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1. Simple rolling circle amplification colorimetric assay based on pH for target DNA detection

Author:
Hamidi, Seyed Vahid; Perreault, Jonathan
Source:
Talanta 2019 v.201 pp. 419-425
ISSN:
0039-9140
Subject:
polymerase chain reaction,   etc   ; DNA; colorimetry; equipment; pH;     Show all 5 Subjects
Abstract:
... Detection and identification of DNA by PCR has opened tremendous possibilities and allows detection of minute quantities of DNA highly specifically. However, PCR remains confined to laboratory settings because of the need of thermocyclers and other analytical equipment. This led to development of isothermal amplification techniques, among which Pad Lock Probe (PLP)-based Rolling Circle Amplificati ...
DOI:
10.1016/j.talanta.2019.04.003

2. Quantification of Legionella DNA certified reference material by digital droplet PCR

Author:
Baume, Maud; Cariou, Astrid; Leveau, Adélaïde; Fessy, Noémie; Pastori, Frédéric; Jarraud, Sophie; Pierre, Sophie
Source:
Journal of microbiological methods 2019 v.157 pp. 50-53
ISSN:
0167-7012
Subject:
quantitative polymerase chain reaction,   etc   ; DNA; Legionella; droplets;     Show all 4 Subjects
Abstract:
... A value was assigned in 2009 to the Legionella DNA Certified Reference Material, and the stability study conducted using quantitative PCR found a low level of degradation. Herein, the Digital Droplet PCR method for Legionella DNA was qualified and used to provide absolute quantification of the CRM. ...
DOI:
10.1016/j.mimet.2018.12.019

3. Ultrasensitive Detection of Pb2+ Based on a DNAzyme and Digital PCR

Author:
Zhang, Tao; Liu, Cong; Zhou, Wuping; Jiang, Keming; Yin, Chenyu; Liu, Cong; Zhang, Zhiqiang; Li, Haiwen
Source:
Journal of Analytical Methods in Chemistry (Online) 2019 v.2019
ISSN:
2090-8873
Subject:
polymerase chain reaction,   etc   ; DNA; droplets; lead;     Show all 4 Subjects
Abstract:
... In this study, an ultrasensitive detection method for aqueous Pb²⁺ based on digital polymerase chain reaction (dPCR) technology and a Pb²⁺-dependent DNAzyme was developed. In the presence of Pb²⁺, the Gr-5 DNAzyme was activated and catalyzed the hydrolytic cleavage of the substrate strand, resulting in an increase in the amount of template DNA available for dPCR and a resultant change in the numbe ...
DOI:
10.1155/2019/3528345

4. Comparison of plasma and urinary microRNA-483-5p for the diagnosis of adrenocortical malignancy

Author:
Decmann, Abel; Bancos, Irina; Khanna, Aakanksha; Thomas, Melinda A.; Turai, Péter; Perge, Pál; Pintér, József Zsolt; Tóth, Miklós; Patócs, Attila; Igaz, Peter
Source:
Journal of biotechnology 2019 v.297 pp. 49-53
ISSN:
0168-1656
Subject:
quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction,   etc   ; adenoma; biomarkers; carcinoma; microRNA; patients;     Show all 7 Subjects
Abstract:
... Minimally invasive circulating microRNAs might be used for the preoperative differentiation of adrenocortical carcinoma (ACC) and adrenocortical adenoma (ACA). So far, the best blood-borne microRNA biomarker of ACC is circulating hsa-miR-483-5p. The expression of urinary hsa-miR-483-5p as a non-invasive marker of malignancy and its correlation with plasma hsa-miR-483-5p, has not been investigated, ...
DOI:
10.1016/j.jbiotec.2019.03.017

5. Detection of phenol contamination in RNA samples and its impact on qRT-PCR results

Author:
Unger, Conny; Lokmer, Nicole; Lehmann, Daniel; Axmann, Ilka M.
Source:
Analytical biochemistry 2019 v.571 pp. 49-52
ISSN:
0003-2697
Subject:
quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction,   etc   ; RNA; absorbance; fluorometry; phenol;     Show all 6 Subjects
Abstract:
... Residual phenol, carried over from RNA purification, can alter RNA concentration measurements and is assumed to inhibit PCR. Here, we demonstrate that Impurities A260 values of spectral content profiling (SCP) UV/Vis measurements correlated with phenol concentration, whereas absorbance ratios of classical UV/Vis systems failed to reliably detect phenol in RNA samples. Phenol contamination led to o ...
DOI:
10.1016/j.ab.2019.02.002

