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Naoumi N, Araya-Farias M, Megariti M, Alexandre L, Papadakis G, Descroix S, Gizeli E. Acoustic detection of a mutation-specific Ligase Chain Reaction based on liposome amplification. Analyst 2024; 149:3537-3546. [PMID: 38758167 DOI: 10.1039/d3an02142d] [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: 05/18/2024]
Abstract
Single nucleotide variants (SNVs) play a crucial role in understanding genetic diseases, cancer development, and personalized medicine. However, existing ligase-based amplification and detection techniques, such as Rolling Circle Amplification and Ligase Detection Reaction, suffer from low efficiency and difficulties in product detection. To address these limitations, we propose a novel approach that combines Ligase Chain Reaction (LCR) with acoustic detection using highly dissipative liposomes. In our study, we are using LCR combined with biotin- and cholesterol-tagged primers to produce amplicons also modified at each end with a biotin and cholesterol molecule. We then apply the LCR mix without any purification directly on a neutravidin modified QCM device Au-surface, where the produced amplicons can bind specifically through the biotin end. To improve sensitivity, we finally introduce liposomes as signal enhancers. For demonstration, we used the detection of the BRAF V600E point mutation versus the wild-type allele, achieving an impressive detection limit of 220 aM of the mutant target in the presence of the same amount of the wild type. Finally, we combined the assay with a microfluidic fluidized bed DNA extraction technology, offering the potential for semi-automated detection of SNVs in patients' crude samples. Overall, our LCR/acoustic method outperforms other LCR-based approaches and surface ligation biosensing techniques in terms of detection efficiency and time. It effectively overcomes challenges related to DNA detection, making it applicable in diverse fields, including genetic disease and pathogen detection.
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Affiliation(s)
- Nikoletta Naoumi
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion, 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Monica Araya-Farias
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - Maria Megariti
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Lucile Alexandre
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Stephanie Descroix
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - Electra Gizeli
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion, 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
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Martínez-Pérez-Cejuela H, Gionfriddo E. Evolution of Green Sample Preparation: Fostering a Sustainable Tomorrow in Analytical Sciences. Anal Chem 2024; 96:7840-7863. [PMID: 38687329 DOI: 10.1021/acs.analchem.4c01328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Affiliation(s)
- H Martínez-Pérez-Cejuela
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
| | - E Gionfriddo
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, United States
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Wang Z, Yan B, Ni Y, Cao Y, Qiu J, He R, Dong Y, Hao M, Wang W, Wang C, Su H, Yi B, Chang L. A portable, integrated microfluidics for rapid and sensitive diagnosis of Streptococcus agalactiae in resource-limited environments. Biosens Bioelectron 2024; 247:115917. [PMID: 38101186 DOI: 10.1016/j.bios.2023.115917] [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: 09/27/2023] [Revised: 11/23/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023]
Abstract
Streptococcus agalactiae (Group B Streptococcus, GBS) has been the leading cause of infections in newborns. Rapid and accurate diagnosis of GBS in pregnant women is a deterministic strategy to prevent newborn infection. Conventional detection methods based on nucleic acid amplification assay have been applied in GBS diagnosis in central laboratories, with demonstrated high sensitivity. However, their heavy dependence on instrumentation and trained technicians forms remarkable obstacles to GBS detection in wide scenarios, including self-testing, and bedside-/community-screening. Furthermore, the structures of GBS bring about extra challenges to the nucleic acid extraction and purification. Novel GBS diagnosis platforms integrating sample processing, amplification, and read-out, are highly desired in clinical. Here, we report a portable, integrated microfluidics that enables rapid extraction of DNA from sampling swabs (<10 min), power-free DNA amplification (<30 min), and simple read-out in GBS detection. The platform works without an external pump, achieving rapid and highly efficient DNA extraction from clinical samples, with a significantly reduced time from 6 h to less than 50 min. Systematic clinical tests based on 47 patient samples validated the high performance of the platform, highlighted with a low limit of detection (LOD, 103 copies/ml), high sensitivity (100%), and specificity (100%). Head-to-head comparisons showed that the device improved the LOD by an order of magnitude than the traditional PCR method, showing a simple yet powerful POCT platform for home-/community-based testing towards GBS (and other pathogens) prevention in remote areas.
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Affiliation(s)
- Zhiying Wang
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China
| | - Bo Yan
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Gansu Province Clinical Research Center for Infertility, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Yali Ni
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Gansu Province Clinical Research Center for Infertility, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Yafei Cao
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Gansu Province Clinical Research Center for Infertility, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; The First Clinical Medical College of Gansu University of Chinese Medicine, Lanzhou, 730000, China
| | - Jie Qiu
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Rui He
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Yan Dong
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Man Hao
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Weikai Wang
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Gansu Province Clinical Research Center for Pediatric, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Cheng Wang
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China
| | - Haixiang Su
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China.
| | - Bin Yi
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Gansu Province Clinical Research Center for Pediatric, Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China.
| | - Lingqian Chang
- Gansu Provincial Maternity and Child-care Hospital (Gansu Provincial Central Hospital), Lanzhou, 730050, China; Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing, 100191, China.
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