Simple visualized readout of suppressed coffee ring patterns for rapid and isothermal genetic testing of antibacterial resistance

Kang, Yoo Kyung; Im, San Hae; Ryu, Jea Sung; Lee, Jae-Hyun; Chung, Hyun Jung

doi:10.1016/j.bios.2020.112566

Cited by 25 publications

(10 citation statements)

References 38 publications

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“…2 b, the band for the ligated padlock probe is observed only when added with the target DNA for mecA, whereas the bands do not appear when target DNA is absence or when added with control target DNAs for other resistance genes NDM-1 and KPC [ 35 , 36 ]. Exo1 treatment of the padlock probe ligated by mecA target DNA resulted in a shift of the band to the (−) electrode, due to the decrease in size by removal of single-strand target DNA which used to be bound to the padlock probe [ 19 ]. This result demonstrates the specificity of the padlock probe, which is able to ligate only upon complementary binding of mecA target DNA.…”

Section: Resultsmentioning

confidence: 99%

“…Ligation and RCA was performed according to a previous report with modification in the materials and procedures [ 19 ]. The sequences for padlock probes, biotin-primers, FAM-probes, and target DNAs are listed in Table 1 .…”

Section: Methodsmentioning

confidence: 99%

“…The amplified products must be detected by colorimetric, fluorescence, optical, or electrochemical means, and usually involves the addition of organic substrates or hybridization probes to induce specific target signals [12][13][14][15][16]. Advanced methods such as detection of RCA products based on hydrogel formation or suppression of coffee ring patterns have been reported as novel approaches to apply genetic testing as a simple and affordable assay while achieving high sensitivity [17][18][19]. However, these strategies require further development as a platform to be available to customers for practical use as a self-diagnostic kit for on-site or home settings.…”

Section: Introductionmentioning

confidence: 99%

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A Lateral Flow Assay for Nucleic Acid Detection Based on Rolling Circle Amplification Using Capture Ligand-Modified Oligonucleotides

et al. 2022

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We introduce a lateral flow assay (LFA) integrated with a modified isothermal nucleic acid amplification procedure for rapid and simple genetic testing. Padlock probes specific for the target DNA were designed for ligation, followed by rolling circle amplification (RCA) using capture ligand-modified oligonucleotides as primers. After hybridization with detection linker probes, the amplified target DNA is flowed through an LFA membrane strip for binding of gold nanoparticles as the substrate for colorimetric detection. We established and validated the “RCA-LFA” method for detection of mecA, the antibiotic resistance gene for methicillin-resistant Staphylococcus aureus (MRSA). The assay was optimized using various concentrations of primers and probes for RCA and LFA, respectively. The sensitivity was determined by performing RCA-LFA using various amounts of mecA target DNA, showing a detection limit of ~ 1.3 fmol. The specificity of the assay was examined using target DNAs for other resistance genes as the controls, which demonstrated positive detection signals only for mecA DNA, when added either individually or in combinations with the control targets. Furthermore, applying the RCA-LFA method using specifically designed probes for RNA-dependent RNA polymerase (RdRp) and receptor binding domain (RBD) gene for SARS-CoV-2, which demonstrated feasibility of the method for viral gene targets. The current method suggests a useful platform which can be universally applied for various nucleic acid targets, allowing rapid and sensitive diagnosis at point-of-care. Supplementary Information The online version contains supplementary material available at 10.1007/s13206-022-00080-1.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A Lateral Flow Assay for Nucleic Acid Detection Based on Rolling Circle Amplification Using Capture Ligand-Modified Oligonucleotides

et al. 2022

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“…Interestingly, the growth dynamics of coffee rings are altered when active particles such as motile bacteria move around in the evaporating droplet [767][768][769][770], and bacterial suspensions can feature acive depinning dynamics. Hence, in the spirit of frugal science, it might be possible to exploit the coffee ring effect to detect antimicrobial resistance [771].…”

Section: E Coffee Ring Effectmentioning

confidence: 99%

Culinary fluid mechanics and other currents in food science

Mathijssen¹,

Lisicki²,

Prakash³

et al. 2022

Preprint

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Innovations in fluid mechanics have refined food since ancient history, while creativity in cooking inspires science in return. Here, we review how recent advances in hydrodynamics are changing food science, and we highlight how the surprising phenomena that arise in the kitchen lead to discoveries and technologies across the disciplines, including rheology, soft matter, biophysics and molecular gastronomy. This review is structured like a menu, where each course highlights different aspects of culinary fluid mechanics. Our main themes include multiphase flows, complex fluids, thermal convection, hydrodynamic instabilities, viscous flows, granular matter, porous media, percolation, chaotic advection, interfacial phenomena, and turbulence. For every topic, we first provide an introduction accessible to food professionals and scientists in neighbouring fields. We then assess the state-of-the-art knowledge, the open problems, and likely directions for future research. New gastronomic ideas grow rapidly as the scientific recipes keep improving too.

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“…(2) In LAMP, three pairs of primers are used with six distinct target regions of the DNA sequence, making it highly specific compared with NASBA ( Trinh et al, 2019 ). (3) LAMP can be achieved with a single step reaction, whereas one additional ligation step is required before amplification for RCA ( Kang et al, 2020 ; Yue et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Rotational diffusometric sensor with isothermal amplification for ultra-sensitive and rapid detection of SARS-CoV-2 nsp2 cDNA

Das

Lin

Kwon

et al. 2022

Biosensors and Bioelectronics

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Simple visualized readout of suppressed coffee ring patterns for rapid and isothermal genetic testing of antibacterial resistance

Cited by 25 publications

References 38 publications

A Lateral Flow Assay for Nucleic Acid Detection Based on Rolling Circle Amplification Using Capture Ligand-Modified Oligonucleotides

A Lateral Flow Assay for Nucleic Acid Detection Based on Rolling Circle Amplification Using Capture Ligand-Modified Oligonucleotides

Culinary fluid mechanics and other currents in food science

Rotational diffusometric sensor with isothermal amplification for ultra-sensitive and rapid detection of SARS-CoV-2 nsp2 cDNA

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