= ColE1 RNA II
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\b[ColE1 RNA II] is the primer-precursor transcript used to initiate <DNA replication> of the <Colicin E1 plasmid>. Part of the nascent <RNA> forms a persistent hybrid with the template <DNA> near the replication start. <Ribonuclease H> processes the hybridized transcript to generate an <RNA primer>, from which DNA synthesis can proceed. Thus a transcript can help start replication without encoding a <protein>.<Control of ColE1 plasmid replication: the process of binding of RNA I to the primer transcript by J. Tomizawa>[Abstract: primer-promoter transcript, persistent RNA–DNA hybrid and RNAase H processing.]{ref}
The regulatory transcript <ColE1 RNA I> binds <ColE1 RNA II> and can prevent the hybrid needed for primer formation. The important distinction is between making an RNA molecule and making a usable primer: a transcript can be present but take a pairing or folding pathway that blocks productive initiation.<Control of ColE1 plasmid replication: the process of binding of RNA I to the primer transcript by J. Tomizawa>[RNA I binding inhibits RNA II hybridization; identification of the RNA-binding product.]{ref}
An idealized bookkeeping example separates the steps. If 100 precursor transcripts are made but only 30 reach the primer-producing state, the number of transcripts is 100 while the number of productive primer events is 30. This is not a measured efficiency or a complete kinetic model; it illustrates why total transcript abundance does not directly count successful <DNA replication> initiations. Changes in RNA production, RNA pairing or processing can have different mechanisms even if they all reduce final plasmid yield.
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