present a wealth of opportunities for advanced drug delivery systems. Their exceptional properties and versatility offers great potential in improving therapeutic efficacy, minimizing side effects, and enabling personalized medicine and the recent patents on 2D nanomaterial.
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Affiliation(s)
- Dilpreet Singh
- University Institute of Pharma Sciences, Chandigarh University, Gharuan, Mohali. 140413, India
| | - G D Gupta
- Department of Pharmaceutical Sciences, ISF College of Pharmacy, Moga, Punjab, 142001, India
| | - Nimish Gupta
- Department of Pharmaceutical Sciences, ISF College of Pharmacy, Moga, Punjab, 142001, India
| | - Princi Verma
- Department of Pharmaceutical Sciences, ISF College of Pharmacy, Moga, Punjab, 142001, India
| | - Abhisek Dey
- Department of Pharmaceutical Sciences, ISF College of Pharmacy, Moga, Punjab, 142001, India
| | - Simranjeet Kaur
- Department of Pharmaceutical Sciences, ISF College of Pharmacy, Moga, Punjab, 142001, India
| | - Akshay Kumar
- Department of Pharmaceutical Sciences, ISF College of Pharmacy, Moga, Punjab, 142001, India
| | - Namandeep Raj
- Department of Pharmaceutical Sciences, ISF College of Pharmacy, Moga, Punjab, 142001, India
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Alarcón-Correa M, Kilwing L, Peter F, Liedl T, Fischer P. Platinum-DNA Origami Hybrid Structures in Concentrated Hydrogen Peroxide. Chemphyschem 2023; 24:e202300294. [PMID: 37640688 DOI: 10.1002/cphc.202300294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
The DNA origami technique allows fast and large-scale production of DNA nanostructures that stand out with an accurate addressability of their anchor points. This enables the precise organization of guest molecules on the surfaces and results in diverse functionalities. However, the compatibility of DNA origami structures with catalytically active matter, a promising pathway to realize autonomous DNA machines, has so far been tested only in the context of bio-enzymatic activity, but not in chemically harsh reaction conditions. The latter are often required for catalytic processes involving high-energy fuels. Here, we provide proof-of-concept data showing that DNA origami structures are stable in 5 % hydrogen peroxide solutions over the course of at least three days. We report a protocol to couple these to platinum nanoparticles and show catalytic activity of the hybrid structures. We suggest that the presented hybrid structures are suitable to realize catalytic nanomachines combined with precisely engineered DNA nanostructures.
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Affiliation(s)
- Mariana Alarcón-Correa
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, 69120, Heidelberg, Germany
| | - Luzia Kilwing
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Florian Peter
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, 69120, Heidelberg, Germany
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Peer Fischer
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120, Heidelberg, Germany
- Institute for Molecular Systems Engineering and Advanced Materials, Heidelberg University, INF 225, 69120, Heidelberg, Germany
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3
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Zhao S, Jia Y, Wang A, Yang J, Yang L. Dual-mode DNA walker-based optical fiber biosensor for ultrasensitive detection of microRNAs. Biosens Bioelectron 2023; 239:115613. [PMID: 37607447 DOI: 10.1016/j.bios.2023.115613] [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: 04/29/2023] [Revised: 08/06/2023] [Accepted: 08/17/2023] [Indexed: 08/24/2023]
Abstract
We present a novel dual-mode DNA-walker based optical fiber biosensor (DMDW-Opt biosensor) for sensitive assay of micro-RNAs in bio-samples. In the sensor system, we develop a new strategy for the cascade amplification, DNA-walker/rolling cycle amplification (RCA), by the use of the residue track of the walker. The strategy can significantly improve the response of the sensor and avoid any tedious operation procedure. Dual-mode readouts, i.e., fluorescence and chemiluminescence, are measured independently without interfering with each other to achieve reliable and accurate analysis. Optical fibers with the surface modified by gold nanoparticles are utilized as the support for fabrication of the sensor, which would be benefit for developing miniaturized and portable sensing devices. The performance of the proposed method is evaluated by using micro-RNAs (MiR-155 and MiR-21) as the analytical target. The method is successfully applied for accurate determination of micoRNAs in human serum and MCF-7 cells. Our method can perform sensitive assays of MiR-155 with limit-of-detection as low as 97.72 fM and 11.22 fM, MiR-21 with limit-of-detection as low as 107.15 fM and 8.32 fM for the fluorescence- and the chemiluminescence-readout respectively, and the biosensor exhibits excellent specificity, reproducibility and storage stability, indicating its valuable potential applications for sensing trace-amount targets in complicated real samples.
