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Quantification of the Detrimental Effect of a Single Primer-Template Mismatch by Real-Time PCR Using the 16S rRNA Gene as an Example

https://doi.org/10.1128/aem.02403-07
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1006/abio.2000.4635openalex-snapshot
Discrimination of Primer 3′-Nucleotide Mismatch by Taq DNA Polymerase during Polymerase Chain Reaction
inferredcites →https://doi.org/10.1007/978-94-009-0215-2openalex-snapshot
Molecular Microbial Ecology Manual
inferredcites →https://doi.org/10.1007/s002489900056openalex-snapshot
Microbial Evolution, Diversity, and Ecology: A Decade of Ribosomal RNA Analysis of Uncultivated Microorganisms
inferredcites →https://doi.org/10.1016/j.mimet.2003.08.009openalex-snapshot
Review and re-analysis of domain-specific 16S primers
inferredcites →https://doi.org/10.1016/j.mimet.2004.02.009openalex-snapshot
Quantification of a novel group of nitrate-reducing bacteria in the environment by real-time PCR
inferredcites →https://doi.org/10.1016/s0167-7012(01)00220-2openalex-snapshot
Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting
inferredcites →https://doi.org/10.1038/345063a0openalex-snapshot
16S rRNA sequences reveal numerous uncultured microorganisms in a natural community
inferredcites →https://doi.org/10.1093/nar/18.4.999openalex-snapshot
Effects of primer-template mismatches on the polymerase chain reaction: Human immunodeficiency virus type 1 model studies
inferredcites →https://doi.org/10.1093/nar/20.17.4567openalex-snapshot
Extension of base mispairs by Taq DNA polymerase: implications for single nucleotide discrimination in PCR
inferredcites →https://doi.org/10.1093/nar/27.8.1810openalex-snapshot
Nucleotide analogs facilitate base conversion with 3' mismatch primers
inferredcites →https://doi.org/10.1093/nar/gnf110openalex-snapshot
The effects of sequence length and oligonucleotide mismatches on 5' exonuclease assay efficiency
inferredcites →https://doi.org/10.1111/j.1574-6941.2007.00283.xopenalex-snapshot
Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis
inferredcites →https://doi.org/10.1111/j.1574-6976.1997.tb00351.xopenalex-snapshot
Determination of microbial diversity in environmental samples: pitfalls of PCR-based rRNA analysis
inferredcites →https://doi.org/10.1126/science.276.5313.734openalex-snapshot
A Molecular View of Microbial Diversity and the Biosphere
inferredcites →https://doi.org/10.1128/aem.67.8.3753-3755.2001openalex-snapshot
Optimization of Annealing Temperature To Reduce Bias Caused by a Primer Mismatch in Multitemplate PCR
inferredcites →https://doi.org/10.1128/jcm.42.7.3317-3320.2004openalex-snapshot
Real-Time PCR Assay for Detection and Genotype Differentiation of Giardia lamblia in Stool Specimens

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DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match
inferred← citeshttps://doi.org/10.1098/rsbl.2025.0647openalex-snapshot
When cryptogenic species are also cryptic: reframing biogeographic uncertainty in the environmental DNA era
inferred← citeshttps://doi.org/10.1101/2024.11.01.621049openalex-snapshot
Trophic Interactions of Anopheles Gambiae Mosquito Larvae in Aquatic Ecosystem: A Metagenomics Approach
inferred← citeshttps://doi.org/10.1101/2025.03.25.645285openalex-snapshot
Assessing the combined performance of supervised learning and spike-in constructs for bias correction in eDNA metabarcoding
inferred← citeshttps://doi.org/10.1101/2025.08.14.25333671openalex-snapshot
Global In-Silico Performance Assessment of the CDC Zika Trioplex Detection System
inferred← citeshttps://doi.org/10.1101/866731openalex-snapshot
Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities and denoising algorithms
inferred← citeshttps://doi.org/10.1111/1462-2920.15553openalex-snapshot
Comprehensive single‐PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S
inferred← citeshttps://doi.org/10.1111/1751-7915.12366openalex-snapshot
Underestimation of ammonia‐oxidizing bacteria abundance by amplification bias in amoA ‐targeted qPCR
inferred← citeshttps://doi.org/10.1111/1751-7915.13627openalex-snapshot
