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Xu X, Fu J, Jiao X, Wang Y, Yao C. DNA-induced assembly of biocatalytic nanocompartments for sensitive and selective aptasensing of aflatoxin B1. Anal Chim Acta 2024; 1295:342328. [PMID: 38355226 DOI: 10.1016/j.aca.2024.342328] [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: 12/18/2023] [Revised: 01/28/2024] [Accepted: 02/01/2024] [Indexed: 02/16/2024]
Abstract
Enzyme cascade with high specificity and catalytic efficiency has significant applications for developing efficient bioanalysis methods. In this work, a sensitive and selective aptasensor was constructed based on the DNA-induced assembly of biocatalytic nanocompartments. Different from the conventional co-immobilization in one pot, the cascade enzymes of glucose oxidase (GOX) and horseradish peroxidase (HRP) were separately encapsulated in ZIF-90 nanoparticles. After conjugating complementary DNA or aptermer on enzyme@ZIF-90, DNA hybridization drove enzyme@ZIF-90 connected into clusters or linked on other DNA modified biocatalytic nanocompartment (such as invertase loaded Fe3O4@SiO2). Owing to the shortened distance between enzymes, the catalytic efficiency of connected clusters was significantly enhanced. However, the specifically interaction between the substrate molecule and aptermer sequence would lead to the disassembly of DNA duplexes, resulting in the gradual "switching-off" of cascade reactions. With aflatoxin B1 (AFB1) as the model substrate, the compartmentalized three-enzyme nanoreactors showed good analytical performance in the linear range from 0.01 ng mL-1 to 50 ng mL-1 with a low detection limit (3.3 pg mL-1). In addition, the proposed aptasensor was applied to detect AFB1 in corn oil and wheat powder samples with total recoveries ranging from 94 % to 109 %. As a result, this DNA-induced strategy for enzyme cascade nanoreactors opens new avenues for stimuli-responsive applications in biosensing.
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Affiliation(s)
- Xuan Xu
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, PR China.
| | - Junfeng Fu
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, PR China
| | - Xiaotong Jiao
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, PR China
| | - Yuqin Wang
- College of Pharmaceutical Sciences, Nanjing Tech University, Nanjing, 211816, PR China
| | - Cheng Yao
- College of Chemistry and Molecular Engineering, Nanjing Tech University, Nanjing, 211816, PR China
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2
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Shik AV, Skorobogatov EV, Bliznyuk UA, Chernyaev AP, Avdyukhina VM, Yu Borschegovskaya P, Zolotov SA, Baytler MO, Doroshenko IA, Podrugina TA, Beklemishev MK. Estimation of doses absorbed by potato tubers under electron beam or X-ray irradiation using an optical fingerprinting strategy. Food Chem 2023; 414:135668. [PMID: 36841105 DOI: 10.1016/j.foodchem.2023.135668] [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: 09/17/2022] [Revised: 01/04/2023] [Accepted: 02/08/2023] [Indexed: 02/15/2023]
Abstract
High-energy electron beam and X-ray processing of foods can be used for extending their storage life and for combating pests and pathogens. Several instrumental techniques are used to estimate irradiation doses in foods, but these methods are complex and laborious, require expensive equipment, and do not always allow to determine low doses. This study was aimed at developing simple methods for detecting irradiation in potato tubers and for dose estimation. We used a "fingerprinting" strategy that does not involve quantitation of any compound; instead, the rate of indicator reactions involving carbocyanine dyes is measured. The dye content was monitored by its near-infrared fluorescence intensity and visible-light absorption. Potatoes not subjected to treatment and those irradiated with different doses (10, 100, 1000, 5000, or 10,000 Gray) could be distinguished by linear discriminant analysis. Thus, the order of magnitude of the absorbed dose can be estimated with 89% ± 3% accuracy for a mixture of tubers of two potato varieties irradiated with an electron beam or with 95% ± 8% accuracy for one variety irradiated with an X-ray source.
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Affiliation(s)
- Anna V Shik
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia.
| | - Evgenii V Skorobogatov
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia
| | - Ulyana A Bliznyuk
- Physics Department, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia; Skobeltsyn Institute of Nuclear Physics, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia.
| | - Alexander P Chernyaev
- Physics Department, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia; Skobeltsyn Institute of Nuclear Physics, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia.
| | | | - Polina Yu Borschegovskaya
- Physics Department, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia; Skobeltsyn Institute of Nuclear Physics, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia.
| | - Sergey A Zolotov
- Physics Department, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia; Skobeltsyn Institute of Nuclear Physics, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia
| | - Maksim O Baytler
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia
| | - Irina A Doroshenko
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia
| | - Tatyana A Podrugina
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia.
| | - Mikhail K Beklemishev
- Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow 119991 GSP-1, Russia.
