An autocatalytic DNA machine with autonomous target recycling and cascade circular exponential amplification for one-pot, isothermal and ultrasensitive nucleic acid detection

2016 ◽  
Vol 52 (74) ◽  
pp. 11108-11111 ◽  
Author(s):  
Xinya Sun ◽  
Li Wang ◽  
Mingsha Zhao ◽  
Changzhi Zhao ◽  
Shufeng Liu

An autonomous target recycling and cascade circular exponential amplification strategy was proposed for the one-pot, isothermal and ultrasensitive detection of target DNA.

2015 ◽  
Vol 51 (100) ◽  
pp. 17756-17759 ◽  
Author(s):  
Shufeng Liu ◽  
Hongwei Gong ◽  
Xinya Sun ◽  
Tao Liu ◽  
Li Wang

A programmable Y-shaped junction probe-mediated modular and cascade amplification strategy was proposed for the one-pot, isothermal and ultrasensitive detection of target DNA.


RSC Advances ◽  
2016 ◽  
Vol 6 (13) ◽  
pp. 10650-10654 ◽  
Author(s):  
Haiping Wei ◽  
Yan Wang ◽  
Hong Zhang ◽  
Haiyan Zhao ◽  
Wei Jiang

A sensitive strategy based on Au nanoparticles fluorescence switch-mediated target recycling amplification for nucleic acid detection.


BIOspektrum ◽  
2020 ◽  
Vol 26 (6) ◽  
pp. 624-627
Author(s):  
Ole Behrmann ◽  
Iris Bachmann ◽  
Frank Hufert ◽  
Gregory Dame

Abstract The COVID-19 pandemic highlights the need for fast and simple assays for nucleic acid detection. As an isothermal alternative to RT-qPCR, we outline the development of a detection scheme for SARS-CoV-2 RNA based on reverse transcription recombinase polymerase amplification (RT-RPA) technology. RPA uses recombination proteins in combination with a DNA polymerase for rapid amplification of target DNA at a constant temperature (39–42 °C) within 10 to 20 minutes and can be monitored in real-time with fluorescent probes.


2019 ◽  
Vol 11 (2) ◽  
pp. 200-204 ◽  
Author(s):  
Lin Tan ◽  
Liu Xu ◽  
Jin-Wen Liu ◽  
Li-Juan Tang ◽  
Hao Tang ◽  
...  

Isothermal amplification techniques for nucleic acid detection have drawn increasing interest recently due to the simplicity and low-cost of instruments.


2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S42-S43
Author(s):  
Rose Lee ◽  
Helena De Puig Guixe ◽  
Jeffrey Dvorin ◽  
James Collins

Abstract Background Malaria control and eradication have been hampered by asymptomatic carriage which serves as a parasite reservoir. Low-density infections (< 100 parasites/microliter) frequently fall below the limit of detection (LOD) of microscopy and rapid diagnostic tests (RDT) which are antigen-based tests. Molecular methods such as polymerase chain reaction are capable of higher sensitivity yet remain impractical for resource-limited settings. We describe development of an isothermal assay using the nucleic acid detection platform SHERLOCK (Specific High-Sensitivity Enzymatic Reporter UnLOCKing), which may also be increasingly important as there has been rising detection of histidine-rich protein 2 (HRP2) gene deletions in Plasmodium spp. HRP2 is the most commonly used antigen in RDTs and deletion of this gene would render many RDTs obsolete. Methods SHERLOCK leverages the endonucleases of CRISPR-associated microbial adaptive immunity. Cas12a is an RNA-guided, DNA-cleaving enzyme, which can be programmed with guide RNAs to cleave nontarget reporter ssDNA. We exploit the nonspecific degradation of labeled ssDNA to detect the presence of the dsDNA target that activated Cas12a (Figure 1). Recombinase polymerase amplification (RPA) coupled with Cas12a detection enables a lower LOD. Plasmodium falciparum whole genomic DNA was compared with parasites cultured in red blood cells (RBCs) with known parasitemia and boiled at 95°C for 5 minutes for lysis of RBCs/parasites then diluted 1:2.5 to prevent solidification. Results This SHERLOCK assay detected simulated Plasmodium falciparum infection at attomolar LODs when applied to whole genomic DNA and simulated samples of infected RBCs spiked into whole blood. The genomic assay detected down to 0.2 parasites/microliter and the simulated sample detected to 10 parasites/microliter in the final reaction volume. In comparison, LODs from the initial input volume was 5aM and 250aM, respectively (Figure 2). Conclusion We demonstrate an isothermal nucleic acid detection platform capable of diagnosis in 60 minutes in a one-pot assay requiring minimal sample preparation and reaching an LOD recommended by the WHO for malaria eradication. In summary, we illustrate the utility of the SHERLOCK platform in application to malaria and global health. Disclosures All Authors: No reported Disclosures.