6. Does vacuum centrifugal concentration reduce yield or quality of nucleic acids extracted from FFPE biospecimens?

Author:
Sánchez, Ignacio; Betsou, Fay; Mathieson, William
Source:
Analytical biochemistry 2019 v.566 pp. 16-19
ISSN:
0003-2697
Subject:
quantitative polymerase chain reaction; reverse transcriptase polymerase chain reaction,   etc   ; DNA; RNA; fluorescence emission spectroscopy; temperature;     Show all 6 Subjects
Abstract:
... Vacuum centrifugal (SpeedVac) concentration is commonly applied to nucleic acids extracted from formalin-fixed paraffin-embedded (FFPE) sections, but with an unknown impact. We concentrated DNA and RNA from FFPE biospecimens using different time/temperature SpeedVac combinations of up to 30 min concentration at 45 °C, then used spectrophotometry, spectrofluorometry, RIN, PERM, DV200, qRT-PCR, DIN ...
DOI:
10.1016/j.ab.2018.10.020

7. The Ultimate qPCR Experiment: Producing Publication Quality, Reproducible Data the First Time

Author:
Taylor, Sean C.; Nadeau, Katia; Abbasi, Meysam; Lachance, Claude; Nguyen, Marie; Fenrich, Joshua
Source:
Trends in biotechnology 2019 v.37 no.7 pp. 761-774
ISSN:
0167-7799
Subject:
quantitative polymerase chain reaction,   etc   ; accuracy; nucleic acids; reproducibility;     Show all 4 Subjects
Abstract:
... Quantitative PCR (qPCR) is one of the most common techniques for quantification of nucleic acid molecules in biological and environmental samples. Although the methodology is perceived to be relatively simple, there are a number of steps and reagents that require optimization and validation to ensure reproducible data that accurately reflect the biological question(s) being posed. This review arti ...
DOI:
10.1016/j.tibtech.2018.12.002

8. Betaine-assisted recombinase polymerase assay with enhanced specificity

Author:
Luo, Guang-Cheng; Yi, Ting-Ting; Jiang, Bing; Guo, Xiao-lan; Zhang, Guo-Yuan
Source:
Analytical biochemistry 2019 v.575 pp. 36-39
ISSN:
0003-2697
Subject:
polymerase chain reaction,   etc   ; DNA; Hepatitis B virus; betaine; enzymes;     Show all 5 Subjects
Abstract:
... Recombinase polymerase amplification (RPA) is a widespread isothermal amplification method and regarded as an excellent candidate to replace polymerase chain reaction. However, the specificity of RPA is not always satisfactory when the sample contains amounts of background DNA. Herein, we report a novel RPA method named betaine-assisted RPA (B-RPA) that uses inexpensive betaine to avoid nonspecifi ...
DOI:
10.1016/j.ab.2019.03.018

9. Comparing real-time PCR and Calcofluor-white with conventional methods for rapid detection of dermatophytes: Across-sectional study

Author:
Motamedi, Marjan; Sharifi Lari, Milad; Pakshir, Keyvan; Zomorodian, Kamiar
Source:
Journal of microbiological methods 2019 v.161 pp. 84-86
ISSN:
0167-7012
Subject:
quantitative polymerase chain reaction,   etc   ; dermatomycoses; keratinophilic fungi; rapid methods; screening;     Show all 5 Subjects
Abstract:
... In this study, the performance of conventional methods, Calcofluor-white, and Real-time PCR methods were compared to establish an effective method for screening dermatomycosis. Our results showed excellent agreement between direct examination with Calcofluor -white (kappa = 0.97) and real-time PCR (kappa = 0.89) in 307 clinical samples. ...
DOI:
10.1016/j.mimet.2019.04.014

10. Fast and efficient symbiotic gene-based duplex PCR approach for the preliminary selection of legume root nodule bacteria

Author:
Silva, Valéria Borges da; Silva, Aleksandro Ferreira da; Silva, Thaise Rosa da; Santos, Jonnathan Whiny Moraes dos; Silva, Jéssica Fernanda da; Souza, Adailson Pereira de; Freitas, Ana Dolores Santiago de; Fernandes-Júnior, Paulo Ivan
Source:
Rhizosphere 2019 v.10 pp. 100144
ISSN:
2452-2198
Subject:
polymerase chain reaction,   etc   ; bacteria; genes; legumes; nodulation; rhizosphere; root nodules;     Show all 7 Subjects
Abstract:
... The isolation of root nodule bacteria (RNB) usually lead to obtainment of several non-rhizobia, mainly those fast-growing bacteria. The plant-authentication experiments to select the nodulating bacteria are time consuming and can be ruined in case of nodulation of negative controls. To speed up this step in rhizobiology research a fast, simple and efficient duplex PCR assay for the amplification o ...
DOI:
10.1016/j.rhisph.2019.100144

