The ColE1 primer transcript (RNA II) hybridizes to the template DNA near the replication origin. The hybridized RNA II is cleaved by RNAase H to form the primer. Hybridization is inhibited by binding of another RNA, RNA I, to RNA II. This binding alters the secondary structure of RNA II even in the region far downstream of the segment where RNA I binds. Similar functional and structural alterations of RNA II are produced by a single base-change within this segment. However, a region of about 200 nucleotides proximal to the 5' end of RNA II that includes the segment can be deleted with little effect on primer formation. By forming an alternative structure, the dispensable region affects folding of a downstream region, and thus participates in regulation of primer formation.