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Affiliation(s)
- Siqi Zhao
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Yaxue Jia
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Anping Wang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Jinlan Yang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China
| | - Li Yang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province, 130024, China.
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4
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Sun LZ, Ying YJ. Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks. NANOSCALE 2023; 15:15794-15809. [PMID: 37740362 DOI: 10.1039/d3nr03747a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
DNA nanorobots have garnered increasing attention in recent years due to their unique advantages of modularity and algorithm simplicity. To accomplish specific tasks in complex environments, various walking strategies are required for the DNA legs of the nanorobot. In this paper, we employ computational simulations to investigate a well-designed DNA-legged nanorobot moving along a nanopore-based track on a planar membrane. The nanorobot consists of a large nanoparticle as the robot core and three single-stranded DNAs (ssDNAs) as the robot legs. The nanopores linearly embedded in the membrane serve as the toeholds for the robot legs. A charge gradient along the pore distribution mainly powers the activation of the nanorobot. The nanorobot can move in two modes: a walking mode, where the robot legs sequentially enter the nanopores, and a jumping mode, where the robot legs may skip a nanopore to reach the next one. Moreover, we observe that the moving dynamics of the nanorobot on the nanopore-based tracks depends on pore-pore distance, pore charge gradient, external voltage, and leg length.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Yao-Jun Ying
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
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Ye T, Deng B, Bai L, Luo X, Yuan M, Cao H, Hao L, Wu X, Yin F, Li Z, Xu F. Butanol accelerated entropy-driven DNA walking machine for rapid and ultrasensitive determination of alkaline phosphatase activity. Talanta 2023; 265:124879. [PMID: 37392708 DOI: 10.1016/j.talanta.2023.124879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/03/2023] [Accepted: 06/22/2023] [Indexed: 07/03/2023]
Abstract
Alkaline phosphatase (ALP) as an important biomarker as well as an index for the pasteurization degree of dairy food. However, there is a dilemma between the sensitivity and time-cost of ALP determination based on nucleic acid amplification approach. Herein, an ultrasensitive and rapid detection method for the ALP assay was developed based on entropy-driven DNA machine. In our design, the ALP catalyzed dephosphorylation of detection probe, which inhibited the digestion effect of lambda exonuclease. The remaining probe as a linker to tether the walking strand proximity to the surface of track strand modified gold nanoparticle, activating entropy-driven DNA machine. Accompany with walking strand moving, a large amount of assembled dye-labelled strand dissociated from gold nanoparticle with fluorescence recovery. More importantly, to further improve the walking efficiency, butanol was introduced to accelerated the signal amplification at interface, which short the incubation time from several hours to 5 min. Under the optimum condition, the change of fluorescence intensity was proportion to the concentration of ALP in the range from 0.05 U L-1 to 5 U L-1 with an ultralow limit of detection of 2.07 × 10-3 U L-1 was achieved, which is superior to other reported methods. Furthermore, the proposed method also successfully applied for the spiked milk sample assay with satisfactory recovery in the range of 98.83%-103.00%. This work proposed a new strategy for the application of entropy-driven DNA machine in the field of rapid and ultrasensitive detection.
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Affiliation(s)
- Tai Ye
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Bitao Deng
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Long Bai
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Xiaorong Luo
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Min Yuan
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Hui Cao
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Liling Hao
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Xiuxiu Wu
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Fengqin Yin
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Zefan Li
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Fei Xu
- Shanghai Engineering Research Center for Food Rapid Detection, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
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Abstract
miRNAs in circulating blood have been regarded as promising biomarkers for the diagnosis of a series of diseases. Development of ultrasensitive, reliable, and convenient methods for miRNA assay is of great significance. Herein, we present a novel electrochemical sensing strategy. The assembly of DNA walker strands on membrane-coated nanomaterials, target-mediated recycling activation, and electrochemical signal enrichment are integrated. Multipedal DNA walking with magnetic cores and a catalytic hairpin assembly at the electrode lead to the increase of electrochemical response, which can be used to probe initial target miRNA. This DNA walking nanomachine shows enhanced signal amplification efficiency and facile magnetic separation steps. It enables rapid analysis of miRNA at the attomole level and performs satisfactorily in samples of human circulating blood. Given the powerful sensitivity, facile operation, and excellent specificity, this magnetic multipedal DNA walker provides a promising way to determine miRNA level for biomedical applications.
