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What Are RNA Primers?

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  • Written By: E.A. Sanker
  • Edited By: John Allen
  • Last Modified Date: 31 March 2014
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Ribonucleic acid (RNA) primers play an essential role in deoxyribonucleic acid (DNA) replication, the copying of DNA molecules that occurs in all living organisms. Replication allows an organism to pass on genetic information, contained in a copy of its DNA, to its offspring. RNA primers help initiate replication on the molecular level. They act in conjunction with several enzymes, or proteins, that catalyze reactions involved in this process.

RNA, like DNA, is molecule consisting of subunits called nucleotides. Each nucleotide in an RNA or DNA chain contains a chemical compound known as a nucleobase. DNA nucleobases are adenine, thymine, guanine, and cytosine. In RNA, the compound uracil is used in place of thymine, but the other nucleobases are the same as in DNA.

Each nucleobase in an RNA or DNA strand chemically bonds with a complementary nucleobase on another DNA or RNA strand to form a base pair, creating a double helix. Adenine pairs with thymine or uracil, while guanine pairs with cytosine. The pattern of repeating units creates a sequence in which genetic information can be stored.

During replication, the enzyme helicase splits the bonds between nucleotides and separates the DNA molecule into its two constituent strands. Another enzyme, DNA polymerase, attaches complementary nucleotides to each single strand. This process creates a duplicate of the original DNA molecule by using each of the two complementary strands as a template.

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DNA polymerase can add nucleotides to a developing strand, but it cannot create a new strand from scratch. This is where RNA primers come in. RNA primers are short strands of about 10 or 11 nucleotides each, and are formed by the enzyme primase. Primase binds to helicase to form a structure known as a primosome. The primosome attaches complementary nucleotides to the single stranded DNA molecule, creating an RNA primer, and the action of RNA primers along the chain sets off DNA polymerase.

The arrangement of atoms within nucleotide molecules causes DNA and RNA strands to have directionality — each strand has a specific orientation. Strand ends are named based on the area of the nucleotide molecule they terminate with. The five-prime (5’) end of a strand terminates with the fifth carbon atom in the molecule’s carbon ring structure. Complementary strands are oriented opposite one another, so the other strand would have a three-prime (3’) end at that location, terminating in its third carbon atom. To visualize this, if one strand of a double helix runs from 5’ to 3’ left to right, the opposite strand must run from 3’ to 5’ left to right.

DNA polymerase can only add nucleotides to the 3’ end, working towards the 5’ end. Only one RNA primer is needed to start this process from the leading strand, which ends in 3’. Replication of the opposite lagging strand is more complicated. DNA polymerase adds nucleotides backwards along this strand intermittently, working in short sequences as the strands are split. Each sequence requires an RNA primer at its beginning, so several RNA primers are needed to replicate the lagging strand.

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