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Altalbawy FMA, Ali E, N Fenjan M, Fakri Mustafa Y, Mansouri S, D O B, Gulnikhol Idiyevna S, Misra N, Alawadi AH, Alsalamy A. Aptamer-Magnetic Nanoparticle Complexes for Powerful Biosensing: A Comprehensive Review. Crit Rev Anal Chem 2024:1-14. [PMID: 38165810 DOI: 10.1080/10408347.2023.2298328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024]
Abstract
The selective and sensitive diagnosis of diseases is a significant matter in the early stages of the cure of illnesses. To elaborate, although several types of probes have been broadly applied in clinics, magnetic nanomaterials-aptamers, as new-generation probes, are becoming more and more attractive. The presence of magnetic nanomaterials brings about quantification, purification, and quantitative analysis of biomedical, especially in complex samples. Elaborately, the superparamagnetic properties and numerous functionalized groups of magnetic nanomaterials are considered two main matters for providing separation ability and immobilization substrate, respectively. In addition, the selectivity and stability of aptamer can present a high potential recognition element. Importantly, the integration of aptamer and magnetic nanomaterials benefits can boost the performance of biosensors for biomedical analysis by introducing efficient and compact probes that need low patient samples and fast diagnosis, user-friendly application, and high repeatability in the quantification of biomolecules. The primary aim of this review is to suggest a summary of the effect of the employed other types of nanomaterials in the fabrication of novel aptasensors-based magnetic nanomaterials and to carefully explore various applications of these probes in the quantification of bioagents. Furthermore, the application of these versatile and high-potential probes in terms of the detection of cancer cells and biomarkers, proteins, drugs, bacteria, and nucleoside were discussed. Besides, research gaps and restrictions in the field of biomedical analysis by magnetic nanomaterials-aptamers will be discussed.
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Affiliation(s)
- Farag M A Altalbawy
- Department of Chemistry, University College of Duba, University of Tabuk, Tabuk, Saudi Arabia
- National Institute of Laser Enhanced Sciences (NILES), University of Cairo, Giza, Egypt
| | - Eyhab Ali
- College of Chemistry, Al-Zahraa University for Women, Karbala, Iraq
| | - Mohammed N Fenjan
- College of Health and Medical Technology, Al-Ayen University, Nasiriyah, Iraq
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, Iraq
| | - Sofiene Mansouri
- Department of Biomedical Technology, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
- Laboratory of Biophysics and Medical Technologies, Higher Institute of Medical Technologies of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Bokov D O
- Institute of Pharmacy, Sechenov First Moscow State Medical University, Moscow, Russia
- Laboratory of Food Chemistry, Federal Research Center of Nutrition, Biotechnology and Food Safety, Moscow, Russia
| | | | - Neeti Misra
- Department of Management, Uttaranchal Institute of Management, Uttaranchal University, Dehradun, India
| | - Ahmed Hussien Alawadi
- Chemistry Department, The Islamic University, Najaf, Iraq
- Chemistry Department, The Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq
- Chemistry Department, The Islamic University of Babylon, Babylon, Iraq
| | - Ali Alsalamy
- Chemistry Department, Imam Ja'afar Al-Sadiq University, Al-Muthanna, Iraq
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2
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Zhang J, Deng Z, Feng H, Shao B, Liu D. A multifunctional fluorescent sensor for Ag + and Hg 2+ detection in seawater. ENVIRONMENTAL MONITORING AND ASSESSMENT 2023; 196:22. [PMID: 38060083 DOI: 10.1007/s10661-023-12217-2] [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: 01/01/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023]
Abstract
In order to detect Ag+ and Hg2+ in seawater, we explored a multifunctional fluorescence sensor. A multifunctional Ag+ and Hg2+ sensor was designed by using gold nanoparticles (AuNPs) as quenching agent, PicoGreen dye as fluorescent probe of base pairing double-stranded deoxyribonucleic acid (DNA), and combining the characteristics of Ag+ making C base mismatch and Hg2+ making T base mismatch. Meanwhile, the DNA logic gate was constructed by establishing logic circuit, truth table, and logic formula. The relevant performances of the sensor were investigated. The results revealed that the sensor can detect Ag+ in the range of 100 to 700 nM with R2 = 0.98129, and its detection limit is 16.88 nM (3σ/slope). The detection range of Hg2+is 100-900 nM with R2 = 0.99725, and the detection limit is 5.59 nM (3σ/slope). An AND-AND-NOR-AND molecular logic gate has been successfully designed. With the characteristics of high sensitivity, multifunction, and low cost, the recommended detection method has the potential to be applied to the detection of Ag+ and Hg2+ in seawater.
