Phosphodiester bond formation (DNA polymerase) template

Metal A (Mg²⁺) lowers the pKa of the primer’s 3′-OH; the 3′-O⁻ attacks Pα of the dNTP in line with the Pα–O–Pβ bond and PPi, held by metal B, leaves. Pyrophosphatase then hydrolyses PPi.

Mechanism step by step

The primer’s 3′-OH attacks the α-phosphate of the incoming dNTP and pyrophosphate leaves (Het = base)

1. In-line attack – Metal A (Mg²⁺, not drawn) lowers the 3′-OH pKa: the proton goes to the solvent as 3′-O attacks Pα opposite the Pα–O–Pβ bond, and PPᵢ (held by metal B) leaves
2. PPᵢ hydrolysis – Inorganic pyrophosphatase makes the reaction irreversible

Key points

• Chains grow 5′→3′ only: the new nucleotide’s α-phosphate is attacked by the primer’s 3′-OH. The template is read 3′→5′, antiparallel.
• Two Mg²⁺ ions: metal A activates the 3′-OH, metal B binds the triphosphate and stabilises the leaving PPᵢ. Both are held by conserved Asp residues.
• The attack is in line (SN2-like at P), so the configuration at Pα is inverted. A free 3′-OH is required: dideoxy (ddNTP) chain terminators stop synthesis.
• RNA polymerase makes the same bond from NTPs but needs no primer. PPᵢ hydrolysis (two phosphoanhydride bonds spent per nucleotide) drives both.

Drawn with 142 atoms, 6 arrows, 8 shapes – every one editable in MolDraw.

Sources

• Nelson & Cox, Lehninger Principles of Biochemistry, 8th ed., 2021, ch. 25 Textbook
• Berg, Tymoczko, Gatto & Stryer, Biochemistry, 9th ed., 2019 Textbook
• Lehman, Bessman, Simms & Kornberg, J. Biol. Chem. 1958, 233, 163 Original paper
• Kornberg, Science 1960, 131, 1503 Original paper
• Steitz & Steitz, Proc. Natl. Acad. Sci. USA 1993, 90, 6498 Original paper