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Chen T, Chen G, Cao S, Tang X, Li W, Liu C, Gou H, Sun P, Mao Y, Pan Q, Zhang P, Zhu X. Dynamic Addressing Molecular Robot (DAMR): An Effective and Efficient Trial-and-Error Approach for the Analysis of Single Nucleotide Polymorphisms. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402140. [PMID: 38884120 DOI: 10.1002/advs.202402140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/28/2024] [Indexed: 06/18/2024]
Abstract
Accurate and efficient molecular recognition plays a crucial role in the fields of molecular detection and diagnostics. Conventional trial-and-error-based molecular recognition approaches have always been challenged in distinguishing minimal differences between targets and non-targets, such as single nucleotide polymorphisms (SNPs) of oligonucleotides. To address these challenges, here, a novel concept of dynamic addressing analysis is proposed. In this concept, by dissecting the regions of the target and creating a corresponding recognizer, it is possible to eliminate the inaccuracy and inefficiency of recognition. To achieve this concept, a Dynamic Addressing Molecular Robot (DAMR), a DNA-based dynamic addressing device is developed which is capable of dynamically locating targets. DAMR is designed to first bind to the conserved region of the target while addressing the specific region dynamically until accurate recognition is achieved. DAMR has provided an approach for analyzing low-resolution targets and has been used for analyzing SNP of miR-196a2 in both cell and serum samples, which has opened new avenues for effective and efficient molecular recognition.
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Affiliation(s)
- Tianshu Chen
- Clinical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
| | - Guifang Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Siyu Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Xiaochen Tang
- Clinical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
| | - Wenxing Li
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Chenbin Liu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Hongquan Gou
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
| | - Pei Sun
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Yichun Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China
| | - Qiuhui Pan
- Clinical Laboratory, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, P. R. China
- Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, 200127, P. R. China
| | - Penghui Zhang
- Department of Laboratory Medicine, Shanghai Pudong New Area People's Hospital, Shanghai, 201299, P. R. China
| | - Xiaoli Zhu
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, 200072, P. R. China
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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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Long Y, Zhao J, Ma W, He C, Pei W, Hou J, Hou C, Huo D. Fe Single-Atom Carbon Dots Nanozyme Collaborated with Nucleic Acid Exonuclease III-Driven DNA Walker Cascade Amplification Strategy for Circulating Tumor DNA Detection. Anal Chem 2024; 96:4774-4782. [PMID: 38477105 DOI: 10.1021/acs.analchem.3c04202] [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: 03/14/2024]
Abstract
Circulating tumor DNA (ctDNA), as a next-generation tumor marker, enables early screening and monitoring of cancer through noninvasive testing. Exploring the development of new methods for ctDNA detection is an intriguing study. In this work, a unique electrochemical biosensor for the ctDNA detector was constructed in the first utilizing Fe single-atom nanozymes-carbon dots (SA Fe-CDs) as a signaling carrier in collaboration with a DNA walker cascade amplification strategy triggered by nucleic acid exonuclease III (Exo III). The electrochemical active surface area of AuNPs/rGO modified onto a glassy carbon electrode (AuNPs/rGO/GCE) was about 1.43 times that of a bare electrode (bare GCE), with good electrical conductivity alongside a high heterogeneous electron transfer rate (5.81 × 10-3 cm s-1), that is, as well as the ability to load more molecules. Sequentially, the DNA walker cascade amplification strategy driven by Exo III effectively converted the target ctDNA into an amplified biosignal, ensuring the sensitivity and specificity of ctDNA. Ultimately, the electrochemical signal was further amplified by introducing SA Fe-CDs nanozymes, which could serve as catalysts for 3,3',5,5'-tetramethylbenzidine (TMB) oxidation with facile responding (Vmax = 0.854 × 10-6 M s-1) and robust annexation (Km = 0.0069 mM). The integration of the triple signal amplification approach achieved detection limits as low as 1.26 aM (S/N = 3) for a linearity spanning from 5 aM to 50 nM. In this regard, our proposal for a biosensor with exceptional assay properties in complicated serum environments had great potential for early and timely diagnosis of cancer.
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Affiliation(s)
- Yanyi Long
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Jiaying Zhao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Wanting Ma
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Congjuan He
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Wen Pei
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Jingzhou Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing 401331, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Engineering and Technology Research Center of Intelligent Rehabilitation and Eldercare, Chongqing City Management College, Chongqing 401331, P. R. China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, P. R. China
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Strategies for Enhancing the Sensitivity of Electrochemiluminescence Biosensors. BIOSENSORS 2022; 12:bios12090750. [PMID: 36140135 PMCID: PMC9496703 DOI: 10.3390/bios12090750] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/02/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022]
Abstract
Electrochemiluminescence (ECL) has received considerable attention as a powerful analytical technique for the sensitive and accurate detection of biological analytes owing to its high sensitivity and selectivity and wide dynamic range. To satisfy the growing demand for ultrasensitive analysis techniques with high efficiency and accuracy in complex real sample matrices, considerable efforts have been dedicated to developing ECL strategies to improve the sensitivity of bioanalysis. As one of the most effective approaches, diverse signal amplification strategies have been integrated with ECL biosensors to achieve desirable analytical performance. This review summarizes the recent advances in ECL biosensing based on various signal amplification strategies, including DNA-assisted amplification strategies, efficient ECL luminophores, surface-enhanced electrochemiluminescence, and ratiometric strategies. Sensitivity-enhancing strategies and bio-related applications are discussed in detail. Moreover, the future trends and challenges of ECL biosensors are discussed.
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