Rapid isothermal detection assay: a probe amplification method for the detection of nucleic acids

Gao, Wenjuan; Li, Xiang; Zeng, Lingwen; Peng, Tao

doi:10.1016/j.diagmicrobio.2007.08.002

Cited by 19 publications

(14 citation statements)

References 30 publications

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“…For example, specific gene sequences of genomic DNA can be detected sensitively and specifically by PG–RCA as long as the sequences include nicking sites. The same assay scheme may be applicable to specific RNA sequence detection since nicking reaction of DNA strands in DNA/RNA hybrids was recently reported (17). Alternatively, PG–RCA can be combined with nucleic-acid probe technology such as cycling probe and invader probe to detect specific DNA or RNA sequences and generate specific 3′-end sequence for PG–RCA detection (18–20).…”

Section: Resultsmentioning

confidence: 93%

Sensitive isothermal detection of nucleic-acid sequence by primer generation–rolling circle amplification

Murakami

Sumaoka

Komiyama

2008

Nucleic Acids Research

193

128

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A simple isothermal nucleic-acid amplification reaction, primer generation–rolling circle amplification (PG–RCA), was developed to detect specific nucleic-acid sequences of sample DNA. This amplification method is achievable at a constant temperature (e.g. 60°C) simply by mixing circular single-stranded DNA probe, DNA polymerase and nicking enzyme. Unlike conventional nucleic-acid amplification reactions such as polymerase chain reaction (PCR), this reaction does not require exogenous primers, which often cause primer dimerization or non-specific amplification. Instead, ‘primers’ are generated and accumulated during the reaction. The circular probe carries only two sequences: (i) a hybridization sequence to the sample DNA and (ii) a recognition sequence of the nicking enzyme. In PG–RCA, the circular probe first hybridizes with the sample DNA, and then a cascade reaction of linear rolling circle amplification and nicking reactions takes place. In contrast with conventional linear rolling circle amplification, the signal amplification is in an exponential mode since many copies of ‘primers’ are successively produced by multiple nicking reactions. Under the optimized condition, we obtained a remarkable sensitivity of 84.5 ymol (50.7 molecules) of synthetic sample DNA and 0.163 pg (∼60 molecules) of genomic DNA from Listeria monocytogenes, indicating strong applicability of PG–RCA to various molecular diagnostic assays.

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Section: Resultsmentioning

confidence: 93%

Sensitive isothermal detection of nucleic-acid sequence by primer generation–rolling circle amplification

Murakami

Sumaoka

Komiyama

2008

Nucleic Acids Research

193

128

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“…The assay was evaluated using 22 different H5 isolates, including H5N1, H5N2, H5N3 and H5N9, and only HPAIV Qinghai-like isolates were positive. Goa et al described a rapid isothermal amplification assay (RIDA) that uses chemically labeled probes and a lateral-flow (LF) immunoassay format for the detection of H5N1 virus 42 . RIDA is a probe amplification method that uses single strand endonuclease nicking to repeatedly nick synthetic probes hybridizing to the same target.…”

Section: Influenza Virusmentioning

confidence: 99%

Molecular diagnosis of respiratory virus infections

Mahony¹,

Petrich²,

Śmieja³

2011

Critical Reviews in Clinical Laboratory Sciences

183

181

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The appearance of eight new respiratory viruses, including the SARS coronavirus in 2003 and swine-origin influenza A/H1N1 in 2009, in the human population in the past nine years has tested the ability of virology laboratories to develop diagnostic tests to identify these viruses. Nucleic acid based amplification tests (NATs) for respiratory viruses were first introduced two decades ago and today are utilized for the detection of both conventional and emerging viruses. These tests are more sensitive than other diagnostic approaches, including virus isolation in cell culture, shell vial culture (SVC), antigen detection by direct fluorescent antibody (DFA) staining, and rapid enzyme immunoassay (EIA), and now form the backbone of clinical virology laboratory testing around the world. NATs not only provide fast, accurate and sensitive detection of respiratory viruses in clinical specimens but also have increased our understanding of the epidemiology of both new emerging viruses such as the pandemic H1N1 influenza virus of 2009, and conventional viruses such as the common cold viruses, including rhinovirus and coronavirus. Multiplex polymerase chain reaction (PCR) assays introduced in the last five years detect up to 19 different viruses in a single test. Several multiplex PCR tests are now commercially available and tests are working their way into clinical laboratories. The final chapter in the evolution of respiratory virus diagnostics has been the addition of allelic discrimination and detection of single nucleotide polymorphisms associated with antiviral resistance. These assays are now being multiplexed with primary detection and subtyping assays, especially in the case of influenza virus. These resistance assays, together with viral load assays, will enable clinical laboratories to provide physicians with new and important information for optimal treatment of respiratory virus infections.

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“…In our research, we firstly amplified the RNA target by NASBA; the amplification time in this step could be shortened because the next step of RIDA reaction would amplify the signal of the products by the fluorescence probe. The traditional RIDA method was detected by quantitative PCR instrument which is unavailable in some resource-limited place (Gao et al, 2008). In our research we found that the result can be simply determined with the naked eye by the color difference between positive and negative results under UV irradiation.…”

Section: Introductionmentioning

confidence: 82%

“…To resolve these problems and improve the sensitivity and specificity, we developed a new diagnosis assay which combined the rapid isothermal detection assay (RIDA) with NASBA. RIDA is a "probe amplification" assay, which uses the single-strand nicking activity of restriction nicking endonucleases to repeatedly cleave synthetic probes hybridizing to the same target sequences (Gao et al, 2008;Shi, 2003). RIDA is achieved through the binding of a reporting probe (RP) to the target ssDNA or RNA, followed by the nicking on the RP with the restriction nicking endonuclease.…”

Section: Introductionmentioning

confidence: 99%

New molecular diagnosis method combined with nucleic acid sequence-based amplification and probe amplification in rapid detection of Enterovirus 71

Hong¹,

Kong²,

Xing³

et al. 2012

Afr. J. Microbiol. Res.

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In this study, a new molecular diagnosis assay for rapid detection of virus RNA was established, which combined nucleic acid sequence-based amplification (NASBA) with rapid isothermal detection assay (RIDA). Using this method, we could rapidly identify Human enterovirus 71 RNA with high sensitivity and specificity; the detection limit of the new method was 10 2 copy/ml. The whole assay was processed in one tube and the result was determined by naked eyes under ultraviolet radiation without capopening, meanwhile, as the products of amplification was RNA which is easily degradative, thus, the aerosol contamination was further decreased. This novel method shows excellent sensitivity, specificity and conveniences, which is easily operated in the elementary medical organizations and resource-limited areas.

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Rapid isothermal detection assay: a probe amplification method for the detection of nucleic acids

Cited by 19 publications

References 30 publications

Sensitive isothermal detection of nucleic-acid sequence by primer generation–rolling circle amplification

Sensitive isothermal detection of nucleic-acid sequence by primer generation–rolling circle amplification

Molecular diagnosis of respiratory virus infections

New molecular diagnosis method combined with nucleic acid sequence-based amplification and probe amplification in rapid detection of Enterovirus 71

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