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Shen P, Liu Y, Qu X, Zhu M, Huang T, Sun Q. An optical keypad lock with high resettability based on a quantum dot-porphyrin FRET nanodevice. NANOSCALE ADVANCES 2023; 5:2986-2993. [PMID: 37260500 PMCID: PMC10228340 DOI: 10.1039/d3na00030c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 05/05/2023] [Indexed: 06/02/2023]
Abstract
Due to their appealing properties, nanomaterials have become ideal candidates for the implementation of computing systems. Herein, an optical keypad lock based on a Förster resonance energy transfer (FRET) nanodevice is developed. The nanodevice is composed of a green-emission quantum dot with a thick silica shell (gQD@SiO2) and peripheric blue-emission quantum dots with ultrathin silica spacer (bQD@SiO2), on which 5,10,15,20-tetrakis(4-sulfophenyl)porphyrin (TSPP) is covalently linked. The nanodevice outputs dual emission-based ratiometric fluorescence, depending on the FRET efficiency of bQD-porphyrin pairs, which is highly sensitive to the metalation of TSPP: values are 59.7%, 44.8%, and 10.1% for bQD-Zn(ii)TSPP, bQD-TSPP, and bQD-Fe(iii)TSPP pairs, respectively. As such, by using the competitive chelation-induced transmetalation of TSPP, the nanodevice is capable of implementing a 3-input keypad lock that is unlocked only by the correct input order of Zn(ii) chelator, iron ions, and UV light. Interestingly, the reversible transmetalation of TSPP permits the reset (lock) operation of the keypad lock with the correct input order of ascorbic acid, Zn(ii), and UV light. Application of the nanodevice is exemplified by the construction of paper and cellular keypad locks, respectively, both of which feature signal readability and/or high resettability, showing high potential for personal information identification and bio-encryption applications.
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Affiliation(s)
- Peng Shen
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Yuqian Liu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Joint International Research Lab of Lignocellulosic Functional Materials, College of Light Industry and Food Engineering, Nanjing Forestry University Nanjing 210037 China
| | - Xiaojun Qu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Mingsong Zhu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Ting Huang
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University Nanjing 210096 China
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Xu S, Liu Y, Zhou S, Zhang Q, Kasabov NK. DNA Matrix Operation Based on the Mechanism of the DNAzyme Binding to Auxiliary Strands to Cleave the Substrate. Biomolecules 2021; 11:1797. [PMID: 34944442 PMCID: PMC8698824 DOI: 10.3390/biom11121797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/21/2021] [Accepted: 11/27/2021] [Indexed: 11/16/2022] Open
Abstract
Numerical computation is a focus of DNA computing, and matrix operations are among the most basic and frequently used operations in numerical computation. As an important computing tool, matrix operations are often used to deal with intensive computing tasks. During calculation, the speed and accuracy of matrix operations directly affect the performance of the entire computing system. Therefore, it is important to find a way to perform matrix calculations that can ensure the speed of calculations and improve the accuracy. This paper proposes a DNA matrix operation method based on the mechanism of the DNAzyme binding to auxiliary strands to cleave the substrate. In this mechanism, the DNAzyme binding substrate requires the connection of two auxiliary strands. Without any of the two auxiliary strands, the DNAzyme does not cleave the substrate. Based on this mechanism, the multiplication operation of two matrices is realized; the two types of auxiliary strands are used as elements of the two matrices, to participate in the operation, and then are combined with the DNAzyme to cut the substrate and output the result of the matrix operation. This research provides a new method of matrix operations and provides ideas for more complex computing systems.