Lost in translation: the quest for Nitrosomonas cluster 7‐specific amoA primers and TaqMan probes
inferred← citeshttps://doi.org/10.1111/1755-0998.12556openalex-snapshot
Vector soup: high‐throughput identification of Neotropical phlebotomine sand flies using metabarcoding
inferred← citeshttps://doi.org/10.1111/1755-0998.13097openalex-snapshot
Exploring the accuracy of amplicon‐based internal transcribed spacer markers for a fungal community
inferred← citeshttps://doi.org/10.1111/1755-0998.13681openalex-snapshot
eDNAssay : A machine learning tool that accurately predicts qPCR cross‐amplification
inferred← citeshttps://doi.org/10.1111/1755-0998.13855openalex-snapshot
Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA
inferred← citeshttps://doi.org/10.1111/1758-2229.12684openalex-snapshot
Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment
inferred← citeshttps://doi.org/10.1111/1758-2229.13189openalex-snapshot
A quantitative sequencing method using synthetic internal standards including functional and phylogenetic marker genes
inferred← citeshttps://doi.org/10.1111/2041-210x.12729openalex-snapshot
Evaluation of short mitochondrial metabarcodes for the identification of Amazonian mammals
inferred← citeshttps://doi.org/10.1111/ejss.12314openalex-snapshot
Bacteria as transporters of phosphorus through soil
inferred← citeshttps://doi.org/10.1111/j.1469-8137.2009.02835.xopenalex-snapshot
DNA‐based species level detection of Glomeromycota: one PCR primer set for all arbuscular mycorrhizal fungi
inferred← citeshttps://doi.org/10.1111/j.1574-6941.2009.00767.xopenalex-snapshot
Effect of carbon addition and predation on acetate-assimilating bacterial cells in groundwater
inferred← citeshttps://doi.org/10.1111/j.1574-6941.2011.01138.xopenalex-snapshot
Exploring the composition and diversity of microbial communities at the Jan Mayen hydrothermal vent field using RNA and DNA
inferred← citeshttps://doi.org/10.1111/j.1574-6968.2011.02302.xopenalex-snapshot
spyder, a new method for in silico design and assessment of 16S rRNA gene primers for molecular microbial ecology
inferred← citeshttps://doi.org/10.1111/j.1758-2229.2010.00219.xopenalex-snapshot
Comparison of primer sets for the study of Planctomycetes communities in lentic freshwater ecosystems
inferred← citeshttps://doi.org/10.1111/j.1758-2229.2011.00318.xopenalex-snapshot
‘Next‐base’ effect on PCR amplification
inferred← citeshttps://doi.org/10.1111/j.1758-2229.2012.00347.xopenalex-snapshot
Abundance of anammox bacteria in different wetland soils
inferred← citeshttps://doi.org/10.1111/jam.14231openalex-snapshot
Effect of the extraction and purification of soil DNA and pooling of PCR amplification products on the description of bacterial and archaeal communities
inferred← citeshttps://doi.org/10.1111/jen.70115openalex-snapshot
Evaluating the Effects of Preservation Method and Storage Duration on Lysis Buffer–Based Non‐Destructive DNA Metabarcoding in Insect Mock Communities
inferred← citeshttps://doi.org/10.1111/jre.12210openalex-snapshot
Quantitative analysis of classical and new putative periodontal pathogens in subgingival biofilm: a case–control study
inferred← citeshttps://doi.org/10.1111/lam.13421openalex-snapshot
Association of the colistin resistance gene mcr‐1 with faecal pollution in water environments in Hanoi, Vietnam
inferred← citeshttps://doi.org/10.1111/mec.13481openalex-snapshot
Assessing vertebrate biodiversity in a kelp forest ecosystem using environmental DNA
inferred← citeshttps://doi.org/10.1111/mec.14776openalex-snapshot
The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative
inferred← citeshttps://doi.org/10.1111/ppa.12017openalex-snapshot
Fast real‐time detection of Potato spindle tuber viroid by RT‐LAMP
inferred← citeshttps://doi.org/10.1111/ppa.13877openalex-snapshot
All‐in‐one Xylella detection and identification: A nanopore sequencing‐compatible conventional PCR
inferred← citeshttps://doi.org/10.1128/aem.00237-12openalex-snapshot
Seasonal Diversity of Planktonic Protists in Southwestern Alberta Rivers over a 1-Year Period as Revealed by Terminal Restriction Fragment Length Polymorphism and 18S rRNA Gene Library Analyses
