Oligonucleotide templates

Ritchie CM, Johnsen KR, Kiser JR, Antoku Y, Dickson RM, Petty JT (2007) Ag nanocluster formation using a cytosine oligonucleotide template. J Phys Chem C 111 175-181... 

Xiong, Y., and Steitz, T. A. (2004). Mechanism of transfer RNA maturation by CCA-adding enzyme without using an oligonucleotide template. Nature 430, 640-645. 

For a given lesion, error-free or error-prone synthesis by a bypass polymerase is often determined by in vitro translesion synthesis assays (Figure 22.21). The assay involves in vitro DNA synthesis by a purified bypass polymerase from an oligonucleotide template containing a site-specific lesion. A DNA primer labeled with 32P at its 5 end is annealed to the damaged template prior to assembling the assay reactions. Following the polymerase reaction, products are separated by electrophoresis... 

To the annealed oligonucleotide/template mixture, add 10pL 10mM ATP, lOpL 25mM dNTPs, 15pL lOOmM DTT, 30 Weiss units T4 DNA ligase, 30 units T7 DNA polymerase. 

Luther et al. have circumvented product inhibition by attaching the template to the surface of a solid support [115]. Two complementary DNA 14-mers, immobilized irreversibly on the support, templated the ligation of four 7-mer DNA substrates. After the coupling step, the product strands were released by denaturation, and subsequently immobilized on fresh support to become a template for the next reaction cycle. This procedure requires several steps, but allows exponential amplification of oligonucleotide templates. 

Seckute J, Yang J, Devaraj NK (2013) Rapid oligonucleotide-templated fluorogenic tetrazine ligations. Nucleic Acids Res 41(15) el48. doi 10.1093/nar/gkt540... 

Another iterative approach to generate an exponential self-replicating system combines solid-phase chemistry with chemical replication of oligonucleotides. At the start of the reciprocal version of this procedure, two complementary oligonucleotide templates are immobihzed onto a solid support. Appropriate nucleotide building blocks can then be recognized on the templates and reacted to form copies of both strands. Treatment of the duplexes with polar... 

Another criterion for functionality of short oligonucleotide templates is the stimulation of their binding to ribosomes by cognate aminoacyl-tRNAs."... 

Similar activation methods allow the chemical cyclization of (solution or solid-phase synthesized) linear oligonucleotides (62,201-204), which recently have been studied for triple-helix formation to oligonucleotide templates (204). 

FIGURE 7.5 General schemes of in vitro runoff transcriptions, (a) The transcription from a dual promoter-carrying plasmid and (b) the transcription from a synthetic oligonucleotide template (ds or ss) linked to a mobile promoter. L, M, and R represent left, middle, and right restriction sites in the multiple cloning site (MCS) which is flanked by T7 and SP6 (or T3) promoter sequences. 

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