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HassanAbadi FK, Reshadinezhad MR, Beiki Z, Dehghanian F. Cascadable-Controllable Self-Assembly DNA Tiles for Large-Scale DNA Logic Circuits. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2024; 18:478-497. [PMID: 38090859 DOI: 10.1109/tbcas.2023.3342704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
In the last few decades, DNA-based self-assembly tiles has become a hot field in research due to its special applications and advantages. The regularity and strong design methods comprise other DNA-based digital circuit design methods. In addition to the obvious advantages of this method, there are challenges in performing computations based on self-assembly tiles, which have hindered the development and construction of large computing circuits with this method. The first challenge is the creation of crystals from DNA molecules in the output, which has led to the impossibility of cascading. The second challenge of this method is the uncontrollability of the reactions of the tiles, which increases the percentage of computing errors. In this article, these two challenges have been solved by changing the structure of leading tiles so that without the activator strand, tiles remain inactive and cannot be connected to other tiles. Also, when the tiles are activated, single-strand DNA will be released after connecting to other tiles, which will be used as the output of the circuit. This output gives the possibility of cascading to self-assembly designed circuits. The method introduced in this article can be a beginning for the re-development of DNA-based circuit design with the self-assembly tile method.
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Zou C. A novel activation function based on DNA enzyme-free hybridization reaction and its implementation on nonlinear molecular learning systems. Phys Chem Chem Phys 2024; 26:11854-11866. [PMID: 38567416 DOI: 10.1039/d3cp02811a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
With the advent of the post-Moore's Law era, the development of traditional silicon-based computers has reached its limit, and there is an urgent need to develop new computing technologies to meet the needs of science, technology, and daily life. Due to its super-strong parallel computing capability and outstanding data storage capacity, DNA computing has become an important branch and hot research topic of new computer technology. DNA enzyme-free hybridization reaction technology is widely used in DNA computing, showing excellent performance in computing power and information processing. Studies have shown that DNA molecules not only have the computing function of electronic devices, but also exhibit certain human brain-like functions. In the field of artificial intelligence, activation functions play an important role as they enable artificial intelligence systems to fit and predict non-linear and complex variable relationships. Due to the difficulty of implementing activation functions in DNA computing, DNA circuits cannot easily achieve all the functions of artificial intelligence. DNA circuits need to rely on electronic computers to complete the training and learning process. Based on the parallel computing characteristics of DNA computing and the kinetic features of DNA molecule displacement reactions, this paper proposes a new activation function. This activation function can not only be easily implemented by DNA enzyme-free hybridization reaction reactions, but also has good nesting properties in DNA circuits, and can be cascaded with other DNA reactions to form a complete DNA circuit. This paper not only provides the mathematical analysis of the proposed activation function, but also provides a detailed analysis of its kinetic features. The activation function is then nested into a nonlinear neural network for DNA computing. This system is capable of fitting and predicting a certain nonlinear function.
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Affiliation(s)
- Chengye Zou
- College of Information Science and Engineering, Yanshan University, Qinhuangdao 066004, China.
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Mousazadeh M, Daneshpour M, Rafizadeh Tafti S, Shoaie N, Jahanpeyma F, Mousazadeh F, Khosravi F, Khashayar P, Azimzadeh M, Mostafavi E. Nanomaterials in electrochemical nanobiosensors of miRNAs. NANOSCALE 2024; 16:4974-5013. [PMID: 38357721 DOI: 10.1039/d3nr03940d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Nanomaterial-based biosensors have received significant attention owing to their unique properties, especially enhanced sensitivity. Recent advancements in biomedical diagnosis have highlighted the role of microRNAs (miRNAs) as sensitive prognostic and diagnostic biomarkers for various diseases. Current diagnostics methods, however, need further improvements with regards to their sensitivity, mainly due to the low concentration levels of miRNAs in the body. The low limit of detection of nanomaterial-based biosensors has turned them into powerful tools for detecting and quantifying these biomarkers. Herein, we assemble an overview of recent developments in the application of different nanomaterials and nanostructures as miRNA electrochemical biosensing platforms, along with their pros and cons. The techniques are categorized based on the nanomaterial used.
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Affiliation(s)
- Marziyeh Mousazadeh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Maryam Daneshpour
- Biotechnology Department, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Livogen Pharmed, Research and Innovation Center, Tehran, Iran
| | - Saeed Rafizadeh Tafti
- Medical Nanotechnology & Tissue Engineering Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, 89195-999, Yazd, Iran.
| | - Nahid Shoaie
- Department of Biotechnology, Tarbiat Modares University of Medical Science, Tehran, Iran
| | - Fatemeh Jahanpeyma
- Department of Biotechnology, Tarbiat Modares University of Medical Science, Tehran, Iran
| | - Faezeh Mousazadeh
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Khosravi
- Medical Nanotechnology & Tissue Engineering Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, 89195-999, Yazd, Iran.
| | - Patricia Khashayar
- Center for Microsystems Technology, Imec and Ghent University, 9050, Ghent, Belgium.
| | - Mostafa Azimzadeh
- Medical Nanotechnology & Tissue Engineering Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, 89195-999, Yazd, Iran.
