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DNA polymorphism a DNA sequence that occurs in 2 or more variant forms Haplotype a combination of alleles at multiple tightly linked loci that are transmitted together over many genereations RFLP variation in the length of a restriction fragment detected by a particular probe due to nucleotide changes at a restriction site ASO a short oligionucleotide probe that hybridize to one allele at a chosen SNP locus SNP definition 2 different nucleotides appear at the same position in genomic DNA from different individuals DNA fingerprinting detection of genotype at a number of linked highly polymorphic loci using one probe minisatellite DNA element composed of tandemly repeated identical sequences locus location on a chromosome 4 classes of DNA polymorphisms -single nucleotide polymorphism -insertion/ deletion -simple sequence repeat (useful for making DNA fingerprints) -copy number variation/ copy number polymorphism SNP -single bp difference -most have no direct effect on activity of genes -very stable (low mutation rate) SNP alleles detected via Southern blots -only works if SNP changes restriction site RFLPs Restriction Fragment Length Polymorphisms -gain or loss of a restriction site SNP detection via PCR -use PCR primers flanking SNP to amplify SNP-containing region -cut PCR product with restriction enzyme & run on gel SNP detection using ASOs (Allele Specific Oligionucleotides) -short probes (<21 nts) hybridize only to perfectly complementary DNA -single bp mismatch prevents hybridization (@ higher temp) SSRs/ Microsatellites Simple Sequence Repeats -Repeat unit lengths:2-5 bp -Mutate by replication errors (repeated sequences have increased tendency to loop out during replication) -most do not affect genes -useful as highly polymorphic markers Huntington's disease -one exception to SSRs not affecting genes -caused by increased number of CAG repeats in coding region of HD gene DNA fingerprints -total number of SSR alleles at multiple unlinked loci