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Affiliation(s)
- Peng Miao
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, People's Republic of China
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7
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Xie Y, Si S, Deng C, Wu H. A sensitive “turn-on” fluorescent biosensor for the detection of biomarkers based on three-dimensional DNA walker. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Ning Y, Wang X, Liu S, Li L, Lu F. A graphene-oxide-based aptasensor for fluorometric determination of chloramphenicol in milk and honey samples utilizing exonuclease III-assisted target recycling and Nb.BbvCI-powered DNA walker cascade amplification. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114449. [PMID: 38321668 DOI: 10.1016/j.ecoenv.2022.114449] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 02/08/2024]
Abstract
Herein, a graphene oxide (GO)-based fluorescence aptasensor was developed for the sensitive and selective detection of chloramphenicol (CAP), based on exonuclease III (Exo III)-assisted target recycling and Nb.BbvCI-driven DNA walker cascade amplification. Interactions between CAP, hairpin1(HP1), hairpin2 (HP2), and 3'-amino modified hairpin3 (HP3) labeled with carboxyfluorescein (FAM) and covalently coupled to GO enabled efficient CAP detection. CAP was quantitatively assayed by measuring fluorescence at excitation/emission wavelengths of 480/514 nm, resulting from the accumulation of released FAM. A good linear range of 1 fM to 1 nM and a limit of detection (LOD) of 0.875 fM (signal-to-noise (S/N)= 3) were achieved. This aptasensor can distinguish the CAP from interference antibiotics with good specificity and selectivity, even if the concentration of the interfering substance is ten-fold higher than the target concentration. Moreover, the developed fluorescence aptasensor was successfully applied for the detection of CAP in spiked milk and honey samples. Thus, this method is potentially applicable for assaying CAP in foods and provides a promising strategy for the development of fluorescence aptasensors for environmental sample analysis.
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Affiliation(s)
- Yi Ning
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, PR China
| | - Xiaoqi Wang
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, PR China
| | - Shiwu Liu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, PR China
| | - Ling Li
- Experimental Center of molecular biology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, PR China
| | - Fangguo Lu
- Department of Microbiology, The Medicine School of Hunan University of Chinese Medicine, Changsha, Hunan 410208, PR China.
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9
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Kilwing L, Lill P, Nathwani B, Singh JKD, Liedl T, Shih WM. Three-phase DNA-origami stepper mechanism based on multi-leg interactions. Biophys J 2022; 121:4860-4866. [PMID: 36045576 PMCID: PMC9808544 DOI: 10.1016/j.bpj.2022.08.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 08/17/2022] [Accepted: 08/25/2022] [Indexed: 01/07/2023] Open
Abstract
Nanoscale stepper motors such as kinesin and dynein play a key role in numerous natural processes such as mitotic spindle formation during cell division or intracellular organelle transport. Their high efficacy in terms of operational speed and processivity has inspired the investigation of biomimetic technologies based on the use of programmable molecules. In particular, several designs of molecular walkers have been explored using DNA nanotechnology. Here, we study the actuation of a DNA-origami walker on a DNA-origami track based on three principles: 1) octapedal instead of bipedal walking for greater redundancy; 2) three pairs of orthogonal sequences, each of which fuels one repeatable stepping phase for cyclically driven motion with controlled directionality based on strain-based step selection; 3) designed size of only 3.5 nm per step on an origami track. All three principles are innovative in the sense that earlier demonstrations of steppers relied on a maximum of four legs on at least four orthogonal sequences to drive cyclic stepping, and took steps much larger than 3.4 nm in size. Using gel electrophoresis and negative-stain electron microscopy, we demonstrate cyclic actuation of DNA-origami structures through states defined by three sets of specific sequences of anchor points. However, this mechanism was not able to provide the intended control over directionality of movement. DNA-origami-based stepper motors will offer a future platform for investigating how increasing numbers of legs can be exploited to achieve robust stepping with relatively small step sizes.
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Affiliation(s)
- Luzia Kilwing
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany; Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts
| | - Pascal Lill
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts
| | - Bhavik Nathwani
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts
| | - Jasleen Kaur Daljit Singh
- School of Chemistry, School of Chemical and Biomolecular Engineering, The University of Sydney Nano Institute, The University of Sydney, Sydney, New South Wales, Australia
| | - Tim Liedl
- Faculty of Physics and Center for NanoScience (CeNS), Ludwig-Maximilians-University, Munich, Germany.
| | - William M Shih
- Department of Cancer Biology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts; Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts.
