Internal Primer
Internal Primer - 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.
09:18
Internal Standards
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2023
Source: Laboratory of Dr. B. Jill Venton - University of Virginia The goal of many chemical analyses is a quantitative analysis, where the amount of a substance in a sample is determined. In order to accurately calculate the concentration of an unknown from a sample, careful sample preparation is key. Every time a sample is handled or transferred, some of the sample can be lost. There are strategies however, for minimizing sample loss. There are also strategies for coping with sample loss and...
02:00
Internal Energy
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2020
The total of all possible kinds of energy present in a substance is called the internal energy (U), sometimes symbolized as E. Suppose a system with initial internal energy, Uinitial, undergoes a change in energy (transfer of work or heat), and the final internal energy of the system is Ufinal. Change in internal energy equals the difference between Ufinal and Uinitial. Although the values for Ufinal and Uinitial cannot be determined for a system, the first law of thermodynamics only...
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.
FAQs
The primer’s 3′ end supplies the starting point that DNA polymerase needs for strand extension. Complementary base pairing positions this end against the target sequence, allowing polymerase to extend the newly formed strand when reaction conditions support the process. This arrangement makes the resulting amplification or sequence read focused on the selected internal region.
Its location within the target directs analysis toward a defined internal segment instead of relying only on the fragment’s outer boundaries. In nested PCR, this internal targeting contributes to increased amplification specificity. The approach can therefore help distinguish the intended target from complex template material and support more confident target identification.
Placement determines which portion of a larger DNA or complementary DNA fragment becomes accessible for sequence reading. An Internal Primer can initiate sequencing within the fragment, allowing researchers to examine a selected region rather than beginning only at an outer boundary. This is useful when the biologically relevant sequence lies inside a longer template.
Two central features are sequence complementarity to the intended target and a properly positioned 3′ end for polymerase extension. The reaction must also provide suitable conditions for that extension to occur. When these requirements align, the primer can focus amplification or sequencing on the intended region and produce interpretable molecular data.
In nested PCR, internal sequence-specific primers are used to direct amplification toward a target region within a larger DNA product. Their placement narrows the analysis to the intended sequence and increases amplification specificity. The resulting product can then support target confirmation or further molecular analysis, particularly when the original template contains complex sequence information.
They are useful when researchers need to amplify a defined segment of complementary DNA generated from gene-expression material. By binding within that cDNA target, the primer directs analysis toward a selected sequence region. This focused amplification can help generate data associated with the transcript-derived template rather than examining an entire larger fragment.
Depending on the application, these primers can produce focused amplification data, sequence information from an internal region, or evidence supporting target identity. In gene-expression work, they help amplify defined cDNA segments. Across these uses, the main outcome is more reliable analysis of selected regions within complex DNA or complementary DNA templates.