inferred← citeshttps://doi.org/10.1128/aem.00474-20openalex-snapshot
Insights into the Function and Horizontal Transfer of Isoproturon Degradation Genes ( pdmAB ) in a Biobed System
inferred← citeshttps://doi.org/10.1128/aem.01315-10openalex-snapshot
Diversity of Phytoplankton Nitrate Transporter Sequences from Isolated Single Cells and Mixed Samples from the East China Sea and mRNA Quantification
inferred← citeshttps://doi.org/10.1128/aem.01630-16openalex-snapshot
Design and Evaluation of Illumina MiSeq-Compatible, 18S rRNA Gene-Specific Primers for Improved Characterization of Mixed Phototrophic Communities
inferred← citeshttps://doi.org/10.1128/aem.01682-22openalex-snapshot
Improved DNA Amplification of the Hallmark IS 900 Element in Mycobacterium avium subsp. paratuberculosis : a Reexamination Based on Whole-Genome Sequence Analysis
inferred← citeshttps://doi.org/10.1128/aem.01910-08openalex-snapshot
Evaluation of Single-Nucleotide Primer Extension for Detection and Typing of Phylogenetic Markers Used for Investigation of Microbial Communities
inferred← citeshttps://doi.org/10.1128/aem.07878-11openalex-snapshot
Simple Absolute Quantification Method Correcting for Quantitative PCR Efficiency Variations for Microbial Community Samples
inferred← citeshttps://doi.org/10.1128/jcm.01741-24openalex-snapshot
CDC dengue typing kit fails to detect dengue virus 2 sylvatic genotype
inferred← citeshttps://doi.org/10.1128/spectrum.00974-21openalex-snapshot
Genetic Homology between Bacteria Isolated from Pulmonary Abscesses or Pyothorax and Bacteria from the Oral Cavity
inferred← citeshttps://doi.org/10.1139/cjm-2017-0100openalex-snapshot
Degenerate ITS7 primer enhances oomycete community coverage and PCR sensitivity to Aphanomyces species, economically important plant pathogens
inferred← citeshttps://doi.org/10.1139/gen-2025-0006openalex-snapshot
Detecting bumble bees in the wild using environmental DNA: development and validation of a qPCR assay for the endangered Franklin’s bumble bee ( Bombus franklini )
inferred← citeshttps://doi.org/10.1152/ajpgi.00013.2024openalex-snapshot
A simple and effective genotyping workflow for rapid detection of CRISPR genome editing
inferred← citeshttps://doi.org/10.1155/2015/892013openalex-snapshot
454-Pyrosequencing Analysis of Bacterial Communities from Autotrophic Nitrogen Removal Bioreactors Utilizing Universal Primers: Effect of Annealing Temperature
inferred← citeshttps://doi.org/10.11606/d.21.2021.tde-15032022-162237openalex-snapshot
Diversidade de Archaea em Diferentes Ecossistemas da Antártica
inferred← citeshttps://doi.org/10.1163/15685411-00002984openalex-snapshot
Development of a quantification method with real-time PCR for three Pratylenchus species causing damage to chrysanthemum in Japan
inferred← citeshttps://doi.org/10.1177/1040638711407479openalex-snapshot
Development and evaluation of a real-time polymerase chain reaction method for the detection of Mycoplasma felis
inferred← citeshttps://doi.org/10.1177/1176934319883612openalex-snapshot
Properties of Samples With Segregating Polymerase Chain Reaction (PCR) Dropout Mutations Within a Species
inferred← citeshttps://doi.org/10.1186/1471-2180-12-66openalex-snapshot
Coverage evaluation of universal bacterial primers using the metagenomic datasets
inferred← citeshttps://doi.org/10.1186/1742-4690-10-41openalex-snapshot
Cell-associated HIV RNA: a dynamic biomarker of viral persistence
inferred← citeshttps://doi.org/10.1186/s12859-025-06046-yopenalex-snapshot
CoMIT: a bioinformatic pipeline for risk-based prediction of COVID-19 test inclusivity
inferred← citeshttps://doi.org/10.1186/s12866-020-1707-0openalex-snapshot
Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea
inferred← citeshttps://doi.org/10.1186/s13036-026-00677-2openalex-snapshot
Multi-technique characterization of gold nanoparticle-based DNA biosensor with smartphone-enabled photometry for accelerated detection of Campylobacter jejuni
inferred← citeshttps://doi.org/10.1186/s13068-018-1174-0openalex-snapshot
Growth promotion of three microalgae, Chlamydomonas reinhardtii, Chlorella vulgaris and Euglena gracilis, by in situ indigenous bacteria in wastewater effluent