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Sheng J, Pi Y, Zhao S, Wang B, Chen M, Chang K. Novel DNA nanoflower biosensing technologies towards next-generation molecular diagnostics. Trends Biotechnol 2022; 41:653-668. [PMID: 36117022 DOI: 10.1016/j.tibtech.2022.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/29/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022]
Abstract
DNA nanoflowers (DNFs) are topological flower-like nanostructures based on ultralong-strand DNA and inorganic metal-ion frameworks. Because of their programmability, biocompatibility, and controllable assembly size for specific responses to molecular recognition stimuli, DNFs are powerful biosensing tools for detecting biomolecules. Here, we review the current state of DNF-based biosensing strategies for in vivo and in vitro detection, with a view of how the field has evolved towards molecular diagnostics. We also provide a detailed classification of DNF-based biosensing strategies and propose their future utility. Particularly as transduction elements, DNFs can accelerate biosensing engineering by signal amplification. Finally, we discuss the key challenges and further prospects of DNF-based biosensing technologies in developing applications of a broader scope.
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Affiliation(s)
- Jing Sheng
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Yan Pi
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400042, China
| | - Shuang Zhao
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Binpan Wang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China
| | - Ming Chen
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China; College of Pharmacy and Laboratory Medicine, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China; State Key Laboratory of Trauma, Burn and Combined Injury, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
| | - Kai Chang
- Department of Clinical Laboratory Medicine, Southwest Hospital, Army Medical University, 30 Gaotanyan, Shapingba District, Chongqing 400038, China.
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Zhou Y, Wang Z, Zhang S, Deng L. An ultrasensitive fluorescence detection template of pathogenic bacteria based on dual catalytic hairpin DNA Walker@Gold nanoparticles enzyme-free amplification. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 277:121259. [PMID: 35489113 DOI: 10.1016/j.saa.2022.121259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/02/2022] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
Integrating the advantages of catalytic hairpin components and multi-foot DNA walker, we designed a 16S rRNA detection probe template for pathogen bacteria, which utilizes DNA ligation quencher and dual catalytic hairpin@DNA walker to induce signal recovery. The dual catalytic hairpin@DNA walker uses the walking position of the target on the AuNP as a foothold to promote the reaction, so that the biosensing of the low-abundance target sequence can induce signal recovery. During the entire experiment, no enzyme is required, which can avoid the limitation of enzyme degradation under unfavorable conditions and the inability to detect the target. Most importantly, the detection template has the advantages of high sensitivity, and its detection limit is significantly better than that of single hairpin DNA walker probe. As the detection system can sensitively and rapidly detect its targeted bacteria and not rely on any enzyme and sophisticated instrumentation, it has great potential for sensitive and specific pathogenic bacteria detection.
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Affiliation(s)
- Yan Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, PR China
| | - Zefeng Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, PR China
| | - Shengnan Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, PR China
| | - Le Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, PR China.
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12
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Borsley S, Leigh DA, Roberts BMW. Chemical fuels for molecular machinery. Nat Chem 2022; 14:728-738. [PMID: 35778564 DOI: 10.1038/s41557-022-00970-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 05/10/2022] [Indexed: 12/11/2022]
Abstract
Chemical reaction networks that transform out-of-equilibrium 'fuel' to 'waste' are the engines that power the biomolecular machinery of the cell. Inspired by such systems, autonomous artificial molecular machinery is being developed that functions by catalysing the decomposition of chemical fuels, exploiting kinetic asymmetry to harness energy released from the fuel-to-waste reaction to drive non-equilibrium structures and dynamics. Different aspects of chemical fuels profoundly influence their ability to power molecular machines. Here we consider the structure and properties of the fuels that biology has evolved and compare their features with those of the rudimentary synthetic chemical fuels that have so far been used to drive autonomous non-equilibrium molecular-level dynamics. We identify desirable, but context-specific, traits for chemical fuels together with challenges and opportunities for the design and invention of new chemical fuels to power synthetic molecular machinery and other dissipative nanoscale processes.
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Affiliation(s)
- Stefan Borsley
- Department of Chemistry, University of Manchester, Manchester, UK
| | - David A Leigh
- Department of Chemistry, University of Manchester, Manchester, UK.
