An RNA primer is a short, single-stranded nucleic acid segment, typically 10 to 12 ribonucleotides long. It serves as a temporary starting point for DNA synthesis, a fundamental process where cells copy their genetic material. This small RNA molecule is essential for initiating DNA replication, ensuring accurate duplication of the cell’s entire DNA genome.
Enabling DNA Replication
DNA replication begins with RNA primers because DNA polymerases, the main enzymes synthesizing new DNA strands, have a limitation. They can only add new DNA nucleotides to an existing strand, specifically to a free 3′-hydroxyl group, and cannot start a new strand from scratch. To overcome this, primase synthesizes a short RNA primer directly onto the DNA template. This primer provides the necessary starting point, allowing DNA polymerase to attach and extend the new DNA chain.
The role of RNA primers differs between the two new DNA strands. On the leading strand, built continuously in the same direction as the replication fork unwinds, only a single RNA primer initiates synthesis. However, the lagging strand is synthesized discontinuously in short segments called Okazaki fragments, as its overall direction is opposite to the replication fork. Each Okazaki fragment requires its own RNA primer to begin synthesis. This repetitive priming ensures the entire lagging strand can be replicated despite the directional constraint.
Why RNA, Not DNA?
The cell’s use of RNA rather than DNA for primers is a strategy with implications for genomic integrity. RNA and DNA have distinct chemical compositions: RNA contains ribose sugar and uracil, while DNA has deoxyribose sugar and thymine. This difference makes RNA primers easily distinguishable from the newly synthesized DNA strand. The RNA acts as a clear “flag” for cellular machinery, signaling their temporary nature and need for removal.
This distinction also plays a role in the cell’s quality control. Laying down a primer can be prone to errors. By using RNA, which is later removed and replaced with DNA, the cell gains an opportunity to proofread and correct initial mistakes made during priming. This ensures the permanent DNA strand is synthesized with high fidelity, minimizing mutations.
The Primer’s Lifecycle
Once an RNA primer has served its purpose by providing a starting point for DNA polymerase, it must be removed to ensure the final DNA strand consists entirely of DNA. This removal involves specific cellular enzymes. In prokaryotes, DNA polymerase I removes RNA primers through its exonuclease activity and simultaneously fills the gap with DNA nucleotides. This dual action is often called nick translation.
In eukaryotic cells, the process is more complex, involving several enzymes. RNase H, which degrades RNA in RNA-DNA hybrids, and Flap Endonuclease 1 (FEN1) work together to remove RNA primers. RNase H cleaves the RNA part, and FEN1 removes remaining RNA or small DNA flaps. After removal, DNA polymerase fills the resulting gap with DNA nucleotides, and DNA ligase then seals nicks between the newly synthesized DNA and the adjacent strand, creating a continuous molecule. This cycle ensures accurate and seamless replication of genetic material.