Random Primer Synthesis
Random Primer Synthesis - 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.
15:22
Nucleoside Triphosphates - From Synthesis to Biochemical Characterization
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Cited by 4 •
2014
The protocol described herein aims to explain and abridge the numerous obstacles in the way of the intricate route leading to modified nucleoside triphosphates. Consequently, this protocol facilitates both the synthesis of these activated building-blocks and their availability for practical applications.
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.
08:33
Hydrogel Synthesis
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2023
Source: Amber N. Barron, Ashlea Patterson, and Taylor D. Sparks, Department of Materials Science and Engineering, The University of Utah, Salt Lake City, UT Hydrogels are a versatile class of cross-linked polymers produced through relatively simple procedures and with generally inexpensive materials. They can be formed from solution and involve a polymer backbone formed from monomer reagents, an initiator which makes the polymer reactive and a crosslinking species which binds the polymer chains...
FAQs
The synthesis uses controlled incorporation of mixed nucleotide reagents during phosphoramidite chemistry. At positions where more than one nucleotide can be incorporated, the product becomes a population rather than one uniform sequence. This diversity creates many possible complementary matches, allowing different molecules in a nucleic-acid sample to receive extension from an available 3′ end.
Primer length, nucleotide composition, and reaction conditions are important design variables because they influence both where the mixed population can anneal and how broadly sequences are represented. No single setting guarantees uniform coverage: these variables can shift the balance between binding specificity and breadth, affecting which transcripts or template regions contribute to the final product.
Extension depends on the primer’s free 3′ end. Once a random oligonucleotide anneals to a complementary stretch, DNA polymerase or reverse transcriptase can extend from that end. This converts transient sequence matching into a nucleic-acid product, which is why the synthesized population can initiate cDNA production, labeling, or amplification across many template locations.
Broad binding distribution can improve representation of transcripts because initiation is not restricted to one known sequence. This is especially useful when templates are complex or only partly characterized. The tradeoff is that broader binding also makes the outcome sensitive to primer length, composition, and reaction conditions, which influence specificity and coverage.
To prepare these primers, phosphoramidite synthesis uses controlled incorporation of mixed nucleotide reagents to create sequence diversity at defined positions. The resulting oligonucleotide population is then introduced into a nucleic-acid reaction where complementary stretches permit annealing and enzymatic extension. The exact length and composition should be considered alongside the intended coverage and specificity.
In RNA-focused work, random primers can initiate cDNA production through reverse transcriptase. Because the population can anneal at multiple complementary stretches, cDNA synthesis need not depend on a single preselected RNA sequence. This makes the approach relevant when researchers want broad transcript representation rather than targeting only a known region.
Random primer synthesis also supports nonspecific DNA labeling and amplification of complex or partially characterized templates. These uses exploit the same broad distribution of potential binding sites, but the desired outcome differs: labeling marks DNA, whereas amplification increases representation of template material. Primer design and reaction conditions remain important for interpreting coverage.