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13
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Wang M, Li X, He F, Li J, Wang HH, Nie Z. The Advances in Designer DNA Nanorobots Enabling Programmable Functions. Chembiochem 2022; 23:e202200119. [DOI: 10.1002/cbic.202200119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Indexed: 11/08/2022]
Affiliation(s)
| | | | - Fang He
- Hunan University College of Chemistry and Chemical Engineering CHINA
| | - Juan Li
- Hunan University College of Biology CHINA
| | - Hong-Hui Wang
- Hunan University College of Biology 410082 Changsha CHINA
| | - Zhou Nie
- Hunan University College of Chemistry and Chemical Engineering Yuelushan, Changsha, Hunan, 410082, P.R.China 410082 Changsha CHINA
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14
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Zhu G, Song P, Wu J, Luo M, Chen Z, Chen T. Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective. Front Bioeng Biotechnol 2022; 9:792489. [PMID: 35071205 PMCID: PMC8777461 DOI: 10.3389/fbioe.2021.792489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.
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Affiliation(s)
- Gan Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jing Wu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minglan Luo
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhipeng Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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15
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Bazrafshan A, Kyriazi ME, Holt BA, Deng W, Piranej S, Su H, Hu Y, El-Sagheer AH, Brown T, Kwong GA, Kanaras AG, Salaita K. DNA Gold Nanoparticle Motors Demonstrate Processive Motion with Bursts of Speed Up to 50 nm Per Second. ACS NANO 2021; 15:8427-8438. [PMID: 33956424 DOI: 10.1021/acsnano.0c10658] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Synthetic motors that consume chemical energy to produce mechanical work offer potential applications in many fields that span from computing to drug delivery and diagnostics. Among the various synthetic motors studied thus far, DNA-based machines offer the greatest programmability and have shown the ability to translocate micrometer-distances in an autonomous manner. DNA motors move by employing a burnt-bridge Brownian ratchet mechanism, where the DNA "legs" hybridize and then destroy complementary nucleic acids immobilized on a surface. We have previously shown that highly multivalent DNA motors that roll offer improved performance compared to bipedal walkers. Here, we use DNA-gold nanoparticle conjugates to investigate and enhance DNA nanomotor performance. Specifically, we tune structural parameters such as DNA leg density, leg span, and nanoparticle anisotropy as well as buffer conditions to enhance motor performance. Both modeling and experiments demonstrate that increasing DNA leg density boosts the speed and processivity of motors, whereas DNA leg span increases processivity and directionality. By taking advantage of label-free imaging of nanomotors, we also uncover Lévy-type motion where motors exhibit bursts of translocation that are punctuated with transient stalling. Dimerized particles also demonstrate more ballistic trajectories confirming a rolling mechanism. Our work shows the fundamental properties that control DNA motor performance and demonstrates optimized motors that can travel multiple micrometers within minutes with speeds of up to 50 nm/s. The performance of these nanoscale motors approaches that of motor proteins that travel at speeds of 100-1000 nm/s, and hence this work can be important in developing protocellular systems as well next generation sensors and diagnostics.
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Affiliation(s)
- Alisina Bazrafshan
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
| | - Maria-Eleni Kyriazi
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO171BJ, U.K
| | - Brandon Alexander Holt
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322 United States
| | - Wenxiao Deng
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
| | - Selma Piranej
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
| | - Hanquan Su
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
| | - Yuesong Hu
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, U.K
- Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, U.K
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322 United States
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Southampton, Southampton, SO171BJ, U.K
- Institute for Life Sciences, University of Southampton, Southampton, SO171BJ, U.K
| | - Khalid Salaita
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322 United States
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30322 United States
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16
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Qi Y, Zhai Y, Fan W, Ren W, Li Z, Liu C. Click Chemistry-Actuated Digital DNA Walker Confined on a Single Particle toward Absolute MicroRNA Quantification. Anal Chem 2020; 93:1620-1626. [DOI: 10.1021/acs.analchem.0c04073] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yan Qi
- Key Laboratory of Applied Surface and Colloid Chemistry, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Ministry of Education, Shaanxi Normal University, Xi’an 710119, Shaanxi Province, P. R. China
| | - Yuqing Zhai
- Key Laboratory of Applied Surface and Colloid Chemistry, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Ministry of Education, Shaanxi Normal University, Xi’an 710119, Shaanxi Province, P. R. China
| | - Wenjiao Fan
- Key Laboratory of Applied Surface and Colloid Chemistry, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Ministry of Education, Shaanxi Normal University, Xi’an 710119, Shaanxi Province, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Ministry of Education, Shaanxi Normal University, Xi’an 710119, Shaanxi Province, P. R. China
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Ministry of Education, Shaanxi Normal University, Xi’an 710119, Shaanxi Province, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry & Chemical Engineering, Ministry of Education, Shaanxi Normal University, Xi’an 710119, Shaanxi Province, P. R. China
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