Deoxyribonucleic acid (DNA) holds the complete genetic instructions necessary for the development, functioning, growth, and reproduction of all known organisms. Before a cell divides, this entire genetic blueprint must be accurately copied through a process known as DNA replication. The enzyme DNA polymerase is responsible for adding new DNA building blocks to the growing strands. However, DNA polymerase is not capable of starting a new strand on its own. This is where the specialized enzyme RNA primase comes into play, initiating DNA synthesis so that the main replication enzymes can begin their work.
The Requirement for a Starting Point
The necessity for RNA primase arises from a fundamental limitation of DNA polymerase. This enzyme is designed only to extend an existing nucleotide chain, meaning it can only add new bases to a chain that is already in progress. It lacks the ability to initiate the synthesis of a new strand completely from scratch, a process known as de novo synthesis.
DNA polymerase requires a pre-existing nucleotide that provides a free 3′-hydroxyl (3′-OH) group. This group acts as the attachment point for the incoming new base, allowing the chemical reaction that forms the phosphodiester bond to proceed. RNA primase is the molecular solution, as it possesses the unique capability to begin synthesizing a chain without needing a pre-existing 3′-OH group.
How Primase Builds the RNA Primer
RNA primase is classified as a type of RNA polymerase, meaning its function is to synthesize RNA molecules. When it encounters a single-stranded DNA template, it catalyzes the addition of ribonucleotides (the building blocks of RNA) to form a short segment called a primer. These ribonucleotides are complementary to the exposed DNA template strand, ensuring the new chain aligns correctly. The resulting RNA primer is typically short, often consisting of 5 to 12 nucleotides in length.
The ability of primase to initiate synthesis de novo allows it to bind the template and two initial ribonucleotides together. The enzyme quickly extends the chain until the primer reaches its predetermined length. Once the short RNA primer is complete, it provides the required free 3′-OH group, creating the starting platform that DNA polymerase needs to begin synthesizing the longer DNA strand.
Priming the Leading and Lagging Strands
The function of RNA primase becomes differentiated because the two strands of the double helix are copied in distinct ways due to their antiparallel orientation. Replication occurs at the replication fork, where the DNA strands are separated, exposing the templates. On the leading strand, DNA synthesis proceeds continuously in the same direction as the opening replication fork. The leading strand requires only a single RNA primer, which is laid down at the beginning of the replication process.
The lagging strand must be synthesized discontinuously, moving in the opposite direction of the replication fork. This necessitates that DNA polymerase repeatedly start and stop, creating short segments of new DNA known as Okazaki fragments. Consequently, RNA primase must repeatedly synthesize a new RNA primer for the start of every Okazaki fragment. This continuous, repeated action means that primase is far more active in this region of the replication fork.
The Removal and Replacement of the Primer
Although the RNA primer is necessary to initiate DNA synthesis, it cannot remain as a permanent part of the final DNA molecule. Since the primers are made of RNA, they must be removed to ensure the genetic code is composed entirely of DNA. The removal process differs between organisms but generally involves specialized nucleases. In prokaryotes, DNA Polymerase I degrades the RNA primer and simultaneously fills the space with DNA nucleotides.
In eukaryotic cells, RNA removal is accomplished by a combination of enzymes. RNase H degrades the RNA component of the RNA-DNA hybrid. Flap Endonuclease 1 (FEN-1) then removes any remaining nucleotides that may form a small flap structure.
Once the RNA is excised, a DNA polymerase enzyme fills the vacant space with the correct deoxyribonucleotides. The final step is performed by DNA ligase, which seals the remaining nick, joining the newly synthesized DNA segments into a continuous strand.