Outer Primers
Outer Primers - 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.
11:06
Method for the Isolation of Francisella tularensis Outer Membranes
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Cited by 11 •
2010
A protocol for separating inner and outer membranes from Francisella tularensis by spheroplasting, osmotic lysis, and sucrose density gradient ultracentrifugation.
03:47
Separation of Inner and Outer Membrane Fractions of Gram-Negative Bacteria
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2025
Source: Cian, M. B. et. al., Separation of the Cell Envelope for Gram-negative Bacteria into Inner and Outer Membrane Fractions with Technical Adjustments for Acinetobacter baumannii. J. Vis. Exp. (2020)This video demonstrates the separation of the inner and outer membrane fractions of Gram-negative bacteria using sucrose gradient ultracentrifugation. The membrane fractions are purified and stored at low temperatures for targeted analysis of membrane-specific components.
FAQs
Their placement determines which DNA segment can be copied during PCR. By binding to sequences on opposite sides of the target, the primers establish amplification boundaries. Polymerase then extends inward from each primer’s 3′ end, copying the intervening sequence. This makes primer position central to analyzing a defined genomic or complementary DNA region.
DNA polymerase extends a primer from its 3′ end after the primer anneals to a complementary strand. This establishes the starting point for copying the intervening DNA sequence during each thermal cycle. Consequently, correct primer annealing and a properly positioned 3′ end determine whether the intended region can be efficiently reproduced for downstream analysis.
Nested PCR separates amplification into two primer pairs. Outer Primers are used in the first reaction to copy a broader defined region, while internal primers are used in the second reaction within that region. Amplification by the internal pair can increase target specificity and reduce amplification of nonspecific products, supporting more selective detection.
The workflow begins with a PCR reaction containing the template and Outer Primers, followed by a second reaction that uses internal primers. The first reaction provides an amplified region containing the intended target, and the second focuses amplification within it. This sequential arrangement is useful when greater specificity is needed for target detection.
Amplification defined by Outer Primers can provide DNA material for sensitive detection, cloning, sequencing, and analysis. The selected primer positions determine the region carried forward into these applications. Because the approach focuses copying on a specified genomic or complementary DNA segment, it helps researchers examine a particular sequence rather than an undefined portion of DNA.
These primers can be used to define regions in either genomic DNA or complementary DNA for amplification and subsequent study. Their flanking placement establishes which sequence is examined, while thermal cycling and polymerase extension reproduce that region. The resulting targeted amplification supports biological analyses that require detection, cloning, sequencing, or characterization of defined DNA segments.