Chapter 5 - Short Tandem Repeat (STR) Loci and Kits

Abstract

STRs (short tandem repeat) have become popular DNA repeat markers because they are easily amplified by the polymerase chain reaction (PCR) without the problems of differential amplification. This is because both alleles from a heterozygous individual are similar in size since the repeat size is small. The number of repeats in STR markers can be highly variable among individuals, which makes these STRs effective for human identification purposes. STR repeats sequences are named by the length of the repeat unit. STR markers are usually identified in one of the two ways: searching DNA sequence databases such as GenBank for regions with more than six or so contiguous repeat units or performing molecular biology isolation methods. STRs are often divided into several categories based on the repeat pattern. Simple repeats contain units of identical length and sequence; compound repeats comprise two or more adjacent simple repeats; and complex repeats may contain several repeat blocks of variable unit length as well as variable intervening sequences. An STR typing kit consists of five components: a PCR primer mixture containing oligonucleotides designed to amplify a set of STR loci, a PCR buffer containing deoxynucleotide triphosphates, MgCl2, and other reagents necessary to perform PCR, a DNA polymerase, which is sometimes premixed with the PCR buffer, an allelic ladder with common alleles for the STR loci being amplified to enable calibration of allele repeat size, and a positive control DNA sample to verify that the kit reagents are working properly.