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Mechanochemical Synthesis of Short DNA Fragments

revised on 18.01.2020, 00:16 and posted on 21.01.2020, 09:12 by James Thorpe, Daniel O'Reilly, Tomislav Friscic, Masad J. Damha
We report the general and rapid synthesis of short DNA fragments of controllable sequence and length using multi-step, one-pot mechanochemical reactions, without bulk solvent or the need to isolate intermediates. We demonstrate, for the first time, the multi-step ball milling synthesis of DNA dimers and trimers via phosphoramidite and H-phosphonate chemistries. The use of mechanochemistry allowed for coupling of phosphoramidite monomers to the 5'-hydroxyl group of nucleosides, iodine/water oxidation of the resulting phosphite triester linkage, and removal of the 5'-dimethoxy (DMTr) protecting group in situ and in good yields (up to 60% over three steps) to produce DNA dimers in one-pot manner. Sulphurization of phosphite triester linkages was possible using elemental sulfur yielding the corresponding phosphorothioate DNA dimers in good yield (up to 80% over two steps). By using H-phosphonate chemistry under milling conditions, it was possible to couple, protect the H-phosphonate linkage, and remove the 5'-DMTr protecting group in situ, enabling an one-pot process with good yields comparable to existing solvent-based procedures (up to 65% over three steps, or ca. 87% per step). This work opens the door to creation of solvent-free methodologies for the assembly of complex DNA and RNA therapeutics.


NSERC Discovery Grant

McGill Sustainability Systems Initiative (MSSI)


Email Address of Submitting Author


McGill University



ORCID For Submitting Author


Declaration of Conflict of Interest

No conflict of interest.

Version Notes

This is version 2


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in Chemistry – A European Journal