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Updated: Aug 7, 2026

Chemical Triphosphorylation of Oligonucleotides
Published on: June 2, 2022
Reaction mechanism of deoxyribonucleotidase: a theoretical study
Fahmi Himo1, Jing-Dong Guo, Agnes Rinaldo-Matthis
1Theoretical Chemistry, Department of Biotechnology, Royal Institute of Technology, ALBANOVA, SE-106 91 Stockholm, Sweden.
Abstract:
The reaction mechanism of human deoxyribonucleotidase (dN) is studied using high-level quantum-chemical methods. dN catalyzes the dephosphorylation of deoxyribonucleoside monophosphates (dNMPs) to their nucleoside form in human cells. Large quantum models are employed (99 atoms) based on a recent X-ray crystal structure. The calculations support the proposed mechanism in which Asp41 performs a nucleophilic attack on the phosphate to form a phospho-enzyme intermediate. Asp43 acts in the first step as an acid, protonating the leaving nucleoside, and in the second step as a base, deprotonating the lytic water. No pentacoordinated intermediates could be located.
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