- Stem Cell Biology Research Center, Yazd Reproductive Sciences Institute, Shahid Sadoughi University of Medical Sciences, 89195-999, Yazd, Iran
- Department of Medical Biotechnology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd 89165-887, Iran
| | - Ebrahim Mostafavi
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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Zhang Q, Wang H, Liu Q, Zeng N, Fu G, Qiu Y, Yang Y, Yuan H, Wang W, Li B. Exosomes as Powerful Biomarkers in Cancer: Recent Advances in Isolation and Detection Techniques. Int J Nanomedicine 2024; 19:1923-1949. [PMID: 38435755 PMCID: PMC10906735 DOI: 10.2147/ijn.s453545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
Exosomes, small extracellular vesicles derived from cells, are known to carry important bioactive molecules such as proteins, nucleic acids, and lipids. These bioactive components play crucial roles in cell signaling, immune response, and tumor metastasis, making exosomes potential diagnostic biomarkers for various diseases. However, current methods for detecting tumor exosomes face scientific challenges including low sensitivity, poor specificity, complicated procedures, and high costs. It is essential to surmount these obstacles to enhance the precision and dependability of diagnostics that rely on exosomes. Merging DNA signal amplification techniques with the signal boosting capabilities of nanomaterials presents an encouraging strategy to overcome these constraints and improve exosome detection. This article highlights the use of DNA signal amplification technology and nanomaterials' signal enhancement effect to improve the detection of exosomes. This review seeks to offer valuable perspectives for the enhancement of amplification methods applied in practical cancer diagnosis and prognosis by providing an overview of how these novel technologies are utilized in exosome-based diagnostic procedures.
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Affiliation(s)
- Qiongdan Zhang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Huizhen Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Qingyi Liu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Ni Zeng
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Gang Fu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Yixing Qiu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Yupei Yang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Hanwen Yuan
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Bin Li
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
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Du J, He JS, Wang R, Wu J, Yu X. Ultrasensitive reporter DNA sensors built on nucleic acid amplification techniques: Application in the detection of trace amount of protein. Biosens Bioelectron 2024; 243:115761. [PMID: 37864901 DOI: 10.1016/j.bios.2023.115761] [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: 08/26/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
The detection of protein is of great significance for the study of biological physiological function, early diagnosis of diseases and drug research. However, the sensitivity of traditional protein detection methods for detecting trace amount of proteins was relatively low. By integrating sensitive nucleic acid amplification techniques (NAAT) with protein detection methods, the detection limit of protein detection methods can be substantially improved. The DNA that can specifically bind to protein targets and convert protein signals into DNA signals is collectively referred to reporter DNA. Various NAATs have been used to establish NAAT-based reporter DNA sensors. And according to whether enzymes are involved in the amplification process, the NAAT-based reporter DNA sensors can be divided into two types: enzyme-assisted NAAT-based reporter DNA sensors and enzyme-free NAAT-based reporter DNA sensors. In this review, we will introduce the principles and applications of two types of NAAT-based reporter DNA sensors for detecting protein targets. Finally, the main challenges and application prospects of NAAT-based reporter DNA sensors are discussed.
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Affiliation(s)
- Jungang Du
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Jin-Song He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Rui Wang
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200438, China.
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China.
| | - Xiaoping Yu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
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Chen Y, Jiang H, Liu X, Wang X. Engineered Electrochemiluminescence Biosensors for Monitoring Heavy Metal Ions: Current Status and Prospects. BIOSENSORS 2023; 14:9. [PMID: 38248386 PMCID: PMC10813191 DOI: 10.3390/bios14010009] [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: 11/04/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 01/23/2024]
Abstract
Metal ion contamination has serious impacts on environmental and biological health, so it is crucial to effectively monitor the levels of these metal ions. With the continuous progression of optoelectronic nanotechnology and biometrics, the emerging electrochemiluminescence (ECL) biosensing technology has not only proven its simplicity, but also showcased its utility and remarkable sensitivity in engineered monitoring of residual heavy metal contaminants. This comprehensive review begins by introducing the composition, advantages, and detection principles of ECL biosensors, and delving into the engineered aspects. Furthermore, it explores two signal amplification methods: biometric element-based strategies (e.g., HCR, RCA, EDC, and CRISPR/Cas) and nanomaterial (NM)-based amplification, including quantum dots, metal nanoclusters, carbon-based nanomaterials, and porous nanomaterials. Ultimately, this review envisions future research trends and engineered technological enhancements of ECL biosensors to meet the surging demand for metal ion monitoring.
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Affiliation(s)
| | | | | | - Xuemei Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; (Y.C.); (H.J.); (X.L.)
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