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Affiliation(s)
- Jingjing Zhang
- College of Applied Science and Technology, Hainan University, Danzhou, 571737, China
| | - Ziqi Deng
- College of Applied Science and Technology, Hainan University, Danzhou, 571737, China
| | - Hongbo Feng
- College of Applied Science and Technology, Hainan University, Danzhou, 571737, China
| | - Bingqian Shao
- College of Applied Science and Technology, Hainan University, Danzhou, 571737, China.
| | - Debing Liu
- College of Applied Science and Technology, Hainan University, Danzhou, 571737, China.
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Na Y, Zhang J, Zhang S, Liang N, Zhao L. Fluorescence Sensor for Zearalenone Detection Based on Oxidized Single-walled Carbon Nanohorns/N-doped Carbon Quantum Dots-aptamer. J Fluoresc 2023:10.1007/s10895-023-03466-y. [PMID: 37831356 DOI: 10.1007/s10895-023-03466-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023]
Abstract
Zearalenone (ZEN), a resorcinolactone toxin, which has been a potential threat to agricultural production and human health. In this study, a sample and rapid fluorescence sensor was established for the detection of ZEN, which is based on the fluorescence properties of N-doped carbon dots-aptamer (NCDs-apt) and the quenching ability of oxidized single-walled carbon nanohorns (oxSWCNHs). NCDs synthesized by one-step hydrothermal method were connected with ZEN-aptamer (ZEN-apt), and oxSWCNHs were added to quench the fluorescence of NCDs-apt. Therefore, an oxSWCNHs/NCDs-apt aptasensor based on fluorescence "on-off" for the determination of ZEN in food was formed. Under optimum conditions, the limit of detection (LOD) of this method was 18 ng/mL and the linear range was 20 ~ 100 ng/mL. The possible interfering substances were investigated, and the results showed excellent selectivity. The recoveries were in the range of 99.5%~114.3%, and the relative standard deviations (RSDs) were not more than 6.5%, which demonstrated that this aptasensor was successfully applied for the detection of ZEN in food samples with satisfactory result.
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Affiliation(s)
- Yue Na
- School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road Shenhe District, Shenyang, 110016, Liaoning, P. R. China
| | - Jiaxin Zhang
- School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road Shenhe District, Shenyang, 110016, Liaoning, P. R. China
| | - Shunhua Zhang
- School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road Shenhe District, Shenyang, 110016, Liaoning, P. R. China
| | - Ning Liang
- School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, 110016, Liaoning Province, China.
| | - Longshan Zhao
- School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road Shenhe District, Shenyang, 110016, Liaoning, P. R. China.
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Ding Y, Zhu W, Huang C, Zhang Y, Wang J, Wang X. Quantum dot-labeled phage-encoded RBP 55 as a fluorescent nanoprobe for sensitive and specific detection of Salmonella in food matrices. Food Chem 2023; 428:136724. [PMID: 37418877 DOI: 10.1016/j.foodchem.2023.136724] [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: 03/20/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
As a commonly pathogenic bacterium, the rapid detection of Salmonella outbreaks and assurance of food safety require a highly efficient detection method. Herein, a novel approach to Salmonella detection using quantum dot-labeled phage-encoded RBP 55 as a fluorescent nanoprobe is reported. RBP 55, a novel phage receptor binding protein (RBP), was identified and characterized from phage STP55. RBP 55 was functionalized onto quantum dots (QDs) to form fluorescent nanoprobes. The assay was based on the combination of immunomagnetic separation and RBP 55-QDs, which formed a sandwich composite structure. The results showed a good linear correlation between the fluorescence values and the concentration of Salmonella (101-107 CFU/mL) with a low detection limit of 2 CFU/mL within 2 h. The method was used to successfully detect Salmonella in spiked food samples. This approach can be used for the simultaneous detection of multiple pathogens by labeling different phage-encoded RBPs using polychromatic QDs in the future.