11. Authentication of nine snapper species by single-strand conformation polymorphism (SSCP) and forensically informative nucleotide sequencing (FINS) methods

Author:
Sivaraman, Balasubramanian; Jeyasekaran, Geevaretnam; Shakila, Robinson Jeya; Aanand, Samraj; Sukumar, Durairaj
Source:
Food control 2019 v.99 pp. 124-130
ISSN:
0956-7135
Subject:
polymerase chain reaction,   etc   ; markets; mitochondria; nucleotide sequences; snapper;     Show all 5 Subjects
Abstract:
... PCR-SSCP and PCR-FINS methods were developed to authenticate nine species of snapper. A highly variable mitochondrial D-loop region was chosen as a target region and three new primers viz., one forward (Fish-DL-F) and two reverse primers (Fish-DL-R and DLFR) were designed. PCR-SSCP was first targeted to amplify 515 bp D-loop fragment using Fish-DL-F/Fish-DL-R primers, but it could not differentiat ...
DOI:
10.1016/j.foodcont.2018.12.047

12. Development of a multiplex-PCR to simultaneously detect acquired linezolid resistance genes cfr, optrA and poxtA in enterococci of clinical origin

Author:
Bender, Jennifer K.; Fleige, Carola; Klare, Ingo; Werner, Guido
Source:
Journal of microbiological methods 2019 v.160 pp. 101-103
ISSN:
0167-7012
Subject:
polymerase chain reaction,   etc   ; Enterococcus; diagnostic techniques; linezolid; resistance genes;     Show all 5 Subjects
Abstract:
... Linezolid-resistant enterococcus spp. are increasingly recognized by diagnostic laboratories. Resistance can be mediated by the expression of cfr, optrA or poxtA. We developed a multiplex-PCR to simultaneously detect all three genes. The PCR is suitable for microbiological diagnostics in order to restrict further spread of resistances in enterococci. ...
DOI:
10.1016/j.mimet.2019.03.025

13. A rapid bioanalytical tool for detection of sequence-specific circular DNA and mitochondrial DNA point mutations

Author:
Zhang, Yuqian; Kaynak, Ahmet; Huang, Taosheng; Esfandiari, Leyla
Source:
Analytical and bioanalytical chemistry 2019 v.411 no.10 pp. 1935-1941
ISSN:
1618-2642
Subject:
polymerase chain reaction,   etc   ; denaturation; mitochondrial DNA; plasmids; point mutation; screening;     Show all 6 Subjects
Abstract:
... Mutations in mitochondrial DNA (mtDNA) have been an essential cause of numerous diseases, making their identification critically important. The majority of mtDNA screening techniques require polymerase chain reaction (PCR) amplification, enzymatic digestion, and denaturation procedures, which are laborious and costly. Herein, we developed a sensitive PCR-free electrokinetic-based sensor combined w ...
DOI:
10.1007/s00216-019-01683-8

14. Performance assessment of digital PCR for the quantification of GM-maize and GM-soya events

Author:
Cottenet, Geoffrey; Blancpain, Carine; Chuah, Poh Fong
Source:
Analytical and bioanalytical chemistry 2019 v.411 no.11 pp. 2461-2469
ISSN:
1618-2642
Subject:
quantitative polymerase chain reaction,   etc   ; guidelines; ingredients; quantitative analysis; transgenic plants;     Show all 5 Subjects
Abstract:
... Accurate quantitative methods are needed to determine the amount of transgenic material in ingredients and comply with labelling GMO thresholds. Quantitative real-time PCR methods are usually applied for GMO quantification, but since a few years, digital PCR (dPCR) has been described as a potential alternative by quantifying DNA molecules directly without any standard curves. In this study, the pe ...
DOI:
10.1007/s00216-019-01692-7

15. A novel template repairing-PCR (TR-PCR) reaction platform for microRNA detection using translesional synthesis on DNA templates containing abasic sites

Author:
ZhouThese authors contributed equally., Dianming; Lin, Xiaohui; Gao, Weichen; Piao, Jiafang; Li, Shufei; He, Ning; Qian, Zhiyong; Zhao, Miao; Gong, Xiaoqun
Source:
Chemical communications 2019 v.55 no.20 pp. 2932-2935
ISSN:
1364-548X
Subject:
polymerase chain reaction,   etc   ; DNA; chemical compounds; chemical reactions; microRNA;     Show all 5 Subjects
Abstract:
... A novel template repairing-PCR technology based on miRNA-primed bypass synthesis at the abasic sites on the PCR template is developed as a sensitive and selective platform for miRNA detection. The assay is expected to show great promise for reverse transcription-free RNA PCR amplification and target-based coding analysis. ...
DOI:
10.1039/c8cc10226k

