scholarly journals Gene specific-loci quantitative and single-base resolution analysis of 5-formylcytosine by compound-mediated polymerase chain reaction

2018 ◽  
Vol 9 (15) ◽  
pp. 3723-3728 ◽  
Author(s):  
Yafen Wang ◽  
Chaoxing Liu ◽  
Xiong Zhang ◽  
Wei Yang ◽  
Fan Wu ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Demethylation ◽  
Chain Reaction ◽  
Single Base ◽  
Active Dna Demethylation ◽  
Key Players ◽  
Resolution Analysis ◽  
Single Base Resolution ◽  
Polymerase Chain

5-Formylcytosine (5fC) is known as one of the key players in the process of active DNA demethylation and displays essential epigenetic functions in mammals.

scholarly journals Bisulfite-free, single base-resolution analysis of 5-hydroxymethylcytosine in genomic DNA by chemical-mediated mismatch

2019 ◽  
Vol 10 (2) ◽  
pp. 447-452 ◽  
Author(s):  
Yafen Wang ◽  
Xiong Zhang ◽  
Fan Wu ◽  
Zonggui Chen ◽  
Xiang Zhou
Keyword(s):  
Genomic Dna ◽  
Dna Demethylation ◽  
Nuclear Reprogramming ◽  
Single Base ◽  
Active Dna Demethylation ◽  
Resolution Analysis ◽  
Single Base Resolution

5-Hydroxymethylcytosine (5hmC) is known as one of the vital players in nuclear reprogramming and the process of active DNA demethylation.

Detection of Single Base Alterations in Genomic DNA by Solid Phase Polymerase Chain Reaction on Oligonucleotide Microarrays

2001 ◽  
Vol 299 (1) ◽  
pp. 24-30 ◽  
Author(s):  
Martin Huber ◽  
Doris Losert ◽  
Reinhard Hiller ◽  
Christian Harwanegg ◽  
Manfred W. Mueller ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Genomic Dna ◽  
Solid Phase ◽  
Oligonucleotide Microarrays ◽  
Chain Reaction ◽  
Single Base ◽  
Polymerase Chain

New Somatic Mutation in the PIG-A Gene Emerges at Relapse of Paroxysmal Nocturnal Hemoglobinuria

Blood ◽  
1998 ◽  
Vol 92 (9) ◽  
pp. 3422-3427 ◽  
Author(s):  
Khédoudja Nafa ◽  
Monica Bessler ◽  
H. Joachim Deeg ◽  
Lucio Luzzatto
Keyword(s):  
Bone Marrow ◽  
Polymerase Chain Reaction ◽  
Longitudinal Study ◽  
Paroxysmal Nocturnal Hemoglobinuria ◽  
Pcr Amplification ◽  
Chain Reaction ◽  
Single Base ◽  
Single Base Pair ◽  
Polymerase Chain ◽  
American Society

We report a detailed longitudinal study of the first patient to be treated (in 1973) for paroxysmal nocturnal hemoglobinuria (PNH) with syngeneic bone marrow transplantation (BMT). The patient subsequently relapsed with PNH in 1983, and still has PNH to date. Analysis of thePIG-A gene in a recent blood sample showed in exon 6 an insertion-duplication causing a frameshift. Polymerase chain reaction (PCR) amplification of the PIG-A exon 6 from bone marrow (BM) slides obtained before BMT showed that the duplication was not present; instead, we found several single base pair substitutions in exons 2 and 6. Thus, relapse of PNH in this patient was not due to persistence of the original clones; rather, it was associated with the emergence of a new clone. These findings support the notion that the BM environment may create selective conditions favoring the expansion of PNH clones.© 1998 by The American Society of Hematology.

scholarly journals 3′ Tth Endonuclease Cleavage Polymerase Chain Reaction (3TEC-PCR) Technology for Single-Base-Specific Multiplex Pathogen Detection using a Two-Oligonucleotide System

2021 ◽  
Vol 22 (11) ◽  
pp. 6061
Author(s):  
Owen Higgins ◽  
Terry J. Smith
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Target Detection ◽  
Pathogen Detection ◽  
Multiplex Detection ◽  
Chain Reaction ◽  
Single Base ◽  
Base Specificity ◽  
Pcr Technology ◽  
Polymerase Chain

Polymerase chain reaction (PCR) is the standard in nucleic acid amplification technology for infectious disease pathogen detection and has been the primary diagnostic tool employed during the global COVID-19 pandemic. Various PCR technology adaptations, typically using two-oligonucleotide dye-binding methods or three-oligonucleotide hydrolysis probe systems, enable real-time multiplex target detection or single-base specificity for the identification of single-nucleotide polymorphisms (SNPs). A small number of two-oligonucleotide PCR systems facilitating both multiplex detection and SNP identification have been reported; however, these methods often have limitations in terms of target specificity, production of variable or false-positive results, and the requirement for extensive optimisation or post-amplification analysis. This study introduces 3′ Tth endonuclease cleavage PCR (3TEC-PCR), a two-oligonucleotide PCR system incorporating a modified primer/probe and a thermostable cleavage enzyme, Tth endonuclease IV, for real-time multiplex detection and SNP identification. Complete analytical specificity, low limits of detection, single-base specificity, and simultaneous multiple target detection have been demonstrated in this study using 3TEC-PCR to identify bacterial meningitis associated pathogens. This is the first report of a two-oligonucleotide, real-time multiplex PCR technology with single-base specificity using Tth endonuclease IV.

scholarly journals Specific detection ofSalmonella entericaserotype Enteritidis using the polymerase chain reaction

1996 ◽  
Vol 116 (2) ◽  
pp. 137-145 ◽  
Author(s):  
K. A. Lampel ◽  
S. P. Keasler ◽  
D. E. Hanes
Keyword(s):  
Polymerase Chain Reaction ◽  
Broth Culture ◽  
Virulence Plasmid ◽  
Specific Detection ◽  
Chain Reaction ◽  
Pcr Assay ◽  
Single Base ◽  
Pcr Product ◽  
Base Mismatch ◽  
Polymerase Chain

SUMMARYAn assay was developed for the specific detection ofSalmonella entericaserotype Enteritidis, using a novel application of the polymerase chain reaction (PCR). This PCR assay is based on the mismatch amplification mutation assay, an allele-specific reaction, and can discriminate Enteritidis from all other salmonella. PCR primers were selected to amplify a 351-base pair (bp) DNA fragment from the salmonella plasmid virulence A (spvA) gene of Enteritidis. A single base difference at position 272 is present between the nucleotide sequence of thespvAgene of Enteritidis and other salmonellae. The downstream PCR primer, that encompasses position 272 of the EnteritidisspvAgene, was designed to contain a single base mismatch at the penultimate position, resulting in a l-base mismatch with Enteritidis and a 2-base mismatch with other salmonellae that harbour the virulence plasmid. The upstream primer was completely homologous with the region immediately 5′ to thespvAgene. When these primers were used and the annealing and extension reactions were performed at the same temperature, the PCR assay was specific for Enteritidis; no PCR product was detected for 40 other serotypes and 28 different genera examined. In pure culture, 120 colony forming units (c.f.u.) could be detected; a PCR product was observed from template derived from a 5 h enrichment broth culture of chicken seeded with 1 c.f.u. per gram of Enteritidis. This PCR assay is specific, reproducible, and less time consuming than the standard bacteriological methods used to detect Enteritidis.

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