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Affiliation(s)
- Shaoxia Xu
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China;
| | - Yuan Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China;
| | - Shihua Zhou
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China;
| | - Qiang Zhang
- Key Laboratory of Advanced Design and Intelligent Computing, Dalian University, Dalian 116622, China;
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China;
| | - Nikola K. Kasabov
- Knowledge Engineering and Discovery Research Institute, Auckland University of Technology, Auckland 1010, New Zealand;
- Intelligent Systems Research Center, Ulster University, Londonderry BT52 1SA, UK
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Zhu L, Yu L, Meng T, Peng Y, Yang X. Contrary Logic Pair Library, Parity Generator/Checker and Various Concatenated Logic Circuits Engineered by a Label-Free and Immobilization-Free Electrochemiluminescence Resonance Energy Transfer System. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102881. [PMID: 34792279 DOI: 10.1002/smll.202102881] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/24/2021] [Indexed: 06/13/2023]
Abstract
Herein, a label-free and immobilization-free electrochemiluminescence resonance energy transfer (ECL-RET) system based on graphitic carbon nitride nanosheets (GCNNs)/Ru(phen)32+ donor/acceptor pair is developed, in which the ECL-RET is regulated by regulating the diffusivity of Ru(phen)32+ molecules toward the negatively charged GCNNs through logically programmed DNA hybridization reactions. The two optical signals of GCNNs (445 nm) and Ru(phen)32+ (593 nm) show completely opposite changes through the same one-time DNA hybridization reaction. Based on this ECL-RET system, a contrary logic pair (CLP) library, a parity generator/checker system for differentiating the erroneous bits during data transmission, the parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits including a six-input logic gate capable of implementing of 64 input combinations for meeting the needs of computational complexity are developed. The ECL-RET-based molecular logic system avoids the time-consuming, costly and inefficient labeling procedures and the laborious processes of immobilization, presenting great potential for building more complicated and advanced logic gates, and providing a refreshing inspiration for the construction of combinatorial logic circuits based on ECL method.
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Affiliation(s)
- Liping Zhu
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Linying Yu
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Tian Meng
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
| | - Yao Peng
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Xiurong Yang
- University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
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Zhu L, Yu L, Yang X. Electrochemical-Based DNA Logic Devices Regulated by the Diffusion and Intercalation of Electroactive Dyes. ACS APPLIED MATERIALS & INTERFACES 2021; 13:42250-42257. [PMID: 34452580 DOI: 10.1021/acsami.1c12650] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Electrochemical-based logic gates are simple to operate, sensitive, controllable, and easy to integrate with silicon-based semiconductor logic devices, showing great application prospects and remaining largely unexplored. Herein, an immobilization-free dual-output electrochemical molecular logic system based on the different diffusivity of electroactive dyes ferrocene (Fc) and methylene blue (MB) toward an indium tin oxide (ITO) electrode under different DNA hybridization reactions was developed. In this system, the hybridization of the catalytic strand IN1 with Fc-modified hairpin DNA H1 triggered an exonuclease III (Exo III) cleavage cycle to obtain free Fc and produce a large number of long double-stranded DNAs via the hybridization chain reaction for intercalating MB, which was previously in the free state. Such a hybridization reaction caused a significant change in the diffusion capacity of MB and Fc toward the ITO electrode, resulting in two electrochemical signals with opposite changes. On this basis, a contrary logic pair library, a parity generator/checker system for differentiating the erroneous bits during data transmission, a parity checker to identify the even/odd natural numbers from 0 to 9, and a series of concatenated logic circuits for meeting the needs of computational complexity were developed. The proposed electrochemical-based molecular logic system greatly expanded the application of the electrochemical method in the construction of logic circuits and provided a conceptual prototype for the development of more advanced and complicated logic devices.
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Affiliation(s)
- Liping Zhu
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Linying Yu
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Xiurong Yang
- University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
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Ning Y, Hu J, Lu F. Aptamers used for biosensors and targeted therapy. Biomed Pharmacother 2020; 132:110902. [PMID: 33096353 PMCID: PMC7574901 DOI: 10.1016/j.biopha.2020.110902] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 01/07/2023] Open
Abstract
Aptamers are single-stranded nucleic acid sequences that can bind to target molecules with high selectivity and affinity. Most aptamers are screened in vitro by a combinatorial biology technique called systematic evolution of ligands by exponential enrichment (SELEX). Since aptamers were discovered in the 1990s, they have attracted considerable attention and have been widely used in many fields owing to their unique advantages. In this review, we present an overview of the advancements made in aptamers used for biosensors and targeted therapy. For the former, we will discuss multiple aptamer-based biosensors with different principles detected by various signaling methods. For the latter, we will focus on aptamer-based targeted therapy using aptamers as both biotechnological tools for targeted drug delivery and as targeted therapeutic agents. Finally, challenges and new perspectives associated with these two regions were further discussed. We hope that this review will help researchers interested in aptamer-related biosensing and targeted therapy research.
