Novel approaches to the synthesis of selenium modified nucleosides, nucleotides and nucleic acids

  • Patrick Conlon

Student thesis: Doctoral ThesisDoctor of Philosophy


Under Finkelstein-type reaction conditions, 2ʹ-deoxy-5ʹ-O-tosylnucleosides reacted cleanly with potassium selenocyanate in refluxing acetonitrile. Following quenching of excess selenocyanate with benzyl bromide and column chromatography, pure materials were isolated. Three novel 2ʹ,5ʹ-dideoxynucleoside-5ʹ-selenocyanate analogues (of dA, dC and dG) and a previously reported compound (5ʹ-deoxythymidine-5ʹ-selenocyanate) were thus prepared on multi-gram scales.
These seleno nucleosides were immobilised on controlled pore glass (CPG) which underwent Michaelis – Arbuzov (M-A) reactions with nucleoside-3ʹ-H-phosphonates. All sixteen possible 5ʹ-phosphoroselenolate-linked canonical dimer motifs were synthesised. The support bound thymidine analogue was also used in the synthesis of a tetranucleotide sequence with a single phosphoroselenolate-linkage at the 3ʹ-terminus ((dCp)3SedT).

In a further demonstration of the utility of M-A chemistry, protected phosphoroselenolate-triester linked dimers were constructed in solution through the high yielding M-A reaction. Subsequent phosphitylation fashioned the corresponding dimer phosphoramidites.
Coupling of these phosphoramidites to solid-supported substrates was optimised under both manual and automated conditions and required only minor modifications to the standard DNA synthesis cycle.

Following initial unmasking of methyl-protected phosphoroselenolate triesters, pure oligodeoxynucleotides were isolated using standard deprotection and purification procedures and subsequently characterised by mass spectrometry and circular dichroism. The CD spectra of both modified and native duplexes derived from self-complementary sequences with A-form, B-form or mixed conformational preferences were essentially superimposable. These sequences were also used to study the effect of the modification upon duplex stability which showed context-dependent destabilisation (-0.4 → -6.3 °C per phosphoroselenolate) when introduced at either the 5′-termini or at juxtaposed central locations within A- or B-form duplexes.

As found with other nucleic acids incorporating selenium, expeditious crystallisation of both a modified A-form decanucleotide and B-form dodecamer duplex was found and the structure of the former solved to a resolution of 1.45 Å using SAD X-ray crystallography. The DNA structure adjacent to the modification was not significantly perturbed. The phosphoroselenolate linkage was found to impart resistance to nuclease activity.
Date of AwardJul 2021
Original languageEnglish
Awarding Institution
  • Queen's University Belfast
SponsorsNorthern Ireland Department for the Economy
SupervisorJoseph Samuel Vyle (Supervisor) & Karl Hale (Supervisor)

Cite this