Inverse Primer Design
Inverse Primer Design - Related Videos
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Primer-Free Aptamer Selection Using A Random DNA Library
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Cited by 20 •
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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.
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Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources
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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.
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Liquid Phase Reactor: Sucrose Inversion
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2023
Source: Kerry M. Dooley and Michael G. Benton, Department of Chemical Engineering, Louisiana State University, Baton Rouge, LA Both batch and continuous flow reactors are used in catalytic reactions. Packed beds, which use solid catalysts and a continuous flow, are the most common configuration. In the absence of an extensive recycle stream, such packed bed reactors are typically modeled as "plug flow". The other most common continuous reactor is a stirred tank, which is assumed to be perfectly...
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Inverse Trigonometric Functions
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2025
Inverse trigonometric functions are fundamental mathematical tools that reverse the actions of standard trigonometric functions. While trigonometric functions map angles to ratios, inverse trigonometric functions perform the opposite operation by mapping a ratio back to its corresponding angle. These functions are essential in various applications, particularly in determining angles when given specific distances, such as calculating elevation angles in navigation and engineering.For a function...
01:25
Inverse Hyperbolic Functions and Their Derivatives
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2026
The shape of a suspension bridge cable hanging under its own weight is described by a catenary curve, which is modeled using the hyperbolic cosine function. This mathematical model accurately captures the balance between gravity and tension acting along the cable. When a particular vertical position on the cable is known, the corresponding horizontal position can be determined using the inverse hyperbolic cosine function, allowing for a detailed analysis of the cable's geometry.Inverse...
FAQs
The primer pair binds within the known sequence but points away from it, so amplification proceeds into the neighboring DNA rather than toward the established region. After restriction fragments are joined into circles, the unknown flanking segment becomes part of the amplifiable template. This orientation allows sequence information to extend beyond the region used for primer design.
Restriction digestion separates genomic DNA into fragments with defined ends, while dilution favors intramolecular ligation, meaning each fragment is more likely to join to itself than to another fragment. Self-ligation produces circular templates containing the known region and its adjacent DNA. These circles create the physical arrangement needed for outward-facing primers to amplify flanking sequence.
The known sequence provides the only established location for primer binding and determines the primers’ outward orientation. Because the adjacent region does not need to be known in advance, the strategy can investigate DNA that is difficult to target directly. This makes the approach useful for extending sequence analysis beyond an existing reference region.
A typical workflow begins by digesting genomic DNA with restriction enzymes. The resulting fragments are diluted to favor intramolecular ligation and circular template formation. Outward-facing primers are then used for PCR, and the amplified product is sequenced. The sequence data can reveal DNA adjacent to the known region used for primer placement.
Sequencing the amplified product can identify DNA flanking a known sequence, including neighboring genomic regions that were not previously characterized. In cancer research, the resulting information may help locate integration sites, define gene rearrangements, or examine structural variation near a known mutation or engineered genomic element.
The approach is valuable when a tumor genome contains a known mutation, integration-related sequence, or engineered element but the surrounding DNA is uncertain. By recovering adjacent sequence, researchers can molecularly characterize nearby rearrangements and structural variants. It therefore supports investigation of how established genomic features connect to less-defined regions in tumor DNA.