Recent developments in nucleic acid identification using solid-phase enzymatic assays

Khodakov, Dmitriy A.; Ellis, Amanda

doi:10.1007/s00604-014-1167-z

Cited by 15 publications

(2 citation statements)

References 99 publications

(175 reference statements)

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“…This advantage allows the rapid on-site detection of amplicons in a time-saving manner by overcoming multiple manipulations required for post-analyses of PCR products (Khodakov & Ellis, 2014;Mercier, Slater, & Mayer, 2003;Shin, Perera, Kim, & Park, 2013).…”

Section: Introductionmentioning

confidence: 99%

Microdevice‐based solid‐phase polymerase chain reaction for rapid detection of pathogenic microorganisms

Pham

Jung

Lee

2018

Biotech & Bioengineering

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We demonstrate the integration of DNA amplification and detection functionalities developed on a lab-on-a-chip microdevice utilizing solid-phase polymerase chain reaction (SP-PCR) for point-of-need (PON) DNA analyses. First, the polycarbonate microdevice was fabricated by thermal bonding  to contain microchambers as reservoirs for performing SP-PCR. Next, the microchambers were subsequently modified with polyethyleneimine and glutaraldehyde for immobilizing amine-modified forward primers. During SP-PCR, the immobilized forward primers and freely diffusing fluorescence-labeled reverse primers cooperated to generate target amplicons, which remained covalently attached to the microchambers for the fluorescence detection. The SP-PCR microdevice was used for the direct identifications of two widely detected foodborne pathogens, namely Salmonella spp. and Staphylococcus aureus, and an alga causing harmful algal blooms annually in South Korea, Cochlodinium polykrikoides. The SP-PCR microdevice would be versatilely applied in PON testing as a universal platform for the fast identification of foodborne pathogens and environmentally threatening biogenic targets.

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Section: Introductionmentioning

confidence: 99%

Microdevice‐based solid‐phase polymerase chain reaction for rapid detection of pathogenic microorganisms

Pham

Jung

Lee

2018

Biotech & Bioengineering

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“…In contrast to traditional PCR, these methods do not require changing the reaction temperature and therefore use time-based measurements instead of cycle based measurements. However, isothermal amplification methods have less clinical use than conventional PCR [3], [4].…”

Section: Introductionmentioning

confidence: 99%

A survey of tools for the analysis of quantitative PCR (qPCR) data

Pabinger

Rödiger

Kriegner

et al. 2014

Biomolecular Detection and Quantification

153

119

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Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions.Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR.Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.

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ChemInform Abstract: Recent Developments in Nucleic Acid Identification Using Solid‐Phase Enzymatic Assays

Khodakov

Ellis

2014

ChemInform

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Recent developments in nucleic acid identification using solid-phase enzymatic assays

Cited by 15 publications

References 99 publications

Microdevice‐based solid‐phase polymerase chain reaction for rapid detection of pathogenic microorganisms

Microdevice‐based solid‐phase polymerase chain reaction for rapid detection of pathogenic microorganisms

A survey of tools for the analysis of quantitative PCR (qPCR) data

ChemInform Abstract: Recent Developments in Nucleic Acid Identification Using Solid‐Phase Enzymatic Assays

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