Primer Probes
Primer Probes - Related Videos
11:14
Primer-Free Aptamer Selection Using A Random DNA Library
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Cited by 20 •
2010
SELEX protocols comprise multiple rounds of selection, each of which require regeneration of bound ligands, which in turn require fixed primer sequences flanking the random library regions. These fixed primer sequences can interfere with the selection process (false positives and negatives). Here we present a primer-free protocol.
15:28
Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
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Cited by 41 •
2009
We present a method of targeted ancient DNA sequence retrieval, which we used to reconstruct the complete mitochondrial genomes of five Neandertal individuals. Comparison of these sequences with present day humans suggests that Neandertals had a long term low effective population size.
10:17
Laboratory Protocol for Genetic Gut Content Analyses of Aquatic Macroinvertebrates Using Group-specific rDNA Primers
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Cited by 7 •
2017
Most common gut content analyses of macroinvertebrates are visual. Requiring intense knowledge about morphological diversity of prey organisms, they miss soft bodied prey and, due to strong comminution of prey, are nearly impossible for some organisms, including amphipods. We provide detailed, novel genetic approaches for macroinvertebrate prey identification in the diet of amphipods.
10:28
Probe-based Real-time PCR Approaches for Quantitative Measurement of microRNAs
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Cited by 33 •
2015
Circulating microRNAs have recently emerged as promising and novel biomarkers for various cancers and other diseases. The goal of this article is to discuss three different probe-based real-time PCR platforms and methods that are available to quantify and determine the abundance of circulating microRNAs.
06:36
A Field Primer for Monitoring Benthic Ecosystems Using Structure-From-Motion Photogrammetry
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Cited by 14 •
2021
We provide a detailed protocol for conducting underwater structure-from-motion photogrammetry surveys to generate 3D models and orthomosaics.
FAQs
Primer pairs anneal to complementary sequences on opposite sides of the selected DNA or RNA-derived target. Their positions define the region that DNA polymerase will copy, while extension from the annealed primers enables repeated amplification. This boundary-setting function determines which sequence enters the assay’s amplified product and supports selective detection.
The probe binds to a complementary sequence located within the amplified region. Its reporter and quencher initially limit detectable fluorescence, but amplification-associated separation of these components allows signal generation. Because the probe must recognize an internal target sequence in addition to primer-binding regions, the signal provides sequence-specific evidence during quantitative PCR.
Primers provide the starting points that DNA polymerase extends, thereby producing additional copies of the selected region. An internal probe does not define the amplification boundaries; instead, it recognizes a sequence within the product and supports signal generation through its reporter and quencher. Combining these roles links target copying with specific detection.
Sequence design affects whether the oligonucleotides recognize the intended target and support reliable signal production. Well-designed sequences improve sensitivity, meaning the assay can detect the selected target, and selectivity, meaning signal is more closely associated with that target. These properties also contribute to quantitative accuracy in measurements based on amplification.
During quantitative PCR, amplification is accompanied by signal from the internal fluorescent probe when its reporter and quencher become separated. Monitoring this signal connects the detection readout to formation of the amplified target. Careful primer and probe design is therefore important when the assay must provide quantitative information rather than simple target identification.
Applications include pathogen detection, genotyping, gene-expression analysis, and mutation screening. In each case, the selected primer and probe sequences are matched to the DNA or RNA target relevant to the question being studied. This flexibility allows the same general assay principle to support diagnostic testing as well as molecular biology research.
They provide a way to connect target-specific recognition with amplification-based measurement. In biological techniques, this supports assays that need to distinguish selected sequences, detect changes such as mutations, or examine gene-expression patterns. Their value comes from coordinating complementary binding, polymerase extension, and probe-generated fluorescence within a single molecular analysis.