Entropy Beacon: A Hairpin-Free DNA Amplification Strategy for Efficient Detection of Nucleic Acids

The easy and rapid spread of bacterial contamination and the risk it poses to human health makes evident the need for analytical methods alternative to conventional time-consuming laboratory-based techniques for bacterial detection. To tackle this demand, biosensors based on isothermal DNA amplification methods have emerged, which avoid the need for thermal cycling, thus facilitating their integration into small and low-cost devices for in situ monitoring. This review focuses on the breakthroughs made on biosensors based on isothermal amplification methods for the detection of bacteria in the field of food safety and environmental monitoring. Optical and electrochemical biosensors based on loop mediated isothermal amplification (LAMP), rolling circle amplification (RCA), recombinase polymerase amplification (RPA), helicase dependent amplification (HDA), strand displacement amplification (SDA), and isothermal strand displacement polymerisation (ISDPR) are described, and an overview of their current advantages and limitations is provided. Although further efforts are required to harness the potential of these emerging analytical techniques, the coalescence of the different isothermal amplification techniques with the wide variety of biosensing detection strategies provides multiple possibilities for the efficient detection of bacteria far beyond the laboratory bench.

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COBAS AMPLICOR: fully automated RNA and DNA amplification and detection system for routine diagnostic PCR

Clinical Chemistry ◽

10.1093/clinchem/42.12.1915 ◽

1996 ◽

Vol 42 (12) ◽

pp. 1915-1923 ◽

Cited By ~ 67

Author(s):

N DiDomenico ◽

H Link ◽

R Knobel ◽

T Caratsch ◽

W Weschler ◽

...

Keyword(s):

Nucleic Acids ◽

Internal Control ◽

Detection System ◽

Dna Amplification ◽

Cross Reactivity ◽

Diagnostic Pcr ◽

Thermal Cycler ◽

Paramagnetic Microparticles ◽

Rna And Dna ◽

Single Reaction

Abstract The COBAS AMPLICOR system automates amplification and detection of target nucleic acids, making diagnostic PCR routine for a variety of infectious diseases. The system contains a single thermal cycler with two independently regulated heating/cooling blocks, an incubator, a magnetic particle washer, a pipettor, and a photometer. Amplified products are captured on oligonucleotide-coated paramagnetic microparticles and detected with use of an avidin-horseradish peroxidase (HRP) conjugate. Concentrated solutions of amplicon or HRP were pipetted without detectable carryover. Amplified DNA was detected with an intraassay CV of < 4.5%; the combined intraassay CV for amplification and detection was < 15%. No cross-reactivity was observed when three different target nucleic acids were amplified in a single reaction and detected with three target-specific capture probes. The initial COBAS AMPLICOR menu includes qualitative tests for diagnosing infections with Chlamydia trachomatis, Neisseria gonorrhoeae, Mycobacterium tuberculosis, and hepatitis C virus. All tests include an optional Internal Control to provide assurance that specimens are successfully amplified and detected.

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Methods for identification of causative agents of dangerous and particularly dangerous infections based on the analysis of nucleic acids

Journal of NBC Protection Corps ◽

10.35825/2587-5728-2018-2-4-22-35 ◽

2018 ◽

Vol 2 (4) ◽

pp. 22-35

Keyword(s):

Nucleic Acids ◽

Dna Amplification ◽

Rapid Identification ◽

Chain Reaction ◽

Biological Contamination ◽

Laboratory Facilities ◽

Trained Personnel ◽

Causative Agents ◽

Polymerase Chain ◽

Goals And Objectives

One of the main tasks of the NBC Protection Troops is accurate and rapid identification of infectious disease causative agents in case of establishing the fact of biological contamination. Different methods based on the analysis of nucleic acids are most preferred for this purpose. Most of them are based on DNA amplification by polymerase chain reaction (PCR). The result is detected by electrophoretic separation of amplification products, as well as by registration of endpoint fluorescent signal (FLASH modification) or in real time (PCR-RT). Other methods of DNA amplification, such as ligase chain reaction (LCR) and isothermal amplification, are also applicable in practice. The article also describes some identification methods based on nucleic acid sequencing: multilocus sequence typing (MLST) method, sequencing of individual genes and complete genome sequencing. It is concluded that the choice of identification method should be based on the goals and objectives, laboratory facilities, availability of trained personnel and funding levels. Despite the fact that the most informative are methods based on sequencing nucleotide sequences, their implementation in the field is difficult so far due to technological requirements

