Mesoscopic Evaluation of DNA Mismatches in PCR Primer-Target Hybridisation to Detect SARS-CoV-2 Variants of Concern

2021 ◽  
pp. 145-150
Author(s):  
Pâmella Miranda ◽  
Vivianne Basílio Barbosa ◽  
Gerald Weber
Keyword(s):  
Dna Mismatches ◽  
Pcr Primer

scholarly journals Degenerate PCR primer design for the specific identification of rhinovirus C

2015 ◽  
Vol 214 ◽  
pp. 15-24 ◽  
Author(s):  
Young Ran Nam ◽  
Uk Lee ◽  
Han Seok Choi ◽  
Kyoung Jin Lee ◽  
Nari Kim ◽  
...  
Keyword(s):  
Primer Design ◽  
Degenerate Pcr ◽  
Specific Identification ◽  
Rhinovirus C ◽  
Pcr Primer

scholarly journals Adenine Release Is Fast in MutY-catalyzed Hydrolysis of G:A and 8-Oxo-G:A DNA Mismatches

2003 ◽  
Vol 278 (32) ◽  
pp. 29587-29592 ◽  
Author(s):  
Joe A. B. McCann ◽  
Paul J. Berti
Keyword(s):  
Dna Mismatches ◽  
Hydrolysis Of

scholarly journals VizPrimer: a web server for visualized PCR primer design based on known gene structure

2011 ◽  
Vol 27 (24) ◽  
pp. 3432-3434 ◽  
Author(s):  
Y. Zhou ◽  
W. Qu ◽  
Y. Lu ◽  
Y. Zhang ◽  
X. Wang ◽  
...  
Keyword(s):  
Gene Structure ◽  
Web Server ◽  
Primer Design ◽  
Pcr Primer

Identifying DNA mismatches at single-nucleotide resolution by probing individual surface potentials of DNA-capped nanoparticles

Nanoscale ◽  
2018 ◽  
Vol 10 (2) ◽  
pp. 538-547 ◽  
Author(s):  
Hyungbeen Lee ◽  
Sang Won Lee ◽  
Gyudo Lee ◽  
Wonseok Lee ◽  
Kihwan Nam ◽  
...  
Keyword(s):  
Kelvin Probe Force Microscopy ◽  
Powerful Method ◽  
Kelvin Probe ◽  
Single Nucleotide ◽  
Force Microscopy ◽  
Surface Potentials ◽  
Dna Mismatches ◽  
Nucleotide Resolution ◽  
Single Nucleotide Resolution

Here, we demonstrate a powerful method to discriminate DNA mismatches at single-nucleotide resolution from 0 to 5 mismatches (χ0 to χ5) using Kelvin probe force microscopy (KPFM).

scholarly journals Minimum Multicolored Subgraph Problem in Multiplex PCR Primer Set Selection and Population Haplotyping

2006 ◽  
pp. 758-766 ◽  
Author(s):  
M. T. Hajiaghayi ◽  
K. Jain ◽  
L. C. Lau ◽  
I. I. Măndoiu ◽  
A. Russell ◽  
...  
Keyword(s):  
Multiplex Pcr ◽  
Pcr Primer

scholarly journals New PCR Primer Pairs Specific for Cryptococcus neoformans Serotype A or B Prepared on the Basis of Random Amplified Polymorphic DNA Fingerprint Pattern Analyses

1999 ◽  
Vol 37 (2) ◽  
pp. 315-320 ◽  
Author(s):  
Francisco Hideo Aoki ◽  
Tamae Imai ◽  
Reiko Tanaka ◽  
Yuzuru Mikami ◽  
Hideaki Taguchi ◽  
...  
Keyword(s):  
Cryptococcus Neoformans ◽  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Primers ◽  
Dna Fingerprint ◽  
Serotype A ◽  
Specific Pcr ◽  
Fingerprint Pattern ◽  
Serotype B ◽  
Pcr Primer

Thirty-three strains of Cryptococcus neoformans were isolated from clinical specimens, including specimens from AIDS patients in Brazil, and were classified into two serotypes; we detected 31 and 2 strains of serotypes A and B, respectively. Random amplified polymorphic DNA (RAPD) fingerprint pattern analyses of these strains of serotypes A and B showed that the patterns were similar for strains of each serotype when three 10-mer primers were used as the RAPD primers. Comparative studies of the fingerprint patterns of the study isolates with those of the reference strains also showed that the RAPD patterns for strains of each serotype were related and that most of the fingerprint bands existed commonly for all strains of each serotype tested. The common RAPD bands (an approximately 700-bp band for serotype A and an approximately 450-bp band for serotype B) were extracted and the DNA sequences were determined. Using this information, we prepared two and one PCR primer pairs which were expected to be specific for C. neoformans serotypes A and B, respectively. Use of each PCR primer combination thus prepared for serotype A or B was 100% successful in identifying the respectiveC. neoformans serotypes, including the 33 clinical isolates tested in the present study. Among these combinations, one for serotype A was found to amplify DNA from C. neoformans serotype B as well as serotype A. Serotype B-specific PCR primer pairs amplified DNA from not only serotype B strains but also from serotype C strains. The usefulness of other serotype-specific PCR primers for clinical C. neoformans isolates is discussed.

An Improved PCR Primer Pair Based on 16S rDNA for the Specific Detection of Salmonella Serovars in Food Samples

2004 ◽  
Vol 67 (7) ◽  
pp. 1335-1343 ◽  
Author(s):  
CHIEN-KU LIN ◽  
CHO-LIEN HUNG ◽  
SHU-CHEN HSU ◽  
CHENG-CHIH TSAI ◽  
HAU-YANG TSEN
Keyword(s):  
Sequence Data ◽  
Complete Sequence ◽  
Food Samples ◽  
Chicken Meat ◽  
Rrna Gene ◽  
Whole Milk ◽  
Sporadic Cases ◽  
Salmonella Serovars ◽  
Primer Annealing ◽  
Pcr Primer

Salmonella serovars are some of the major bacterial pathogens that can cause sporadic cases and outbreaks of foodborne illness. Based on the sequence data in the V3 region of the 16S rRNA gene, two PCR primer pairs have been designed for the detection of all serovars of Salmonella. However, none of these primers were specific for Salmonella because complete sequence homology with certain non-Salmonella strains has been found within each of them. Thus, the specificities of these two primer pairs could not rely on only one of the two primers. In this study, we modified our previous 16SFI primer by extending one base at the 5′ end and three bases at the 3′ end. The modified primer, 16S-Sal, was designed with one or more mismatched bases near the 3′ end of the primer annealing to the corresponding sequences of non-Salmonella strains. Such modification eliminates interference from Citrobacter freundii and Enterobacter cloacae as occurs with the 16SFI primer. When 16S-Sal and a degenerate primer, 16S-CCR, were used as a primer pair, detection specificity of Salmonella serovars was achieved. Because this primer pair was used for PCR detection of the salmonellae in food samples, such as whole milk and chicken meat, as low as 1 to 9 CFU/g (ml) of the food sample could be detected when a 8-h preculture step was performed prior to the PCR. For chicken meat, the endogenous microflora did not interfere with the PCR results.

scholarly journals Novel computational methods for increasing PCR primer design effectiveness in directed sequencing

2008 ◽  
Vol 9 (1) ◽  
Author(s):  
Kelvin Li ◽  
Anushka Brownley ◽  
Timothy B Stockwell ◽  
Karen Beeson ◽  
Tina C McIntosh ◽  
...  
Keyword(s):  
Computational Methods ◽  
Primer Design ◽  
Design Effectiveness ◽  
Pcr Primer
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