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Affiliation(s)
- Yifeng Ding
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Wenjuan Zhu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Chenxi Huang
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yiming Zhang
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Jia Wang
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaohong Wang
- Key Laboratory of Environment Correlative Dietology, Huazhong Agricultural University, Wuhan 430070, China; College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Detection Method for Tomato Leaf Mildew Based on Hyperspectral Fusion Terahertz Technology. Foods 2023; 12:foods12030535. [PMID: 36766063 PMCID: PMC9914460 DOI: 10.3390/foods12030535] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
Leaf mildew is a common disease of tomato leaves. Its detection is an important means to reduce yield loss from the disease and improve tomato quality. In this study, a new method was developed for the multi-source detection of tomato leaf mildew by THz hyperspectral imaging through combining internal and external leaf features. First, multi-source information obtained from tomato leaves of different disease grades was extracted by near-infrared hyperspectral imaging and THz time-domain spectroscopy, while the influence of low-frequency noise was removed by the Savitzky Golay (SG) smoothing algorithm. A genetic algorithm (GA) was used to optimize the selection of the characteristic near-infrared hyperspectral band. Principal component analysis (PCA) was employed to optimize the THz characteristic absorption spectra and power spectrum dimensions. Recognition models were developed for different grades of tomato leaf mildew infestation by incorporating near-infrared hyperspectral imaging, THz absorbance, and power spectra using the backpropagation neural network (BPNN), and the models had recognition rates of 95%, 96.67%, and 95%, respectively. Based on the near-infrared hyperspectral features, THz time-domain spectrum features, and classification model, the probability density of the posterior distribution of tomato leaf health parameter variables was recalculated by a Bayesian network model. Finally, a fusion diagnosis and health evaluation model of tomato leaf mildew with hyperspectral fusion THz was established, and the recognition rate of tomato leaf mildew samples reached 97.12%, which improved the recognition accuracy by 0.45% when compared with the single detection method, thereby achieving the accurate detection of facility diseases.
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Feng T, Yan S, Wang Z, Fan X. A facile fluorescence turn-on biosensor customized for monitoring of protein kinase activity based on carboxylic carbon nanoparticles-peptide complexes. LUMINESCENCE 2022; 37:922-929. [PMID: 35322517 DOI: 10.1002/bio.4237] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 11/12/2022]
Abstract
In this study, we present a facile and low-cost approach for detecting protein kinase A (PKA) by assembling a purpose-designed carboxyfluorescein (FAM)-labeled peptide with carboxylic carbon nanoparticles (CNPs). Fluorescence of the FAM-labeled peptide gradually decreases to low background signal as a result of the electron transfer from CNPs to FAM-labeled peptide via the peptide, which acts as a bridge. The reaction in the sensor in the presence of adenosine 5'-triphosphate and PKA phosphorylates the substrate peptide and disrupts the electrostatic repulsive force between the CNPs and the peptide, thus altering the spectroscopic signal of the system. The change in fluorescence signal was directly proportional to the PKA concentration in the range of 0-1.8 U/mL with a detection limit of 0.04 U/mL. These results suggest that PKA activity can be effectively measured using the developed PKA biosensor. Moreover, the fluorescence biosensor was successfully used in the investigation of PKA in spiked human embryonic kidney (HEK) 293 cells lysates, indicating its potential applications in protein kinase-related biochemical fundamental research.
