sizes. DQCAR alleles associated with non-DQ1-associated haplotypes had perfect CA repeat sequences, and the variation seen in allele size was attributable to the difference in the number of CA repeats. These results indicated that several mutational mechanisms are involved in the generation of allelic diversity within the same microsatellite locus. Different mutation rates at the same locus must therefore be taken into account when using microsatellites as markers in disease evolution studies.
Single PCR primers complementary to microsatellite repeats were used to amplify genomic DNA samples from plants, humans, yeasts, and Escherichia coli. Most primers generated distinct amplification products, which gave banding patterns on gel electrophoresis which acted as fingerprints for identifying them. However, some of the plant species primers produced fingerprints with the E, coli template DNA as well, and further studies showed that these bands were generated by mismatch priming in a way similar to random amplified polymorphic DNAs. This has serious implications for using amplification products of microsatellites for further studies.
Microsatellite enrichment is thought to result from the accumulated effects of replication slippage mutations (Metzger, Bytof and Wills, 2000). Enrichment is assayed by comparing observed frequency to expected frequency from random association of nucleotides. Enrichment of microsatellites in non-coding sequences occurs for all microsatellite types in a similar exponential fashion within the length of the microsatellite. However, in the coding region, repeats appear to be under much more stringent control. Tri- and hexanucleotide repeats are found consistently in significant excess over a wide range of lengths in both coding and non-coding regions, but other repeat types are much less frequent in coding than in non-coding regions. These findings suggest that differences between coding and non-...