Summary of the inverse PCR process.

Inverse polymerase chain reaction (Inverse PCR) is a variant of the polymerase chain reaction that is used to amplify DNA with only one known sequence. One limitation of conventional PCR is that it requires primers complementary to both termini of the target DNA, but this method allows PCR to be carried out even if only one sequence is available from which primers may be designed.

Inverse PCR is especially useful for the determination of insert locations. For example, various retroviruses and transposons randomly integrate into genomic DNA. To identify the sites where they have entered, the known, "internal" viral or transposon sequences can be used to design primers that will amplify a small portion of the flanking, "external" genomic DNA. The amplified product can then be sequenced and compared with DNA databases to locate the sequence which has been disrupted.

The inverse PCR method involves a series of restriction digests and ligation that "invert" the target DNA, resulting in known sequences at either end of the unknown sequence. Then, like other polymerase chain reaction processes, the DNA is amplified by the temperature-sensitive DNA polymerase:

1. Target DNA is lightly digested into fragments of a few kilobases by an restriction enzyme.
2. Under low DNA concentrations, self-ligation is induced to give a circular DNA product.
3. The target DNA is cut once within the known internal sequence. This gives a linear product with known terminal sequences, suitable for PCR.
4. PCR is carried out as usual, with primers complementary for sections of the known internal sequence.

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