2019 ◽  
Vol 55 (45) ◽  
pp. 6453-6456 ◽  
Author(s):  
Ze-Zhou Yang ◽  
Zhi-Bin Wen ◽  
Xin Peng ◽  
Ya-Qin Chai ◽  
Wen-Bin Liang ◽  
...  

A fluorescent assay for the ultrasensitive detection of miRNA-21 is based on immobilization of PPIX as signal indicators in massive G-quadruplex structures obtained by target recycling, three-dimensional DNA walker and RCA coupled cascade nucleic acid amplification.


NANO ◽  
2020 ◽  
Vol 15 (08) ◽  
pp. 2050110
Author(s):  
Zhikun Zhang ◽  
Xiaojie Ye ◽  
Qingqing Liu ◽  
Cuixia Hu ◽  
Jimmy Yun ◽  
...  

Nucleic acid detection is becoming increasingly important in the diagnostics of genetic diseases for biological analysis. We herein propose gold nanoparticles as probe for colorimetric detection of nucleic acids with branched DNA nanostructures, which enables a novel and simple colorimetric biosensor. In our system, the target DNA specifically triggered two short-chain ssDNA probes to generate branched DNA nanostructures (Y-shape DNA), which prevent AuNPs from aggregation in aqueous NaCl solution. On the contrary, when the target DNA did not exist, gold nanoparticles were unstable and aggregated easily because there is no anti-aggregation function from Y-shape DNA. Sensor response was found to be proportional to the target DNA concentration from 5 to 100[Formula: see text]nM, with detection limits determined as 5[Formula: see text]nM. The developed platform is for colorimetric nucleic acid detection without enzymes, label and modification holds great promise for practical applications.


2020 ◽  
Author(s):  
Jia Liu ◽  
Yi Chen ◽  
Kefan Xie ◽  
Xiaohong Chen

Abstract At present, several countries, such as Germany and India, have employed a pool testing method on the nucleic acid testing of COVID-19 for the shortage of detection kits. In this method, the testing is performed on several samples of the cases together as a bunch. If the test result of the bunch is negative, then it is shown that none of the cases in the bunch has been infected with the novel coronavirus. On the contrary, if the test result of the bunch is positive, then the samples are tested one by one to confirm which cases are infected. We verified that the pool testing method of COVID-19 is effective in the situation of the shortage of nucleic acid detection kits based on probabilistic modeling. Moreover, the following interesting results are also obtained. (1) If the infection rate is extremely low, while the same number of detection kits are used, the expected number of cases that can be tested by the pool testing method is far more than that by the one-by-one testing method. (2) The pool testing method is effective only when the infection rate is less than 0.3078. While the infection rate decreases from 0.3078 to 0.0018, the optimal sample sizes in one bunch increases from 3 to 25. In general, the higher the infection rate, the smaller the optimal sample size in one bunch. (3) If N samples are tested by the pool testing method, while the sample size in one bunch is G, the number of detection kits required is in the interval (N/G, N). Additionally, the lower the infection rate, the fewer detection kits are needed. Therefore, the pool testing method is not only suitable for the situation of the shortage of detection kits, but also the situation of the overall or sampling detection for a large population.


2021 ◽  
Author(s):  
hongyu liu ◽  
Yuhao You ◽  
Youzhuo Zhu ◽  
Heng Zheng

Detection of nucleic acids have become significantly important in molecular diagnostics, genetics therapy, mutation analysis, forensic investigations and biomedical development, and so on. In recent years, exonuclease Ⅲ (Exo III)...


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