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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
| | - Jue Hu
- Department of Microbiology, 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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Logic Gates Based on DNA Aptamers. Pharmaceuticals (Basel) 2020; 13:ph13110417. [PMID: 33238657 PMCID: PMC7700249 DOI: 10.3390/ph13110417] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 02/08/2023] Open
Abstract
DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.
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A molecular device: A DNA molecular lock driven by the nicking enzymes. Comput Struct Biotechnol J 2020; 18:2107-2116. [PMID: 32913580 PMCID: PMC7451616 DOI: 10.1016/j.csbj.2020.08.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 07/28/2020] [Accepted: 08/01/2020] [Indexed: 11/22/2022] Open
Abstract
As people are placing more and more importance on information security, how to realize the protection of information has become a hotspot of current research. As a security device, DNA molecular locks have great potential to realize information protection at the molecular level. However, building a highly secure molecular lock is still a serious challenge. Therefore, taking advantage of the DNA strand displacement and enzyme control technology, we constructed a molecular lock with a self-destructive mechanism. This molecular lock is mainly composed of logic circuits and takes nicking enzymes as inputs. To build this molecular lock, we first constructed a series of cascade circuits, including a YES–YES cascade circuit and a YES–AND cascade circuit. Then, an Inhibit logic gate was constructed to explore the inhibitory properties between different combinations of two nicking enzymes. Finally, using the characteristics of mutual inhibition between several enzymes, a DNA molecular lock driven by three nicking enzymes was constructed. In this molecular device, only the correct sequence of nicking enzymes can be input to ensure the normal operation of the molecular lock. Once the wrong password is entered, the device will be destroyed and cannot be recovered, which effectively prevents intruders from cracking the lock through exhaustive methods. The molecular lock has the function of simulating an electronic keyboard, which can realize the protection of information at the molecular level, and provides a new implementation method for building more advanced and complex molecular devices.
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Liu Y, Guo Q, Qu X, Sun Q. Supramolecularly Assembled Ratiometric Fluorescent Sensory Nanosystem for "Traffic Light"-Type Lead Ion or pH Sensing. ACS APPLIED MATERIALS & INTERFACES 2018; 10:30662-30669. [PMID: 30136835 DOI: 10.1021/acsami.8b10007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The combination of functional nucleic acids and nanomaterials enables the continuous development of hybrid nanosystems that have found wide applications including chemo/biosensing. Herein, we report the supramolecular assembly of a "sesame biscuit"-like superstructural nanosystem based on aptamer, quantum dot (QD), and graphene oxide (GO), and its diverse applications in Pb2+ and pH sensing. The nanosystem was assembled via adsorbing silica-encapsulated green-emitting QD onto the edge of GO by ionic interaction, followed by absorbing aptamer-modified red-emitting QD onto the GO surface via the π-stacking interaction. The nanosystem showed the characteristic of the nonquenched green fluorescence due to silica encapsulation and quenched red fluorescence owing to nanomaterial surface energy transfer. The nanosystem responded to Pb2+/pH in ratiometric fluorescence: the red fluorescence varied upon analyte-driven conformational changes of the aptamer, whereas the green one remained constant. Under optimized conditions, the nanosystem was demonstrated to be capable of quantifying Pb2+ with a detection limit of 11.7 pM, as well as pH with a sensing resolution of 0.1 pH unit. More importantly, the ratiometric nanosystem facilitated visualization of analytes in a distinct "traffic light" manner, which was exemplified by semiquantification of exogenous Pb2+ in living cells. To demonstrate practicality, fluorescent test strips were fabricated by immobilizing the nanosystem on paper. The fluorescent test strips displayed traffic light-type fluorescence color changes, with the capacity for on-site, naked-eye detection of Pb2+ in real samples, as well as point-of-care pH testing in routine urinalysis.
