DNA synthesis in the 5' 3' direction

    The upper diagram shows a di-nucleotide (with green bases), with a tri-phosphate group attached to the 5' carbon of the first (upper) nucleotide, a 3'  5' phosphodiester bond linking the 3' carbon of the upper nucleotide to the 5' carbon of the lower nucleotide, and an exposed 3' carbon with an attached -OH group on the second (lower) nucleotide. Addition of the third nucleotide (with a blue base) onto the bottom of the second nucleotide requires clipping of the outer two PO4 groups and formation of a new 3'  5' phosphodiester bond. The original 5' end on the first nucleotide remains unmodified, and the new 3' end is from the newly-added third nucleotide. Polynucleotides thus "grow" from an unchanging 5' end by succesive modification of the 3' end: we define this as growing in the 5'3' direction. Do NOT attempt to think about the process any other way:

Nucleic acid synthesis processes occur only in the 5'3' direction.

Figure ©2012 TA Brown, Introduction to Genetics (1st ed.); additional text ©2014 by Steven M. Carr