The sugar component of a nucleotide has a ring of five carbon atoms, which are labeled as 1’, 2’, 3’, 4’, and 5’ in the figure on the right. The 5’ atom is joined onto the phosphate group in the nucleotide and eventually to the 3’ end of the neighboring nucleotide. The 3’ atom is joined onto another neighboring nucleotide in the nucleic acid chain. As a result, we call the two ends of the nucleotide the 5’-end and the 3’-end (pronounced “five prime end” and ”three prime end”, respectively).
When we zoom out to the level of the double helix, we can see in the figure below that any DNA fragment is oriented with a 3’ atom on one end and a 5’ atom on the other end. As a standard, a DNA strand is always read in the 5' → 3' direction. Note that the orientations run opposite to each other in complementary strands.