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Affiliation(s)
- Tingting Feng
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.,Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Shuzhu Yan
- Institute of Pharmaceutical and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, China
| | - Zheng Wang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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Khojastehnezhad A, Taghavi F, Yaghoobi E, Ramezani M, Alibolandi M, Abnous K, Taghdisi SM. Recent achievements and advances in optical and electrochemical aptasensing detection of ATP based on quantum dots. Talanta 2021; 235:122753. [PMID: 34517621 DOI: 10.1016/j.talanta.2021.122753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/07/2021] [Accepted: 07/28/2021] [Indexed: 12/23/2022]
Abstract
The design and fabrication of high sensitive and selective biosensing platforms areessential goals to precisely recognize biomaterials in biological assays. In particular, determination of adenosine triphosphate (ATP) as the main energy currency of the cells and one of the most important biomolecules in living organisms is a pressing need in advanced biological detection. Recently, aptamer-based biosensors are introduced as a new direct strategy in which the aptamers (Apts) directly bind to the different targets and detect them on the basis of conformational changes and physical interactions. They can also be conjugated to optical and electronic probes such as quantum dot (QD) nanomaterials and provide unique QD aptasensing platforms. Currently, these Apt-based biosensors with excellent recognition features have attracted extensive attention due to the high specificity, rapid response and facile construction. Therefore, in this review article, recent achievements and advances in aptasensing detection of ATP based on different detection methods and types of QDs are discussed. In this regard, the optical and electrochemical aptasensors have been categorized based on detection methods; fluorescence (FL), electrochemiluminescence (ECL) and photoelectrochemical (PEC) and they have been also divided to two main groups based on QDs; metal-based (M-based) and carbon-based (C-based) materials. Then, their advantages and limitations have been highlighted, compared and discussed in detail.
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Affiliation(s)
- Amir Khojastehnezhad
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Faezeh Taghavi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Elnaz Yaghoobi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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8
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Development of novel blue emissive carbon dots for sensitive detection of dual metal ions and their potential applications in bioimaging and chelation therapy. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106706] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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9
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Mendez-Gonzalez D, Silva-Ibáñez PP, Valiente-Dies F, Calderón OG, Mendez-Gonzalez JL, Laurenti M, Egatz-Gómez A, Díaz E, Rubio-Retama J, Melle S. Oligonucleotide sensor based on magnetic capture and photoligation of upconverting nanoparticles in solid surfaces. J Colloid Interface Sci 2021; 596:64-74. [PMID: 33838326 DOI: 10.1016/j.jcis.2021.02.093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/25/2021] [Accepted: 02/21/2021] [Indexed: 10/21/2022]
Abstract
In this work, we present a luminescence platform that can be used as point of care system for determining the presence and concentration of specific oligonucleotide sequences. This sensor exhibited a limit of detection as low as 50 fM by means of: (i) the use of single-stranded DNA (ssDNA) functionalized magnetic microparticles that captured and concentrated ssDNA-upconverting nanoparticles (ssDNA-UCNPs) on a solid support, when the target sequence (miR-21-5p DNA-analogue) was in the sample, and (ii) a photoligation reaction that covalently linked the ssDNA-UCNPs and the ssDNA magnetic microparticles, allowing stringent washes. The presented sensor showed a similar limit of detection when the assays were conducted in samples containing total miRNA extracted from human serum, demonstrating its suitability for detecting small specific oligonucleotide sequences under real-like conditions. The strategy of combining UCNPs, magnetic microparticles, and a photoligation reaction provides new insight into low-cost, rapid, and ultra-sensitive detection of oligonucleotide sequences.
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Affiliation(s)
- Diego Mendez-Gonzalez
- Department of Chemistry in Pharmaceutical Sciences, Complutense University of Madrid, E-28040 Madrid, Spain.
| | - Pedro P Silva-Ibáñez
- Department of Chemistry in Pharmaceutical Sciences, Complutense University of Madrid, E-28040 Madrid, Spain; Department of Animal Science, University of Concepción, Chillán, Chile
| | - Fernando Valiente-Dies
- Department of Chemistry in Pharmaceutical Sciences, Complutense University of Madrid, E-28040 Madrid, Spain; GISC, Department of Materials Physics, Complutense University of Madrid, E-28040 Madrid, Spain
| | - Oscar G Calderón
- Department of Optics, Complutense University of Madrid, E-28037 Madrid, Spain
| | - Juan L Mendez-Gonzalez
- Institute of Optics, Consejo Superior de Investigaciones Científicas (CSIC), E-28006 Madrid, Spain
| | - Marco Laurenti
- Department of Chemistry in Pharmaceutical Sciences, Complutense University of Madrid, E-28040 Madrid, Spain; Instituto de Ciencia de Materiales de Madrid, c/Sor Juana Inés de la Cruz, Cantoblanco, 28049 Madrid, Spain; Instituto Ramón y Cajal de Investigación Sanitaria, Hospital Universitario Ramón y Cajal, 28034 Madrid, Spain
| | - Ana Egatz-Gómez
- Department of Optics, Complutense University of Madrid, E-28037 Madrid, Spain; Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85281, United States
| | - Elena Díaz
- GISC, Department of Materials Physics, Complutense University of Madrid, E-28040 Madrid, Spain
| | - Jorge Rubio-Retama
- Department of Chemistry in Pharmaceutical Sciences, Complutense University of Madrid, E-28040 Madrid, Spain
| | - Sonia Melle
- Department of Optics, Complutense University of Madrid, E-28037 Madrid, Spain.
