Diagnostic performance of isothermal strand displacement amplification of Mycobacterium tuberculosis IS 6110 in tissue samples

Alnimr, Amani; Alnemer, Areej

doi:10.1016/j.ijmyco.2012.09.001

Cited by 4 publications

(3 citation statements)

References 29 publications

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“…The design of HyCaSD was based on strand-displacement amplification, a method which is known to have high amplification kinetics and efficiency. − The HyCaSD method was designed to exponentially amplify the target RNA. It exhibited an excellent sensitivity with LOD in the femtomolar range.…”

Section: Resultsmentioning

confidence: 99%

Hybridization Cascade Plus Strand-Displacement Isothermal Amplification of RNA Target with Secondary Structure Motifs and Its Application for Detecting Dengue and Zika Viruses

et al. 2019

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Biological RNA generally comprises secondary structure motifs which cause a problem for target RNA detection by isothermal amplification methods. The complexity of the secondary structures makes RNA targets inaccessible for probe hybridization, resulting in decreased sensitivity and selectivity. This is particularly important because the hybridization step of the isothermal amplification method requires a limited temperature range. A strand-displacement strategy can enhance the hybridization efficiency between the probe and target RNA with secondary structure motifs. A short, singlestranded segment within the secondary structure can be used as a toehold for initiating strand displacement. The strategy has been used to establish a highly sensitive isothermal amplification by a combination of a hairpin probe hybridization and stranddisplacement amplification. The hairpin probe is placed on the single-stranded segment of the target RNA's secondary structure to initiate strand displacement. The probe's hybridization cascade provides a template for exponential amplification in two directions by strand-displacement amplification, designated hybridization cascade plus strand-displacement isothermal amplification (HyCaSD). The method requires no reverse transcription step. HyCaSD showed an excellent sensitivity with the limit of detection in the femtomolar (fM) range for synthetic targets as well as viral RNAs. Discrimination between DENV/ ZIKV and JEV/CHIKV was successfully demonstrated using real viruses. Therefore, HyCaSD is a promising platform that can be further developed for diagnostic applications.

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Section: Resultsmentioning

confidence: 99%

Hybridization Cascade Plus Strand-Displacement Isothermal Amplification of RNA Target with Secondary Structure Motifs and Its Application for Detecting Dengue and Zika Viruses

et al. 2019

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“…Commercial platforms are also available e.g ., BDProbeTec™ ET System with inbuilt heating and centrifugation system that separates the DNA from the samples. A number of pathogens have been validated using Mycobacterium tuberculosis , 86 Chlamydia trachomatis and Neisseria gonorrhoeae . 87 …”

Section: Direct Amplification Studies Using Isothermal or Pcr Polymermentioning

confidence: 99%

Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices

et al. 2017

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Antimicrobial resistance (AMR) is recognized as a global threat to human health. Rapid detection and characterization of AMR is a critical component of most antibiotic stewardship programs. Methods based on amplification of nucleic acids for detection of AMR are generally faster than culture-based approaches but they still require several hours to more than a day due to the need for transporting the sample to a centralized laboratory, processing of sample, and sometimes DNA purification and concentration. Nucleic acids-based point-of-care (POC) devices are capable of rapidly diagnosing antibiotic-resistant infections which may help in making timely and correct treatment decisions. However, for most POC platforms, sample processing for nucleic acids extraction and purification is also generally required prior to amplification. Direct amplification, an emerging possibility for a number of polymerases, has the potential to eliminate these steps without significantly impacting diagnostic performance. This review summarizes direct amplification methods and their implication for rapid measurement of AMR. Future research directions that may further strengthen the possibility of integrating direct amplification methods with POC devices are also summarized.

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“…Furthermore, the multiplexing capability of qRT–PCR is quite limited due to the intrinsic requirement for multiple primers and signaling probes. Since the early 1990s, several types of isothermal nucleic acid amplification techniques for the identification of miRNA such as strand displacement amplification (SDA), 6 nucleic acid sequence-based amplification (NASBA), 7 rolling-circle amplification (RCA), 8 loop-mediated amplification (LAMP), 9 isothermal chain amplification (ICA), 10 and exponential amplification reaction (EXPAR) 11 have been employed as a central element in on-site applications. However, they still have the following drawbacks that compromise their widespread use: (i) multiple primer designs and complicated steps are required, 12 (ii) a single target can be identified at a time, (iii) the valid range of target length is limited, and (iv) the sensitivity needs to be improved.…”

mentioning

confidence: 99%

Ultrasensitive multiplexed miRNA detection based on a self-priming hairpin-triggered isothermal cascade reaction

Song

Lee

Park³

2022

Chem. Commun.

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Diagnostic performance of isothermal strand displacement amplification of Mycobacterium tuberculosis IS 6110 in tissue samples

Cited by 4 publications

References 29 publications

Hybridization Cascade Plus Strand-Displacement Isothermal Amplification of RNA Target with Secondary Structure Motifs and Its Application for Detecting Dengue and Zika Viruses

Hybridization Cascade Plus Strand-Displacement Isothermal Amplification of RNA Target with Secondary Structure Motifs and Its Application for Detecting Dengue and Zika Viruses

Implications of direct amplification for measuring antimicrobial resistance using point-of-care devices

Ultrasensitive multiplexed miRNA detection based on a self-priming hairpin-triggered isothermal cascade reaction

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