Repetitive DNA Sequences: Some Considerations for Simple Sequence Repeats

Abstract Three topics are treated in this paper: (1) can the polymorphism evident in the length of many simple sequence repeats (SSRs) or microsatellites be explained as a result of unequal mitotic crossing over? We conclude that although this mechanism may be a reasonable explanation for polymorphisms of minisatellite sequences, it is less attractive for SSRs, because they are considerably shorter and some of the rates of generation of new length alleles are extremely high. A more likely mechanism is some form of slipped strand mispairing, whether occuring during normal DNA replication or during replication accompanying recombination. (2) Some results are presented on the number of mono- and di-nucleotide repeats in the human genome. For each high scoring locus, an optimal alignment is made of the actual with an ideal SSR; from such alignments, the relative numbers of insertions/deletions (indels), transitions and transversions are obtained for each class of SSR. (3) An elementary derivation of the number of equivalence classes of SSRs of any word length, n , is given.

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