Directionality, in molecular biology, refers to the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon atoms in the nucleotide sugar-ring numerically gives rise to a 3' end and a 5' end. The relative positions of structures along a strand of nucleic acid, including genes, transcription factors, and polymerases are usually noted as being either upstream (towards the 5' end) or downstream (towards the 3' end).

The importance of having this type of naming convention is easily demonstrated by the fact that nucleic acids can only be synthesized in vivo in a 5' to 3' direction, as the polymerase used to construct new strands must attach a new nucleotide to the 3' hydroxyl (-OH) group via a phosphodiester bond. Traditionally DNA and RNA sequences are written going from 5' to 3'.

3' end

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The 3' (pronounced "three prime") end of a strand is so named due to it terminating at the hydroxyl (-OH) 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.

Molecular biologists can use nucleotides that lack a 3'-hydroxyl (dideoxyribonucleotides) to interrupt the replication of DNA. This technique is known as both the Dideoxy termination method and the Sanger method, and was used to work out the order of nucleotides in DNA.

The 3' end is also the site of post-translational polyadenylation, which attaches a chain of 50 to 250 adenosine residues to messenger RNA immediately after translation. This chain helps in determining how long the messenger RNA lasts in the cell, and therefore how much protein is produced from it.

5' end

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The 5' (pronounced "five prime") end is named as the strand terminates at the chemical group attached to the fifth carbon in the sugar-ring. If a phosphate group is attached to the 5' end, ligation of two nucleotides can occur, via a phosphodiester bond from the 5'-phosphate to the 3'-hydroxyl group of another nucleotide. If it is removed no ligation can occur. Molecular biologists can use this phenomenon to their advantage by removing the 5'-phosphate with a phosphatase to prevent any unwanted nucleic acid ligation.

The 5' end is the site at which post-translational capping occurs, a process which is vital to producing mature messenger RNA. Capping ensures the stability of the messenger RNA while it undergoes translation, providing resistance to the degradive effects of exonucleases. It consists of a methylated nucleotide (methylguanosine) attached the messenger RNA in a rare 5' to 5' triphosphate linkage.

References

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DNA | Molecular genetics | RNA