Orthogonal Primers
Orthogonal Primers - Related Videos
01:26
Orthogonal Trajectories
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2026
Orthogonal trajectories describe the geometric relationship between two families of curves that intersect each other at right angles. One illustrative case involves a family of parabolas that open sideways along the x-axis. These curves share a common shape but differ by a scaling parameter, resulting in a set of curves that all pass through the origin and widen at different rates.Determining Orthogonal TrajectoriesTo identify the orthogonal trajectories for these parabolas, the first step...
10:32
Orthogonal Protein Purification Facilitated by a Small Bispecific Affinity Tag
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Cited by 7 •
2012
A novel and highly efficient two-step affinity chromatography protocol has been developed and is described in detail. The method is based on a small purification tag with two inherent affinities and is applicable to a wide range of target proteins with different properties.
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.
08:43
Calibration Procedures for Orthogonal Superposition Rheology
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Cited by 4 •
2020
We present a detailed calibration protocol for a commercial orthogonal superposition rheology technique using Newtonian fluids including end-effect correction factor determination methods and recommendations for best practices to reduce experimental error.
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.
FAQs
Complementary base pairing provides the primary recognition signal, while primer length and sequence influence how selectively each primer binds its intended template. A suitable design minimizes matching with other primers and unrelated genomic regions. These properties allow several primer pairs to function together while limiting unintended amplification between targets in the same reaction.
Annealing temperature influences whether primer-template interactions are stable enough to support amplification without favoring weaker, unintended matches. Secondary structures within a primer or target can hide binding sites or alter accessibility. Evaluating both factors helps preserve selective binding and reduces conditions that could produce inefficient or misleading amplification.
Unintended homology can let a primer recognize an off-target genomic region or another assay component, creating cross-talk among reactions. Primer-dimer formation consumes primers and can generate products unrelated to the intended template. Screening for both problems is therefore central to maintaining specificity, especially when multiple primer pairs share one reaction mixture.
Begin by matching each primer pair to its intended DNA target, then examine sequence complementarity against other primers and relevant genomic regions. Check for potential primer-dimer interactions and secondary structures, and consider annealing temperature during evaluation. Designs that show minimal unintended homology and interaction are better candidates for parallel amplification or sequencing assays.
They are useful when a single mixture must amplify or identify several distinct DNA targets. In multiplex PCR, selective primer interactions help different reactions proceed with less cross-talk. For targeted genotyping, this supports parallel analysis of selected genomic regions while reducing misleading amplification, making complex samples more efficient to examine.
In synthetic biology, distinct engineered sequences may need to be monitored within the same experimental system. Carefully screened primers can direct amplification or sequencing toward separate intended targets without substantial interaction among assay components. This enables parallel detection of genetic constructs and helps distinguish specific signals from amplification caused by unintended sequence relationships.