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Zhang J, Xu H, Li C, Wang Y, Liu D, Zhao S. A label-free logic gate hairpin aptasensor for sensitive detection of ATP based on graphene oxide and PicoGreen dye. J Anal Sci Technol 2021. [DOI: 10.1186/s40543-021-00262-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Abstract
Background
In this paper, a simple, enzyme-free, label-free fluorescence, high sensitivity logic gate hairpin aptasensor was developed for adenosine triphosphate (ATP) detection based on graphene oxide (GO) and PicoGreen dye.
Methods
Using single-strand deoxyribonucleic acid (DNA) and adenosine triphosphate (ATP) as input signal and fluorescence signal as output signal, if single-strand DNA (DNA-L), single-strand DNA (DNA-S), and ATP were present at the same time, one segment of DNA-L formed a hairpin ring with ATP, and the other segment of DNA-L formed a completely complementary hairpin stem with DNA-S. The hairpin DNA was detached from the GO surface, and PicoGreen dye was embedded into the hairpin stem, and the fluorescence signal was enhanced. The molecular logic gate was constructed through the establishment of logic histogram, logic circuit, truth table, and logic formula. The biosensor-related performances including sensitivity, selectivity, and linearity were investigated, respectively.
Results
We have successfully constructed a AND logic gate. The detection limit of ATP is 138.0 pmol/L (3σ/slope) with detection range of 50–500 nmol/L (R2 = 0.98951), and its sensitivity is 4.748 × 106–6.875 × 108 a.u. (mol/L)−1.
Conclusions
The logic gate hairpin aptamer sensor has the advantages of high sensitivity, low detection limit, and low cost, and can be successfully applied to the detection of adenosine triphosphate (ATP) in actual human urine samples.
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Kazemifard N, Ensafi AA, Dehkordi ZS. A review of the incorporation of QDs and imprinting technology in optical sensors – imprinting methods and sensing responses. NEW J CHEM 2021. [DOI: 10.1039/d1nj01104a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This review aims to cover the simultaneous method of using molecularly imprinted technology and quantum dots (QDs) as well as its application in the field of optical sensors.
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Affiliation(s)
- Nafiseh Kazemifard
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111
- Iran
| | - Ali A. Ensafi
- Department of Chemistry
- Isfahan University of Technology
- Isfahan 84156-83111
- Iran
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12
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Khoshbin Z, Housaindokht MR, Izadyar M, Bozorgmehr MR, Verdian A. Recent advances in computational methods for biosensor design. Biotechnol Bioeng 2020; 118:555-578. [PMID: 33135778 DOI: 10.1002/bit.27618] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/25/2020] [Accepted: 10/29/2020] [Indexed: 01/20/2023]
Abstract
Biosensors are analytical tools with a great application in healthcare, food quality control, and environmental monitoring. They are of considerable interest to be designed by using cost-effective and efficient approaches. Designing biosensors with improved functionality or application in new target detection has been converted to a fast-growing field of biomedicine and biotechnology branches. Experimental efforts have led to valuable successes in the field of biosensor design; however, some deficiencies restrict their utilization for this purpose. Computational design of biosensors is introduced as a promising key to eliminate the gap. A set of reliable structure prediction of the biosensor segments, their stability, and accurate descriptors of molecular interactions are required to computationally design biosensors. In this review, we provide a comprehensive insight into the progress of computational methods to guide the design and development of biosensors, including molecular dynamics simulation, quantum mechanics calculations, molecular docking, virtual screening, and a combination of them as the hybrid methodologies. By relying on the recent advances in the computational methods, an opportunity emerged for them to be complementary or an alternative to the experimental methods in the field of biosensor design.
