Amplification with Arbitrary Primers

Abstract

Several methods have been published that rely on the use of short oligonucleotide primers with arbitrary sequences to amplify discrete DNA fragments by the polymerase chain reaction (PCR) (1,2). Typically, a single arbitrary primer is used in each reaction and amplification is achieved when the same sequence is present in inverted orientation at two sites separated by less than a few kilobases. These methods have several advantages:

• 1. They can be used to produce quickly large numbers of discrete DNA fragments without prior sequence information;

• 2. Owing to the random nature of the process, the amplified fragments are likely to be evenly distributed across a genomic region;

• 3. Because they do not rely on the presence of species-specific repetitive sequences (e.g., Alu repeats [3]), they can be used to analyze the genome of any species.