Fourteen expanded trinucleotide loci have been found to cause neurological diseases including Huntington's Disease, myotonic dystrophy type 1 and spinocerebellar ataxia. The repeat sequence and allele sizes vary between each locus, and the flanking DNA is assumed to play a significant role in repeat instability. The aim of this project was to characterise the behaviour and mutability of two trinucleotide repeat loci with the same repeat sequence, but with different flanking DNA sequences. Comparing the mutation rates and average length changes of these loci in the male germline demonstrated a clear effect of the influence of the flanking sequence. The ERDAI locus has low %GC content in the flanking sequence and displays a low mutation rate, even for large length alleles, whereas CTG18.1 has a relatively high %GC content and demonstrates an increased mutation rate and average length change for similarly sized alleles. Utilising the sensitive SP-PCR technique gives a clear insight into how the CTG18.1 locus has responded dramatically to defects in mismatch repair, both in MMR deficient cell lines and HNPCC tissues, and possibly in an ovarian tumour. This investigation has also revealed a possible dominant negative mutation in the hMLH1 gene which maintains its influence on an expanded CTG18.1 allele in two generations of a HNPCC family. In conclusion, we have successfully characterised the behaviour of two trinucleotide repeat loci which highlights the significant effect of flanking DNA sequence on the stability of triplet repeats