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Affiliation(s)
- Zahra Khoshbin
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Mohammad Izadyar
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Asma Verdian
- Department of Food Safety and Quality Control, Research Institute of Food Science and Technology (RIFST), Mashhad, Iran
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13
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Saberi Z, Rezaei B, Rezaei P, Ensafi AA. Design a fluorometric aptasensor based on CoOOH nanosheets and carbon dots for simultaneous detection of lysozyme and adenosine triphosphate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 233:118197. [PMID: 32146425 DOI: 10.1016/j.saa.2020.118197] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 02/20/2020] [Accepted: 02/23/2020] [Indexed: 06/10/2023]
Abstract
Simultaneous detection of biomarkers and biomolecules with great analytical performance still is challenging. A simple fluorometric dual-functional aptasensor was designed to detect Lysozyme (LYS) and adenosine triphosphate (ATP) as models of a protein and a small molecule simultaneously. The sensing principle of the aptasensor is based on the interactions between cobalt oxyhydroxide CoOOH nanosheets as fluorescence quencher and carbon dots (CDs) as fluorophores. The aptamer labeled with CDs was able to assemble on CoOOH nanosheets and consequently, the fluorescence signal was quenched. With addition target analytes to the system, the aptamers folded around of targets with a strong and specific affinity. Therefore, the labeled aptamer with CDs was detached from CoOOH nanosheets and the fluorescence signal was restored. The fluorescence spectral overlap of these two CDs is the main limitation for the simultaneous analysis. The least squared support vector machine (LS-SVM) was applied to resolve this problem. Under optimal conditions, when LS-SVR was used, detection limits were found 4.0 and 1.8 nmol L-1 for ATP and LYS. The parallel biosensor is capable of monitoring ATP and LYS levels in the biological samples with satisfactory results.
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Affiliation(s)
- Zeinab Saberi
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Islamic Republic of Iran
| | - Behzad Rezaei
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Islamic Republic of Iran.
| | - Parisa Rezaei
- Department of Medical Laboratory Science, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Ali Asghar Ensafi
- Department of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Islamic Republic of Iran
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Yang HW, Ju SP, Lin YS. Predicting the Most Stable Aptamer/Target Molecule Complex Configuration Using a Stochastic-Tunnelling Basin-Hopping Discrete Molecular Dynamics Method: A Novel Global Minimum Search Method for a Biomolecule Complex. Comput Struct Biotechnol J 2019; 17:812-820. [PMID: 31316725 PMCID: PMC6611977 DOI: 10.1016/j.csbj.2019.06.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/10/2019] [Accepted: 06/18/2019] [Indexed: 02/06/2023] Open
Abstract
This study proposed a novel global minimum search method for predicting the most stable biomolecule complex, which combines the strengths of three global minimum search methods (stochastic tunnelling, basin hopping, and discrete molecular dynamics) to efficiently improve the spatial domain search ability of the stochastic tunnelling-basin hopping (STUN-BH) method from our previous study. The epithelial cell adhesion molecule (EpCAM, PDB code: 4MZV) was used as a benchmark target molecule for the EpCAM aptamer EpA (AptEpA). For the most stable AptEpA/EpCAM complex predicted by our new method, the AptEpA was attached to the entangling loop fragments of the two EpCAM molecules with the most AptEpA residues. After the AptEpA/EpCAM complex had equilibrated with the water environment through a molecular dynamics simulation at 300 K for 10 ns, stable hydrogen bonds formed between the bases of AptEpA and EpCAM residues of the secondary structures, which included the alpha helix and beta sheet becoming less stable in the water environment. Those hydrogen bonds formed between the bases of AptEpA and EpCAM loop fragment residues remained stable in the water environment.
