PCA Principles
Much like how primers are designed such that there is a forward primer and a reverse primer capable of allowing DNA polymerase to fill the entire template sequence, PCA uses the same technology but with multiple oligonucleotides. While in PCR the customary size of oligonuleotides used is 18 base pairs, in PCA lengths of up to 50 are used to ensure uniqueness and correct hybridization.
Each oligonucleotide is designed to be either part of the top or bottom strand of the target sequence. As well as the basic requirement of having to be able to tile the entire target sequence, these oligonucleotides must also have the usual properties of similar melting temperatures, hairpin free, and not too GC rich to avoid the same complications as PCR.
During the polymerase cycles, the oligonucleotides anneal to complementary fragments and then are filled in by polymerase. Each cycle thus increases the length of various fragments randomly depending on which oligonucleotides find each other. It is critical that there is complementarity between all the fragments in some way or a final complete sequence will not be produced as polymerase requires a template to follow.
After this initial construction phase, additional primers encompassing both ends are added to perform a regular PCR reaction, amplifying the target sequence away from all the shorter incomplete fragments. A gel purification can then be used to identify and isolate the complete sequence.
Read more about this topic: Polymerase Cycling Assembly
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