3' end/5' end
A nucleic acid
strand is inherently directional, and the "5 prime end" has a free hydroxyl (or
phosphate) on a 5' carbon and the "3 prime end" has a free hydroxyl (or
phosphate) on a 3' carbon (carbon atoms in the sugar ring are numbered from 1'
to 5'; ). That's simple enough for an RNA strand or for single-stranded (ss) DNA.
However, for double-stranded (ds) DNA it's not so obvious - each strand has a 5'
end and a 3' end, and the 5' end of one strand is paired with the 3' end of the
other strand (it is "antiparallel"; ). One would
talk about the 5' end of ds DNA only if there was some reason to emphasize one
strand over the other - for example if one strand is the sense strand of a gene.
In that case, the orientation of the sense strand establishes the direction .
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