Helicase-dependent amplification: use in OnChip amplification and potential for point-of-care diagnostics

Andresen, Dennie; Nickisch‐Rosenegk, Markus von; Bier, Frank F.

doi:10.1586/erm.09.46

Cited by 38 publications

(21 citation statements)

References 28 publications

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“…Pemov et al described a gel element array where multiplex PCR occurs on and within gel element arrays and is enhanced by pseudomonoplex PCR in solution (38) A similar method is described by Li et al (39), except that the microarray was constructed with gene-specific, universally tagged amplification primers immobilized within microwells. Helicasedependent, solid-phase amplification has also been demonstrated and provides an opportunity to simplify the attendant instrumentation by eliminating the need for a thermal cycler (40). In all cases, however, solid-phase amplification is limited (in part) by the kinetics of (low-copy-number) target hybridization to the array surface during the initial rounds of the amplification reaction.…”

Section: Discussionmentioning

confidence: 99%

Profiling In Situ Microbial Community Structure with an Amplification Microarray

Chandler

Knickerbocker

Bryant

et al. 2013

Appl Environ Microbiol

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The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO 3 ؊ ) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO 3 , but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications.

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Section: Discussionmentioning

confidence: 99%

Profiling In Situ Microbial Community Structure with an Amplification Microarray

Chandler

Knickerbocker

Bryant

et al. 2013

Appl Environ Microbiol

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“…The isothermal amplification techniques, which include Loop-Mediated Isothermal Amplification (LAMP) [13], [14], Helicase-Dependent Amplification (HDA) [15], Recombinase Polymerase Amplification (RPA) [16], Rolling Circle Amplification (RCA) [17], are important innovations in the development of clinical diagnosis systems, because they can deliver a qualitative positive or negative response to pathogen detection, particularly when the target is in low amounts, within a short period of time (circa 1–2 hour). Of these LAMP and HDA have been developed commercially [18].…”

Section: Resultsmentioning

confidence: 99%

A Novel Cassette Method for Probe Evaluation in the Designed Biochips

et al. 2014

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A critical step in biochip design is the selection of probes with identical hybridisation characteristics. In this article we describe a novel method for evaluating DNA hybridisation probes, allowing the fine-tuning of biochips, that uses cassettes with multiple probes. Each cassette contains probes in equimolar proportions so that their hybridisation performance can be assessed in a single reaction. The model used to demonstrate this method was a series of probes developed to detect TORCH pathogens. DNA probes were designed for Toxoplasma gondii, Chlamidia trachomatis, Rubella, Cytomegalovirus, and Herpes virus and these were used to construct the DNA cassettes. Five cassettes were constructed to detect TORCH pathogens using a variety of genes coding for membrane proteins, viral matrix protein, an early expressed viral protein, viral DNA polymerase and the repetitive gene B1 of Toxoplasma gondii. All of these probes, except that for the B1 gene, exhibited similar profiles under the same hybridisation conditions. The failure of the B1 gene probe to hybridise was not due to a position effect, and this indicated that the probe was unsuitable for inclusion in the biochip. The redesigned probe for the B1 gene exhibited identical hybridisation properties to the other probes, suitable for inclusion in a biochip.

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“…HDA has been shown to be effective for various samples, from urine [112] and vaginal swabs [112] to blood [110,111] and stool [108,109]. Therefore, the HDA has a great potential for using it in portable pointof-care devices [113].…”

Section: E Colimentioning

confidence: 99%

Isothermal Amplification and Quantification of Nucleic Acids and its Use in Microsystems

Tröger¹,

Niemann²,

Gärtig³

et al. 2015

J Nanomed Nanotechnol

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Nucleic acid amplification technologies (NAATs) offer the most sensitive tests in the clinical laboratory. These techniques are used as a powerful tool for screening and diagnosis of infectious diseases. Isothermal methods, as an alternative to polymerase chain reaction (PCR), require no thermocycling machine and can mostly be performed with reduced time, high throughput, and accurate and reliable results.However, current molecular diagnostic approaches generally need manual analysis by qualified and experienced personal which is a highly complex, time-consuming and labor-intensive task. Thus, the demand for simpler, miniaturized systems and assays for pathogen detection is steadily increasing. Microfluidic platforms and lab-on-a-chip devices have many advantages such as small sample volume, portability and rapid detection time and enable point-of-care diagnosis.In this article, we review several isothermal amplification methods and their implementation in microsystems in relation to quantification of nucleic acids. miniaturized systems can be diverse. The majority of publications are focussed on clinical diagnostics including foodborne organisms for environmental monitoring [10][11][12]. In case of an infectious disease, cultivation and phenotypic characterization are still the standard methods of microbiologists which need days up to weeks to obtain a diagnostic result. Hence, scientists started to make use of nucleic acid amplification methods to accelerate the analysis. The most widespread and well known technique for this purpose is the polymerase chain reaction (PCR) [10,13], which exploits the activity of the DNA polymerase. The method is based on a thermal cycling process consisting of repeated cycles of heating and cooling steps allowing for DNA melting, sequence specific primer binding and enzymatic amplification of the target nucleic acid. The quantitative assessment of target copies is possible by using a real-time PCR approach, where a concentration dependent signal (e.g. fluorescence) increases over time [14]. The latter enables the user to easily assess the pathogen load of patient samples [15][16][17][18]. Since the first example of a PCR on a miniaturized system in 1994 [19,20], numerous devices were presented, which integrate not just the amplification, but also sample preparation and detection steps [9,[21][22][23][24][25][26][27][28]. Just a few of those microsystems have reached the market so far, but some have shown a fascinating potential to replace the classical laboratory-oriented state-of-the art [29][30][31][32][33]. setups has been shown to obtain a similar result [34]. A smaller heat capacity allows for rapid changes in temperature beneficial for the PCR time as well as a higher parallelism of multiple genetic samples [34].However, a major drawback of the integration of PCR to microsystems is the necessity of sophisticated instrumentation. The reaction requires a thermal cycling instrumentation, space and considerable expertise [35]. Therefore, isothermal reactions for the ta...

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Helicase-dependent amplification: use in OnChip amplification and potential for point-of-care diagnostics

Cited by 38 publications

References 28 publications

Profiling In Situ Microbial Community Structure with an Amplification Microarray

Profiling In Situ Microbial Community Structure with an Amplification Microarray

A Novel Cassette Method for Probe Evaluation in the Designed Biochips

Isothermal Amplification and Quantification of Nucleic Acids and its Use in Microsystems

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