<P> Directionality, in molecular biology and biochemistry, is the end - to - end chemical orientation of a single strand of nucleic acid . In a single strand of DNA or RNA, the chemical convention of naming carbon atoms in the nucleotide sugar - ring means that there will be a 5 ′ - end, which frequently contains a phosphate group attached to the 5 ′ carbon of the ribose ring, and a 3 ′ - end (usually pronounced "five prime end" and "three prime end"), which typically is unmodified from the ribose - OH substituent . In a DNA double helix, the strands run in opposite directions to permit base pairing between them, which is essential for replication or transcription of the encoded information . </P> <P> Nucleic acids can only be synthesized in vivo in the 5 ′ - to - 3 ′ direction, as the polymerases that assemble various types of new strands generally rely on the energy produced by breaking nucleoside triphosphate bonds to attach new nucleoside monophosphates to the 3 ′ - hydroxyl (- OH) group, via a phosphodiester bond . 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). (See also upstream and downstream .) </P>

What is the 5' and 3' end of dna
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