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Ribosomal RNA gene as a high-copy number nucleo-biomarker is extremely conserved among bacteria which limits its application to the discriminative detection approaches. We have developed a colorimetric isothermal amplification method called "single specific primer-LAMP (SSP-LAMP)" requiring only one specific primer for the amplification of the target and applied to the identification of the 16S rRNA gene in the Shigella genus. A region with high sequence homology in the genus and low homology with other bacteria was considered as the most appropriate. In that regard, a 23 bp sequence in the 16S rRNA gene of the genus was targeted based on the alignment of the gene with fifty-three closely related bacterial species, and a single specific primer along with five degenerate primers were designed. Using hydroxy-naphthol blue (HNB) as an indicator and gel electrophoresis, the proposed approach of SSP-LAMP was able to detect S. boydii, S. sonnei, S. flexneri and S. dysenteriae specifically while other species remained unidentified. The SSP-LAMP method could provide a rapid one-pot point-of-care method for molecular diagnostics of pathogens in many circumstances mainly samples with high genetic homogeneity., (Copyright © 2021 Elsevier Inc. All rights reserved.)

A comparative review of the most common isothermal methods is provided. In the last two decades, the challenge of using isothermal amplification systems as an alternate to the most extensive and long-standing nucleic acids-amplifying method-the polymerase chain reaction-has arisen. The main advantage of isothermal amplification is no requirement for expensive laboratory equipment for thermal cycling. Considerable efforts have been made to improve the current techniques of nucleic acid amplification and the development of new approaches based on the main drawbacks of each method. The most important and challenging goal was to achieve a low-cost, straightforward system that is rapid, specific, accurate, and sensitive., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Lack of an appropriate detection method for isothermal RNA amplification technique, known as nucleic acid sequence-based amplification (NASBA), is considered as a major defect for its vast applications. In that regard, novel detection methods as fast, specific, and sensitive as the gold nanoprobe detection technique are highly demanded and non-crosslinking gold nanoprobes are regarded as the ideal choice. In this study, we attempted to integrate these two techniques (RNA amplification and nanoprobe detection) into a single detection-associated amplification method. In that line, essential adjustments such as amplicon dilution, disturbing reagent extraction, ion adjustment, and modification of the hybridization protocol were needed due to the ribonucleic acid nature of NASBA products and the presence of some interfering reagents in the amplification reaction environment. The adjustments successfully resulted in the gold nanoparticle-based detection of NASBA products with naked eyes in a whole operational time of less than 3.5h (including nucleic acid extraction, amplification, and detection). Furthermore, the developed assay was successfully applied to detect dnaK messenger RNA of Salmonella typhimurium. The developed colorimetric method facilitated the detection step of NASBA leading to an ideal methodology for rapid assays and serves as an ideal alternative to the highly expensive reverse transcription polymerase chain reaction (RT-PCR) approach., (Copyright © 2012 Elsevier Inc. All rights reserved.)