A furanose (sugar-ring) molecule with carbon atoms labeled using standard notation. The 5′ is upstream; the 3′ is downstream. DNA and RNA are synthesized in the 5′-to-3′ direction.
Directionality, in
base pairing between them, which is essential for replication or transcription
of the encoded information.
Nucleic acids can only be synthesized
hydroxyl (−OH) group, via a phosphodiester bond. The relative positions of structures along strands of nucleic acid, including genes and various protein binding sites, are usually noted as being either upstream (towards the 5′-end) or downstream (towards the 3′-end). (See also upstream and downstream
.)
Directionality is related to, but different from,
plastids use N-formylmethionine instead) at the N terminus of the protein. By convention, single strands of DNA and RNA
sequences are written in a 5′-to-3′ direction except as needed to illustrate the pattern of base pairing.
5′-end
In the DNA segment shown, the 5′ to 3′ directions are down the left strand and up the right strand.
The 5′-end (pronounced "five prime end") designates the end of the DNA or RNA strand that has the fifth carbon in the
The 3′-end (three prime end) of a strand is so named due to it terminating at the
hydroxyl group of the third carbon in the sugar-ring, and is known as the tail end. The 3′-hydroxyl is necessary in the synthesis of new nucleic acid molecules as it is ligated
(joined) to the 5′-phosphate of a separate nucleotide, allowing the formation of strands of linked nucleotides.
The 3′-end of nascent messenger RNA is the site of post-transcriptional polyadenylation, which attaches a chain of 50 to 250 adenosine residues to produce mature messenger RNA. This chain helps in determining how long the messenger RNA lasts in the cell, influencing how much protein is produced from it.
The 3′-flanking region is a region of DNA that is not copied into the mature mRNA, but which is present adjacent to 3′-end of the gene. It was originally thought that the 3′-flanking DNA was not transcribed at all, but it was discovered to be transcribed into RNA and quickly removed during processing of the primary transcript to form the mature mRNA. The 3′-flanking region often contains sequences that affect the formation of the 3′-end of the message. It may also contain enhancers or other sites to which proteins may bind.
The
polyA tail
is considered to be 3′-untranslated. The 3′-untranslated region may affect the translation efficiency of the mRNA or the stability of the mRNA. It also has sequences which are required for the addition of the poly(A) tail to the message, including the hexanucleotide AAUAAA.
