DNA Outer Structure
Country: United States
Date: February 2006
What does the 3' and 5' side of a gene mean?
3' and 5' refer to the number 3 and 5 carbon atoms of the sugar molecule
deoxyribose. The first nucleotide in a strand of DNA has a 5' carbon atom
that is not bonded to another nucleotide; it is therefore said to be free,
thus the term free 5' end. The last nucleotide in a strand of DNA has a 3'
carbon atom that is not attached to another nucleotide, thus the term free
3' end. When you look at a double-stranded DNA molecule that is in the
vertical position, if the strand on the left has a free 5' nucleotide at the
bottom, the strand on the right will have a free 3' at the bottom. The two
strand are said to be anti-parallel, i.e. parallel but running in opposite
direction 5' > 3' directions. DNA and mRNA is synthesized in the 5' > 3'
direction so that means the template strands of DNA are read from the 3' to
5' during replication and transcription. So there is 5' and 3' *side* of DNA
but rather 5' and 3' ends.
Ron Baker, Ph.D.
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Update: June 2012