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Bharati M, Rana L, Gupta R, Sharma A, Jha PK, Tomar M. Realization of a DNA biosensor using inverted Lamb wave MEMS resonator based on ZnO/SiO 2/Si/ZnO membrane. Anal Chim Acta 2023; 1249:340929. [PMID: 36868768 DOI: 10.1016/j.aca.2023.340929] [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: 10/22/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
A novel technique based on inverted Lamb wave MEMS resonator has been exploited for the realization of a DNA biosensor. Zinc oxide based Lamb wave MEMS resonator in the inverted configuration of ZnO/SiO2/Si/ZnO is fabricated for label free and efficient detection of Neisseria meningitidis, responsible for bacterial meningitis. Meningitis remains a devastating endemic in sub-Saharan Africa. Its early detection can prevent the spread and its lethal complications. The developed biosensor shows a very high sensitivity of 310 Hz(ngμl-1)-1 and very low detection limit of 82 pgμl-1 for symmetric mode of the Lamb wave device while the antisymmetric mode shows a sensitivity of 202 Hz(ngμl-1)-1 and the limit of detection of 84 pgμl-1. This very high sensitivity and very low detection limit of the Lamb wave resonator can be attributed to very high mass loading effect on the membranous structure of Lamb wave device, unlike the bulk substrate based devices. The indigenously developed MEMS based inverted Lamb wave biosensor shows high selectivity, long shelf life and good reproducibility. The ease of operation, low processing time and possibility of wireless integration of the of the Lamb wave DNA sensor paves a path towards the promising application in the field of meningitidis detection. The use of fabricated biosensor can be extended to other viral and bacterial detection applications as well.
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Affiliation(s)
- Manisha Bharati
- Department of Physics and Astrophysics, University of Delhi, Delhi, 110007, India
| | - Lokesh Rana
- Department of Physics, Zakir Husain Delhi College, University of Delhi, Delhi, 110002, India
| | - Reema Gupta
- Department of Physics, Hindu College, University of Delhi, Delhi, 110007, India
| | - Anjali Sharma
- Department of Physics, ARSD College, University of Delhi, Delhi, 110021, India; Institute of Eminence, University of Delhi, Delhi, 110007, India
| | - Pradip K Jha
- Department of Physics, DDU College, University of Delhi, New Delhi, 110078, India
| | - Monika Tomar
- Institute of Eminence, University of Delhi, Delhi, 110007, India; Department of Physics, Miranda House, University of Delhi, Delhi, 110007, India.
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Das B, Toraman S. Deep transfer learning for automated liver cancer gene recognition using spectrogram images of digitized DNA sequences. Biomed Signal Process Control 2022. [DOI: 10.1016/j.bspc.2021.103317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Khoje ZB, kumarVootla S, David M. Brain DNA damage analysis in pesticide exposed wistar albino rats (Rattus norvegicus): a chemometric approach. J Biomol Struct Dyn 2022; 41:2211-2220. [PMID: 35067187 DOI: 10.1080/07391102.2022.2029566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Brain the most important organ which controls most of the regulations in the body is composed of neurons and glia. As brain has a high metabolic rate and reduced cell renewal capability, the lipids, proteins and nucleic acids become the major targets of damage. In the present study carbofuran (CF) induced brain DNA damage in male wistar albino rats at sub-lethal doses (Control-A; B-1.0, C-0.5 and D-0.3 mg/kg BW) while the groups B1,C1, D1, B2, C2, D2 and B3, C3, D3 represents the exposure duration 30, 60 and 90 days each respectively. FTIR spectroscopy based chemometric analysis of functional groups in nucleic acids are reported, changes in band area and band frequencies were examined to understand the DNA damage by constructing heat map. Significant changes were observed in the band frequency, band areas, bandwidth and intensity values (p < 0.05, 0.01, 0.001). The principal component analysis was analyzed to study the alterations at the molecular level, which revealed maximum variance of 74% in groups A, B1, C1, D1 and C2 and 13.7% variance in B2, D2, B3, C3 and D3. The present study provides significant details to analyse DNA damage using non-conventional approach and can also be used for detecting DNA damage in several neural diseases and disorders and emphasizes on using FTIR spectral data through chemometric approach to analyse the DNA damage.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zabin Begum Khoje
- Department of Studies in Zoology, Karnatak University, Dharwad, Karnataka, India
| | - Shyam kumarVootla
- Department of Studies in Microbiology and Biotechnology, Karnatak University, Dharwad, Karnataka, India
| | - Muniswamy David
- Department of Studies in Zoology, Karnatak University, Dharwad, Karnataka, India
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Gaikwad PS, Sarma C, Negi A, Pare A. Alternate Food Preservation Technology. Food Chem 2021. [DOI: 10.1002/9781119792130.ch10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Radiation-Induced Effect on Spin-Selective Electron Transfer through Self-Assembled Monolayers of ds-DNA. MAGNETOCHEMISTRY 2021. [DOI: 10.3390/magnetochemistry7070098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Stability of the DNA molecule is essential for the proper functioning and sustainability of all living organisms. In this study, we investigate the effect of gamma radiation (γ-radiation) on spin-selective electron transfer through double strand (ds)DNA molecules. Self-assembled monolayers (SAMs) of 21-base long DNA are prepared on Au-coated Ni thin film. We measure the spin polarization (%) of the SAMs of ds-DNA using the spin-dependent electrochemical technique. We use a Cs-based γ-radiation source to expose the SAMs of ds-DNA immobilized on thin films for various time intervals ranging from 0–30 min. The susceptibility of DNA to γ-radiation is measured by spin-dependent electrochemistry. We observe that the efficiency of spin filtering by ds-DNA gradually decreases when exposure (to γ-radiation) time increases, and drops below 1% after 30 min of exposure. The change in spin polarization value is related either to the conformational perturbation in DNA or to structural damage in DNA molecules caused by ionizing radiation.
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Varrà MO, Fasolato L, Serva L, Ghidini S, Novelli E, Zanardi E. Use of near infrared spectroscopy coupled with chemometrics for fast detection of irradiated dry fermented sausages. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.107009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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