Low-Stringency Single Specific Primer-Amplified DNA Analysis by Capillary Electrophoresis

Polymerase chain reaction (PCR) amplification is a relatively fast, sensitive method for characterizing discrete segments of the human genome for identity testing. Most PCR-based typing assays that discriminate single nucleotide polymorphisms (SNPs) require further manipulation of the amplification product to identify the polymorphic sites. A more simplified assay, PCR products would be directly analyzed to determine whether DNA extracted from two different sources was a match or a mismatch. Examples of direct PCR assays to distinguish SNPs are allele-specific PCR (1), arbitrary primed PCR (AP-PCR) (2), DNA amplification fingerprinting (DAF) (3), and randomly amplified polymorphic DNA (RAPD) (4). AP-PCR, DAF, and RAPD involve random amplification of genomic DNA using low stringency primer annealing to generate a DNA banding pattern or profile. Sequence differences are detected without identifying the specific variations. However, the concentration of the DNA and the degree of DNA degradation can alter the profile, and the application of these techniques for human identification has not been adequately demonstrated.