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Affiliation(s)
- Hung-Wei Yang
- Institute of Medical Science and Technology, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Shin-Pon Ju
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan.,Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Yu-Sheng Lin
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
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A label-free fluorometric aptasensor for adenosine triphosphate (ATP) detection based on aggregation-induced emission probe. Anal Biochem 2019; 578:60-65. [PMID: 31095938 DOI: 10.1016/j.ab.2019.05.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/09/2019] [Accepted: 05/12/2019] [Indexed: 12/17/2022]
Abstract
Based on Aggregation-Induced Emission (AIE), the development of a label-free, simple and sensitive fluorometric aptasensor for adenosine triphosphate (ATP) detection is described. With ATP present, the aptamers will combine with ATP and the conformation of the aptamer will switch from a random coil to an antiparallel G-quadruplex, which impedes the digestion by exonuclease I (Exo I). Addition of 4,4 -(1E,1E)-2,2-(anthracene-9,10-diyl) bis (ethene-2,1-diyl) bis (N,N, N-trimethyl-benzenaminium iodide) (DSAI) into the solution will cause aggregation of DSAI on the surface of the aptamer/ATP complex and consequently give rise to strong emission. Additionally, a good linear relationship was observed under optimized conditions between the fluorescence intensities and the logarithm of ATP concentrations (R2 = 0.9908). The established aptamer sensor was highly sensitive and exhibited a low limit of detection of 32.8 nM, with superior specificity for ATP. It was also used in the quantification of ATP levels in human serum samples and demonstrated satisfactory recoveries in the scope of 93.2%-107.6%. The cellular ATP assay results indicated that the developed method can be used for monitoring ATP concentrations in cell extracts without the interference of other substances in the cells. This method offers several advantages such as simplicity, rapidity, low cost and excellent selectivity, which make it hold great potential for the detection of ATP in bioanalytical and biological studies.
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16
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A Label-Free Fluorescent DNA Machine for Sensitive Cyclic Amplification Detection of ATP. MATERIALS 2018; 11:ma11122408. [PMID: 30501020 PMCID: PMC6316892 DOI: 10.3390/ma11122408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/25/2018] [Accepted: 11/26/2018] [Indexed: 12/21/2022]
Abstract
In this study, a target recycled amplification, background signal suppression, label-free fluorescent, enzyme-free deoxyribonucleic acid (DNA) machine was developed for the detection of adenosine triphosphate (ATP) in human urine. ATP and DNA fuel strands (FS) were found to trigger the operation of the DNA machine and lead to the cyclic multiplexing of ATP and the release of single stranded (SS) DNA. Double-stranded DNA (dsDNA) was formed on graphene oxide (GO) from the combination of SS DNA and complementary strands (CS′). These double strands then detached from the surface of the GO and in the process interacted with PicoGreen dye resulting in amplifying fluorescence intensity. The results revealed that the detection range of the DNA machine is from 100 to 600 nM (R2 = 0.99108) with a limit of detection (LOD) of 127.9 pM. A DNA machine circuit and AND-NOT-AND-OR logic gates were successfully constructed, and the strategy was used to detect ATP in human urine. With the advantage of target recycling amplification and GO suppressing background signal without fluorescent label and enzyme, this developed strategy has great potential for sensitive detection of different proteins and small molecules.
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Zhang J, Yang C, Niu C, Liu C, Cai X, Du J, Chen Y. A Label-Free Fluorescent AND Logic Gate Aptasensor for Sensitive ATP Detection. SENSORS 2018; 18:s18103281. [PMID: 30274300 PMCID: PMC6210427 DOI: 10.3390/s18103281] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 11/16/2022]
Abstract
In this study, a label-free fluorescent, enzyme-free, simple, highly sensitive AND logic gate aptasensor was developed for the detection of adenosine triphosphate (ATP). Double-stranded deoxyribonucleic acid (DNA) with cohesive ends was attached to graphene oxide (GO) to form an aptasensor probe. ATP and single-stranded DNA were used as input signals. Fluorescence intensity of PicoGreen dye was used as an output signal. The biosensor-related performances, including the logic gate construction, reaction time, linearity, sensitivity, and specificity, were investigated and the results showed that an AND logic gate was successfully constructed. The ATP detection range was found to be 20 to 400 nM (R² = 0.9943) with limit of detection (LOD) of 142.6 pM, and the sensitivity range was 1.846 × 10⁶ to 2.988 × 10⁶ M-1. This method for the detection of ATP has the characteristics of being simple, low cost, and highly sensitive.
