Synthetic oligonucleotide synthesis

Each primer is a synthetic oligonucleotide of about 20 bases prepared so that then-sequences are complementary to the (previously determined) sequences that flank the tar get regions on opposite strands Thus one primer is annealed to one strand the other to the other strand The 3 hydroxyl end of each primer points toward the target region The stage is now set for DNA synthesis to proceed from the 3 end of each primer [Figure 28 14(c )] The solution contains a DNA polymerase and Mg " m addition to the... 

Synthetic organic polymers, which are used as polymeric supports for chromatography, as catalysts, as solid-phase supports for peptide and oligonucleotide synthesis, and for diagnosis, are based mainly on polystyrene, polystyrene-divinylbenzene, polyacrylamide, polymethacrylates, and polyvinyl alcohols. A conventional suspension of polymerization is usually used to produce these organic polymeric supports, especially in large-scale industrial production. 

Synthetic oligonucleotides are very important tools in the study and manipulation of DNA, including such techniques as site-directed mutagenesis and DNA amplification by the polymerase chain reaction. The techniques for chemical synthesis of oligonucleotides are highly developed. Very efficient automated methodologies based on solid phase synthesis are used extensively in fields that depend on the availability of defined DNA sequences.52... 

Colin2 came to a similar conclusion in a review of this subject area. He emphasizes that it is important to distinguish early on the difference between purification costs (e.g., equipment, solvents, packing material) and production costs (purification and cost of making the crude sample). He noted that a crude sample resulting from a multistep synthesis can itself be very expensive and will enable one to tolerate much higher purification costs. This is indeed the case in purification of synthetic oligonucleotides, where even very steep purification costs are a fraction of the costs of even the raw materials required for synthesis, let alone the total cost of synthesis. 

Warren, W. and Vella, G., Analysis and purification of synthetic oligonucleotides by high-performance liquid chromatography, in Oligonucleotide Synthesis Protocols, Agrawal, S., Ed., Humana Press, Totowa, NJ, 1993, 235. 

Furthermore, synthetic oligonucleotide blocks were connected by the same RNA ligase, culminating in the synthesis of E. coli tRNAf and of modified tRNA s. ... 

The PCR procedure has an elegant simplicity. Two synthetic oligonucleotides are prepared, complementary to sequences on opposite strands of the target DNA at positions just beyond the ends of the segment to be amplified. The oligonucleotides serve as replication primers that can be extended by DNA polymerase. The 3 ends of the hybridized probes are oriented toward each other and positioned to prime DNA synthesis across the desired DNA segment (Fig. 9-16). (DNA polymerases... 

To enable a covalent labeling of target molecules, the dyes are functionalized with reactive groups. These are either phosphoramidites for the labeling of synthetic oligonucleotides (solid-phase synthesis), or uridine-5 -triphosphates for enzymatic coupling in PCR (random primed labeling... 

Fig. 6. Physical detection of reciprocal translocations. The chromosomes shown are identical to those in Fig. S. Vertical arrows represent recognition sites for a single restriction enzyme horizontal arrows correspond to synthetic oligonucleotide primers and lines below the chromosomes indicate the sizes of restriction or PCR fragments. In (A), the alteration in restriction fragment size as a result of exchange is illustrated. Such alterations can be detected by Southern analysis using the duplicated sequence as a probe. In (B), the production of a PCR product from one of the exchange chromosomes is illustrated. Neither parental chromosome directs synthesis of a PCR product.

---