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Affiliation(s)
- Yuqian Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Qingsheng Guo
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Xiaojun Qu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering , Southeast University , Nanjing 210096 , China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education, School of Biological Science & Medical Engineering , Southeast University , Nanjing 210096 , China
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Li M, Wang Z, Liang J, Yao H, Shen L, Liu H, Fan L. A chemical/molecular 4-input/2-output keypad lock with easy resettability based on red-emission carbon dots-Prussian blue composite film electrodes. NANOSCALE 2018; 10:7484-7493. [PMID: 29637973 DOI: 10.1039/c8nr01258j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this work, a resettable 4-input/2-output keypad lock system based on red-emission carbon dots (rCDs) and Prussian blue (PB) modified electrodes was developed. Electrochromic PB layers were first electrochemically deposited on the indium tin oxide (ITO) electrode surface. An admixture of rCDs and chitosan (Chi) was then cast on the surface of PB layers, forming rCDs-Chi/PB film electrodes. UV-vis absorption of the films was sensitive to the applied potential since the blue PB constituent of the films would be transformed to nearly colorless Prussian white (PW) at the reduction potential of -0.2 V and then from PW back to PB at the oxidation potential of 0.4 V, and the transformation between PB and PW would also influence the fluorescence emission of the rCD constituent in the films. The addition of cysteine (Cys) in the testing solution could reduce the PB in the films into PW and generate an amperometric electrocatalytic current at 0.4 V. Meanwhile, the addition of Fe3+ in solution could greatly quench the fluorescence from the rCD component in the films. Thus, the responses of UV-vis absorbance, fluorescence emission and amperometric current of the rCDs-Chi/PB film electrode system exhibited potential-, Cys- and Fe3+-responsive switching properties. Based on the aforementioned work, a combinational logic gate circuit with 3 inputs and 3 outputs was established. In particular, on the same platform, a novel chemical/molecular 4-input/2-output keypad lock with easy resettability was elaborately designed with amperometric current and fluorescence peak intensity as two different types of outputs, so that a higher security level could be achieved.
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Affiliation(s)
- Menglu Li
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China.
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Graphene oxide-based fluorometric determination of methicillin-resistant Staphylococcus aureus by using target-triggered chain reaction and deoxyribonuclease-assisted recycling. Mikrochim Acta 2018; 185:183. [PMID: 29594725 DOI: 10.1007/s00604-018-2702-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/21/2018] [Indexed: 12/22/2022]
Abstract
The authors describe a method for the fluorometric determination of methicillin-resistant Staphylococcus aureus (MRSA) by exploiting target-triggered chain reactions and deoxyribonuclease I (DNase I)-aided target recycling. It is making use of a carboxy-fluorescein (FAM)-labeled single-stranded probe containing two sections. One is complementary to the 5' terminus of the target, while the 3' terminus of the other target is adsorbed on the surface of graphene oxide (GO) via π-stacking interactions without the target (16S rRNA). This adsorption results in quenching of the fluorescence of the label and protects it from being cleaved by DNase I. However, upon addition of the target, DNA/RNA hybrids are repelled by GO. This leads to fluorescence recovery as measured at excitation/emission wavelengths of 480/514 nm due to a chain reaction that is triggered by the target. The signal is strongly amplified by using DNase I-mediated target recycling. The 16S rRNA of MRSA can be detected by this method in the 1 to 30 nM concentration range, and the detection limit is 0.02 nM. The method was applied to analyze bacterial samples, and the detection limit is as low as 30 CFU . mL-1. The assay is highly sensitive and selective and in our percpetion has a large potential in diagnosis of drug-resistant bacteria. Graphical abstract Schematic of the graphene oxide-based fluorescent bioassay for Methicillin-resistant Staphylococcus aureus detection by using target-triggered chain reaction and deoxyribonuclease I-aided signal amplification.
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