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Exonuclease III–assisted cascade signal amplification strategy for label-free and ultrasensitive electrochemical detection of nucleic acids

Biosensors and Bioelectronics ◽

10.1016/j.bios.2016.09.036 ◽

2017 ◽

Vol 87 ◽

pp. 732-736 ◽

Cited By ~ 37

Author(s):

Erhu Xiong ◽

Xiaoxia Yan ◽

Xiaohua Zhang ◽

Yunqing Liu ◽

Jiawan Zhou ◽

...

Keyword(s):

Nucleic Acids ◽

Electrochemical Detection ◽

Signal Amplification ◽

Label Free ◽

Exonuclease Iii ◽

Amplification Strategy

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Nucleic acids in mummified plant seeds: biochemistry and molecular genetics of pre-Columbian maize

Genetics Research ◽

10.1017/s0016672300029943 ◽

1991 ◽

Vol 58 (3) ◽

pp. 193-201 ◽

Cited By ~ 32

Author(s):

Franco Rollo ◽

Franco Maria Venanzi ◽

Augusto Amici

Keyword(s):

Nucleic Acids ◽

Polyacrylamide Gel Electrophoresis ◽

Dna Amplification ◽

Degree Of Polymerization ◽

Base Pairs ◽

Plant Seeds ◽

Maize Seeds ◽

Maize Populations ◽

Polymerase Chain ◽

Seed Dna

SummaryNucleic acids fractions were isolated from pre-Columbian maize seeds and characterized using different approaches such as polyacrylamide gel electrophoresis, anti-DNA antibody binding, HPLC fractionation, molecular hybridization with cloned genes, and DNA amplification by the polymerase chain reaction. The nucleic acids were found to be very depolymerized (≤140 base pairs in length) and composed mainly of ribosomal RNA. Despite the very low amount and degree of polymerization of seed DNA, specific maize nuclear Mul, Mu4, Mu8 and, possibly, Mu5 element components could be detected, thanks to the use of amplification systems as short as 90 bp. The results suggest that evaluation of the relative proportions of Mu-type element components and, possibly, other maize genomic components in single mummified kernels, may offer a new key to the study of ancient maize populations.

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Highly sensitive dual mode electrochemical platform for microRNA detection

Scientific Reports ◽

10.1038/srep36719 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 38

Author(s):

Pawan Jolly ◽

Marina R. Batistuti ◽

Anna Miodek ◽

Pavel Zhurauski ◽

Marcelo Mulato ◽

...

Keyword(s):

Nucleic Acids ◽

Dynamic Range ◽

Electrochemical Impedance ◽

Limit Of Detection ◽

Dual Mode ◽

Electrode Surfaces ◽

Microrna Detection ◽

Highly Sensitive ◽

Detection Mode ◽

Amplification Strategy

Abstract MicroRNAs (miRNAs) play crucial regulatory roles in various human diseases including cancer, making them promising biomarkers. However, given the low levels of miRNAs present in blood, their use as cancer biomarkers requires the development of simple and effective analytical methods. Herein, we report the development of a highly sensitive dual mode electrochemical platform for the detection of microRNAs. The platform was developed using peptide nucleic acids as probes on gold electrode surfaces to capture target miRNAs. A simple amplification strategy using gold nanoparticles has been employed exploiting the inherent charges of the nucleic acids. Electrochemical impedance spectroscopy was used to monitor the changes in capacitance upon any binding event, without the need for any redox markers. By using thiolated ferrocene, a complementary detection mode on the same sensor was developed where the increasing peaks of ferrocene were recorded using square wave voltammetry with increasing miRNA concentration. This dual-mode approach allows detection of miRNA with a limit of detection of 0.37 fM and a wide dynamic range from 1 fM to 100 nM along with clear distinction from mismatched target miRNA sequences. The electrochemical platform developed can be easily expanded to other miRNA/DNA detection along with the development of microarray platforms.

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