--- title: "Phosphodiester bond formation (DNA polymerase) Template | MolDraw" url: https://www.moldraw.com/templates/dna-phosphodiester-bond/ description: "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…" lang: en publisher: Scidart Academy generated: 2026-11-13 --- [MolDraw](https://www.moldraw.com/) › [Templates](https://www.moldraw.com/templates/) › [Biochemistry](https://www.moldraw.com/templates/biochemistry/) › Phosphodiester bond formation (DNA polymerase) [Biochemistry](https://www.moldraw.com/templates/biochemistry/)Premium # Phosphodiester bond formation (DNA polymerase) template ![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.](https://www.moldraw.com/templates/dna-phosphodiester-bond.webp) [Edit in MolDraw](https://www.moldraw.com/)Download with Pro Premium template. Preview and edit it free in MolDraw; downloading and exporting it is part of [MolDraw Pro](https://www.moldraw.com/pricing). 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](https://openlibrary.org/isbn/9781319228002) Textbook - [Berg, Tymoczko, Gatto & Stryer, Biochemistry, 9th ed., 2019](https://openlibrary.org/isbn/9781319114657) Textbook - [Lehman, Bessman, Simms & Kornberg, J. Biol. Chem. 1958, 233, 163](https://pubmed.ncbi.nlm.nih.gov/13563462/) Original paper - [Kornberg, Science 1960, 131, 1503](https://doi.org/10.1126/science.131.3412.1503) Original paper - [Steitz & Steitz, Proc. Natl. Acad. Sci. USA 1993, 90, 6498](https://doi.org/10.1073/pnas.90.14.6498) Original paper ## How to use this template 1. Press **Edit in MolDraw**. The template opens on the canvas of the free MolDraw editor. 2. Change anything: move structures, edit atoms and labels, recolour highlights or delete what you do not need. 3. Add your own structures, arrows and text next to it, or combine several templates on one page. 4. Export the drawing as PNG, SVG or PDF for slides, worksheets, theses and papers. ## Frequently asked questions ### Is the Phosphodiester bond formation (DNA polymerase) template free? You can preview the Phosphodiester bond formation (DNA polymerase) template here and open and edit it in MolDraw for free. Downloading or exporting it is part of MolDraw Pro, together with the other premium templates. ### Can I edit the Phosphodiester bond formation (DNA polymerase) template? Yes. It opens as an ordinary MolDraw drawing, so every structure, arrow, label and colour can be changed, and you can add your own content around it. ### Is the chemistry checked? Every structure is checked with RDKit and every curly arrow passes MolDraw’s electron-flow audit. The sources used are listed on this page. ### Are the biochemical pathways drawn with structures? Yes. 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