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The SMART™ oligonucleotide which has an oligo(G) sequence at its 3′ end, base-pairs with the deoxycytidine stretch, creating an extended template.
It is hypothesized that clinical lymph node relapse could be the direct consequence of a suboptimal PLND at the initial treatment or a progression outside the boundaries of the standard extended template.
In this case, the template inherits the vocabulary, constraints, resources, and relationships defined in the extended template.
An extended template is defined for each point as a combination of three parts, of a local descriptor at the sampling point, of its directional vector pointing to the given landmark position, and thirdly, of the local likelihood pattern around the landmark positions.
A oligo dT) primer [CDS III/3' PCR Primer 5'-AAG CAG TGG TAT CAA CGC AGA GTA C(T 30-3'] was used to prime the first-strand synthesis reaction, and the SMART IV Oligo (5'-AAG CAG TGG TAT CAA CGC AGA GTA CGC rGrGrG-3') served as a short, extended template at the 5' end of the mRNA.
The SMART II oligonucleotide (Clontech), which has extra G nucleotides at its 3' end, was used to create an extended template useful for full-length cDNA enrichment.
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hPol κ extended template-primers in the order M1dG dC > M1dG dG > M1dG dT ∼ M1dG dA, but neither hPol ι nor Rev1 extended M1dG-containing template-primers.
Single nucleotide incorporation experiments indicate that hPol κ extended template-primers containing dC opposite M1dG approximately 10-fold more efficiently than template-primers containing other deoxynucleotides opposite the adduct when it is contained in the 3′-GXC-5′ sequence.
This extends template stripping to high-melting-point solids, such as W, and transparent conductors, such as ITO, both of which are difficult to pattern with conventional methods.
Support for this hypothesis is provided by the observation that hPol κ is very inefficient at extending template-primers containing dC PdG termini (27).
Human Pol κ inserted dCMP opposite the exocyclic lesions less efficiently than hPol ι did, but hPol κ was able to extend template-primers containing dNMPs opposite the adducts.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com