16. A selective genome-guided method for environmental Burkholderia isolation

Author:
Haeckl, F. P. Jake; Baldim, João L.; Iskakova, Dasha; Kurita, Kenji L.; Soares, Marisi G.; Linington, Roger G.
Source:
Journal of industrial microbiology & biotechnology 2019 v.46 no.3-4 pp. 345-362
ISSN:
1367-5435
Subject:
polymerase chain reaction,   etc   ; Burkholderia; agar; culture media; isolation techniques; microbiology;     Show all 6 Subjects
Abstract:
... The genus Burkholderia is an emerging source of novel natural products chemistry, yet to date few methods exist for the selective isolation of strains of this genus from the environment. More broadly, tools to efficiently design selection media for any given genus would be of significant value to the natural products and microbiology communities. Using a modification of the recently published SMAR ...
DOI:
10.1007/s10295-018-02121-x

17. Cytogenetic microarray in structurally normal and abnormal foetuses: a five years experience elucidating increasing acceptance and clinical utility

Author:
Lallar, Meenakshi; Srivastava, Priyanka; Rai, Archana; Saxena, Deepti; Mandal, Kausik; Phadke, Shubha R.
Source:
Journal of genetics 2019 v.98 no.1 pp. 6
ISSN:
0022-1333
Subject:
polymerase chain reaction,   etc   ; aneuploidy; fetus; fluorescence; karyotyping; microarray technology; risk;     Show all 7 Subjects
Abstract:
... The aim of the present study was to evaluate the diagnostic yield of prenatal cytogenetic microarray (CMA) in structurally normal and abnormal foetuses and record the acceptance rate of CMA for prenatal diagnosis over a course of five years. In 128 structurally normal and abnormal foetuses, CMA was performed along with foetal karyotype, after exclusion of aneuploidy by quantitative fluorescence po ...
DOI:
10.1007/s12041-018-1050-5

18. Pooling of genital swabs for detection by PCR of Taylorella equigenitalis, the cause of contagious equine metritis

Author:
Mawhinney, I.; Errington, J.; Stamper, N.; Torrens, N.; Engelsma, M. Y.; Roest, H. I. J.
Source:
Equine veterinary journal 2019 v.51 no.2 pp. 227-230
ISSN:
0425-1644
Subject:
polymerase chain reaction,   etc   ; Taylorella equigenitalis; contagious equine metritis; horses; screening;     Show all 5 Subjects
Abstract:
... BACKGROUND: Sets of genital swabs are routinely taken from horses to screen for the presence of Taylorella equigenitalis, the cause of contagious equine metritis. Typically, two to four different sites are swabbed at a time and tested by culture or PCR. OBJECTIVES: This study explored the feasibility of pooling these swabs for a single PCR test per animal instead of testing each swab individually. ...
DOI:
10.1111/evj.12986

19. DNA-Compatible [3 + 2] Nitrone–Olefin Cycloaddition Suitable for DEL Syntheses

Author:
Gerry, Christopher J.; Yang, Zhenhua; Stasi, Michele; Schreiber, Stuart L.
Source:
Organic letters 2019 v.21 no.5 pp. 1325-1330
ISSN:
1523-7052
Subject:
polymerase chain reaction,   etc   ; DNA; chemical structure; cycloaddition reactions; organic compounds;     Show all 5 Subjects
Abstract:
... The limited scope of DNA-compatible chemistry restricts the types of chemical features that can be incorporated into DNA-encoded libraries (DELs). Here, a method to synthesize DNA-conjugated polycyclic isoxazolidines via a [3 + 2] nitrone–olefin cycloaddition is described. The reaction is compatible with many olefin-containing substrates and diverse N-alkylhydroxylamines. The ability to perform su ...
DOI:
10.1021/acs.orglett.9b00017

20. Droplet digital PCR for quantification of PML-RARα in acute promyelocytic leukemia: a comprehensive comparison with real-time PCR

Author:
Yuan, Dandan; Cui, Ming; Yu, Shuping; Wang, Huimin; Jing, Rongrong
Source:
Analytical and bioanalytical chemistry 2019 v.411 no.4 pp. 895-903
ISSN:
1618-2642
Subject:
quantitative polymerase chain reaction,   etc   ; detection limit; droplets; genes; leukemia; patients;     Show all 6 Subjects
Abstract:
... Real-time quantitative PCR (qPCR) has been widely implemented for molecular testing, but there are still some inherent limitations that hamper its usefulness. Droplet digital PCR (ddPCR), which can provide direct, standards-free quantification, has recently received increasing attention. In our study, a comprehensive comparison of ddPCR with qPCR in relation to the quantification of PML-RARα was p ...
DOI:
10.1007/s00216-018-1508-6