RNA primers
Summary
RNA primers are short RNA strands made by primase that pair with the DNA template and give DNA polymerase a free 3′-OH to extend, since it cannot start a strand on its own. The lagging strand needs a new primer for each Okazaki fragment.
Detail
Meaning: DNA polymerases can only add nucleotides to an existing 3′-OH, so they cannot start a strand from nothing. Primase, a specialized RNA polymerase, builds a short RNA segment complementary to the template, and DNA polymerase then extends the primer's 3′ end with deoxyribonucleotides.
On the MCAT: Passages show a replication fork and ask where primers are needed. The leading strand needs one primer at the origin; the lagging strand needs a new primer for each Okazaki fragment. In prokaryotes, DNA polymerase III extends primers, DNA polymerase I removes the RNA with its 5′→3′ exonuclease activity and fills the gap with DNA, and DNA ligase seals the nick. Questions may ask what results if primase or ligase is missing. Primer removal at the end of the lagging strand also underlies telomere shortening, which telomerase offsets.
Common confusion: Primers are not made by DNA polymerase, and they do not stay in the final DNA. Primase makes them from RNA nucleotides (U pairs with template A), and they are later replaced with DNA. Helicase unwinds the helix but makes no primer.
Sources
- Lehninger Principles of Biochemistry
- Biochemistry (Berg, Tymoczko, Stryer)
- Molecular Biology of the Cell
Written for the MCAT and checked before it was published. For study reference only. Spotted an error? Let us know.