Directionality (molecular biology)

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Directionality (molecular biology)

Definition

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Directionality, in molecular biology and biochemistry, is 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 5′-end and a 3′-end (usually pronounced "five prime end" and "three prime end"). The relative positions of structures along a strand 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). This naming convention is important because nucleic acids can only be synthesized in vivo in the 5′-to-3′ direction, as the polymerase that assembles new strands only appends new nucleotides to the 3′-hydroxyl (-OH) group, via a phosphodiester bond. Directionality is related to, but independent from sense. In coding DNA, codons read 5′–ATG–⋯–3′ on the sense strand, and 3′–TAC–⋯–5′ on the complementary antisense strand. Thus only the antisense strand will translate to sense mRNA. By convention, single strands of DNA and RNA sequences are written in 5′-to-3′ direction.