The
ribosomal DNA (
rDNA) repeats of Saccharomyces cerevisiae contain an autonomously replicating sequence (ARS) that colocalizes with a chromosomal origin of replication. We show that a minimal sequence necessary for full ARS function corresponds to a 107-bp
rDNA fragment which contains three 10-of-11-bp matches to the ARS consensus sequence. Point mutations in only one of the 10-of-11-bp matches, GTTTAT GTTTT, inactivate the
rDNA ARS, indicating that this consensus sequence is essential. A perfect match to a revised ARS consensus is present but not essential. Sequences up to 9 bp 5' from the essential consensus are dispensable. A broad
DNA region directly 3' to the essential consensus is required and is easily unwound as indicated by: (i)
hypersensitivity to nicking of an approximately 100-bp region by
mung bean nuclease in a negatively supercoiled plasmid and (ii) helical instability determined by thermodynamic analysis of the nucleotide sequence. A correlation between
DNA helical instability and replication efficiency of wild-type and mutated ribosomal ARS derivatives suggests that a broad region 3' to the essential ARS consensus functions as
a DNA unwinding
element. Certain point mutations that do not stabilize the
DNA helix in the 3' region but reduce ARS efficiency reveal an
element distinct from, but overlapping, the
DNA unwinding
element. The nucleotide sequence of the functionally important constituents in the ARS appears to be conserved among the
rDNA repeats in the chromosome.