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Affiliation(s)
- Jingjing Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Information Science & Technology, College of Materials and Chemical Engineering, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Chunzheng Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Information Science & Technology, College of Materials and Chemical Engineering, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Chaoqun Niu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Information Science & Technology, College of Materials and Chemical Engineering, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Chen Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Information Science & Technology, College of Materials and Chemical Engineering, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Xuepin Cai
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Information Science & Technology, College of Materials and Chemical Engineering, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Jie Du
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Information Science & Technology, College of Materials and Chemical Engineering, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
| | - Yong Chen
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Information Science & Technology, College of Materials and Chemical Engineering, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China.
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Khramtsov P, Kropaneva M, Kalashnikova T, Bochkova M, Timganova V, Zamorina S, Rayev M. Highly Stable Conjugates of Carbon Nanoparticles with DNA Aptamers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:10321-10332. [PMID: 30089209 DOI: 10.1021/acs.langmuir.8b01255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Conjugates of carbon nanoparticles and aptamers have great potential in many areas of biomedicine. In order to be implemented in practice, such conjugates should keep their properties throughout long storage period in commonly available conditions. In this work, we prepared conjugates of carbon nanoparticles (CNP) with DNA aptamers using streptavidin-biotin reaction. Obtained conjugates possess superior stability and kept their physical-chemical and functional properties during 30 days at +4 °C and -20 °C. Proposed approach to conjugation allows loading of about 100-120 pM of biotinylated aptamer per 1 mg of streptavidin-coated CNP (CNP-Str). Aptamer-functionalized CNP-Str have zeta potential of -34 mV at pH 7, mean diameter of 168-177 nm, and polydispersity index of 0.080-0.140. High reproducibility of functionalization was confirmed by preparation of several batches of CNP-aptamer with the same size distribution and aptamer loading using independently synthesized parent CNP-Str nanoparticles. Stability of CNP-aptamer conjugates was significantly enhanced by postsynthesis addition of EDTA that prevents nuclease degradation of immobilized aptamers. Obtained nanoparticles were stable at pH ranging from 6 to 10. Optical properties of CNP-aptamer nanoparticles were also studied and their ability to quench fluorescence via Förster resonance energy transfer was shown. Taking into account properties of CNP-aptamer conjugates, we suppose they may be used in both homo- and heterogeneous colorimetric, fluorescent, and aggregation-based assays.
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Affiliation(s)
- Pavel Khramtsov
- Department of Microbiology and Immunology, Biology Faculty , Perm State National Research University , 614000 , 15 Bukireva Street , Perm , Russia
- Laboratory of Ecological Immunology, Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences - branch of PSRC UB RAS, 614081 , 13 Goleva Street , Perm , Russia
| | - Maria Kropaneva
- Department of Microbiology and Immunology, Biology Faculty , Perm State National Research University , 614000 , 15 Bukireva Street , Perm , Russia
- Laboratory of Ecological Immunology, Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences - branch of PSRC UB RAS, 614081 , 13 Goleva Street , Perm , Russia
| | - Tatyana Kalashnikova
- Department of Microbiology and Immunology, Biology Faculty , Perm State National Research University , 614000 , 15 Bukireva Street , Perm , Russia
| | - Maria Bochkova
- Laboratory of Ecological Immunology, Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences - branch of PSRC UB RAS, 614081 , 13 Goleva Street , Perm , Russia
| | - Valeria Timganova
- Laboratory of Ecological Immunology, Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences - branch of PSRC UB RAS, 614081 , 13 Goleva Street , Perm , Russia
| | - Svetlana Zamorina
- Department of Microbiology and Immunology, Biology Faculty , Perm State National Research University , 614000 , 15 Bukireva Street , Perm , Russia
- Laboratory of Ecological Immunology, Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences - branch of PSRC UB RAS, 614081 , 13 Goleva Street , Perm , Russia
| | - Mikhail Rayev
- Department of Microbiology and Immunology, Biology Faculty , Perm State National Research University , 614000 , 15 Bukireva Street , Perm , Russia
- Laboratory of Ecological Immunology, Institute of Ecology and Genetics of Microorganisms of the Ural Branch of the Russian Academy of Sciences - branch of PSRC UB RAS, 614081 , 13 Goleva Street , Perm , Russia
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