inferred← citeshttps://doi.org/10.1186/s13568-019-0870-xopenalex-snapshot
The differences of bacterial communities in the tissues between healthy and diseased Yesso scallop (Patinopecten yessoensis)
inferred← citeshttps://doi.org/10.1264/jsme2.me18071openalex-snapshot
Improvements in Bacterial Primers to Enhance Selective SSU rRNA Gene Amplification of Plant-associated Bacteria by Applying the LNA Oligonucleotide-PCR Clamping Technique
inferred← citeshttps://doi.org/10.1264/jsme2.me18169openalex-snapshot
The Honeybee Gut Microbiota Is Altered after Chronic Exposure to Different Families of Insecticides and Infection by Nosema ceranae
inferred← citeshttps://doi.org/10.12692/ijb/9.1.430-434openalex-snapshot
Effect of single nucleotide mismatch at 3′-end of the primers in selected candidate micro RNA breast cancer genes
inferred← citeshttps://doi.org/10.12935/jvma.79.e187openalex-snapshot
Development of a Real-Time RT-PCR Assay for Detecting H9 Subtype Avian Influenza Viruses
inferred← citeshttps://doi.org/10.1371/journal.pone.0035887openalex-snapshot
PCR Primers for Metazoan Mitochondrial 12S Ribosomal DNA Sequences
inferred← citeshttps://doi.org/10.1371/journal.pone.0038094openalex-snapshot
High-Throughput Sequencing of 16S rRNA Gene Amplicons: Effects of Extraction Procedure, Primer Length and Annealing Temperature
inferred← citeshttps://doi.org/10.1371/journal.pone.0042149openalex-snapshot
A Comprehensive Evaluation of PCR Primers to Amplify the nifH Gene of Nitrogenase
inferred← citeshttps://doi.org/10.1371/journal.pone.0044224openalex-snapshot
Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing
inferred← citeshttps://doi.org/10.1371/journal.pone.0075850openalex-snapshot
Evaluation of Four Endogenous Reference Genes and Their Real-Time PCR Assays for Common Wheat Quantification in GMOs Detection
inferred← citeshttps://doi.org/10.1371/journal.pone.0105592openalex-snapshot
Development of a Prokaryotic Universal Primer for Simultaneous Analysis of Bacteria and Archaea Using Next-Generation Sequencing
inferred← citeshttps://doi.org/10.1371/journal.pone.0128122openalex-snapshot
Deconstructing the Polymerase Chain Reaction: Understanding and Correcting Bias Associated with Primer Degeneracies and Primer-Template Mismatches
inferred← citeshttps://doi.org/10.1371/journal.pone.0157402openalex-snapshot
PCR Strategies for Complete Allele Calling in Multigene Families Using High-Throughput Sequencing Approaches
inferred← citeshttps://doi.org/10.1371/journal.pone.0161841openalex-snapshot
Uncovering Trophic Interactions in Arthropod Predators through DNA Shotgun-Sequencing of Gut Contents
inferred← citeshttps://doi.org/10.1371/journal.pone.0174609openalex-snapshot
MIPE: A metagenome-based community structure explorer and SSU primer evaluation tool
inferred← citeshttps://doi.org/10.1371/journal.pone.0179443openalex-snapshot
DNA extraction replicates improve diversity and compositional dissimilarity in metabarcoding of eukaryotes in marine sediments
inferred← citeshttps://doi.org/10.1371/journal.pone.0218159openalex-snapshot
A novel data processing method CyC* for quantitative real time polymerase chain reaction minimizes cumulative error
inferred← citeshttps://doi.org/10.1371/journal.pone.0240136openalex-snapshot
Diet composition analysis provides new management insights for a highly specialized endangered small mammal
inferred← citeshttps://doi.org/10.1371/journal.pone.0264008openalex-snapshot
Infection clusters can elevate risk of diagnostic target failure for detection of SARS-CoV-2
inferred← citeshttps://doi.org/10.1371/journal.pone.0275263openalex-snapshot
Abundance, efficiency, and stability of reference transcript expression in a seasonal rodent: The Siberian hamster
inferred← citeshttps://doi.org/10.1371/journal.pone.0292559openalex-snapshot
A novel metric to improve mismatched primer selection and quantification accuracy in amplifying DNA repeats for quantitative polymerase chain reactions
inferred← citeshttps://doi.org/10.14299/ijser.2015.02.001openalex-snapshot
Identification of Medicinal Mangrove Rhizophora apiculata Blume: Morphological, Chemical and DNA Barcoding Methods
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