Synthesis of selenium-derivatized nucleosides, nucleotides, phosphoramidites, triphosphates and nucleic acids

A selenium-containing compound having the structure of formula I:

• (a) R1 is a nucleic acid base selected from adenine, 8-selenoadenine, guanine, 6-selenoguanine, 8-selenoguanine, cytosine, and 2-selenocytosine;
• or is a protected nucleic acid base selected from protected adenine, 8-selenoadenine, guanine, 6-selenoguanine, 8-selenoguanine, cytosine, and 2-selenocytosine;
• (b) R2 is H, HO, alkyl-O, TBDMS-O, TOM-O group, ACE-O group, orthoester group, diselenide, or alkyl-Se;
• (c) R3 is H, HO, alkyl-O, TBDMS-O, diselenide, alkyl-Se, phosphoramidite, phosphoroselenoamidite, phosphate, a 5′ linked nucleotide, a 5′ linked seleno-nucleotide, a 5′ linked oligonucleotide, a 5′ linked seleno-oligonucleotide, a 5′ linked nucleic acid chain, or a 5′ linked seleno-nucleic acid chain, wherein any phosphorus atom of a bridging phosphate of the 5′ linked seleno-nucleotide, the 5′ linked seleno-oligonucleotide, or the 5′ linked seleno-nucleic acid chain is bonded to non-selenium atoms;
• (d) R4 is H, HO, HSe, diselenide, alkyl-Se, alkyl-O, DMTr-O, TBDMS-O, (alkyl-O)3 Si—O, phosphate, diphosphate, diphosphoroselenoate, triphosphate, or triphosphoroselenoate, a 3′ linked nucleotide, a 3′ linked seleno-nucleotide, a 3′ linked oligonucleotide, a 3′ linked seleno-oligonucleotide, a 3′ linked nucleic acid chain, or a 3′ linked seleno-nucleic acid chain, wherein any phosphorus atom of a bridging phosphate of the 3′ linked seleno-nucleotide, the 3′ linked seleno-oligonucleotide, or the 3′ linked seleno-nucleic acid chain is bonded to non-selenium atoms;
• and
• (e) X is an oxygen atom or a selenium atom;
• wherein at least one of R1, R2, R3, R4 or X comprises at least one selenium atom, and wherein alkyl is a saturated or unsaturated, branched or unbranched hydrocarbon group having between 1 and 24 carbon atoms.

A process for preparing a compound having the structure of formula I:

• wherein:
• (a) R1 is a nucleic acid base selected from adenine, 8-selenoadenine, guanine, 6-selenoguanine, 8-selenoguanine, cytosine, and 2-selenocytosine;
• or is a protected nucleic acid base selected from protected adenine, 8-selenoadenine, guanine, 6-selenoguanine, 8-selenoguanine, cytosine, and 2-selenocytosine;
• (b) R2 is H, HO, alkyl-O, TBDMS-O, TOM-O group, ACE-O group, orthoester group, diselenide, alkyl-Se, or Z1;
• (c) R3 is H, HO, alkyl-O, TBDMS-O, diselenide, alkyl-Se, phosphoramidite, phosphoroselenoamidite, phosphate, a 5′ linked nucleotide, a 5′ linked seleno-nucleotide, a 5′ linked oligonucleotide, a 5′ linked seleno-oligonucleotide, a 5′ linked nucleic acid chain, or a 5′ linked seleno-nucleic acid chain, or Z2, wherein any phosphorus atom of a bridging phosphate of the 5′ linked seleno-nucleotide, the 5′ linked seleno-oligonucleotide, or the 5′ linked seleno-nucleic acid chain is bonded to non-selenium atoms;
• (d) R4 is H, HO, HSe, diselenide, alkyl-Se, alkyl-O, DMTr-O, TBDMS-O, (alkyl-O)3 Si—O, phosphate, diphosphate, diphosphoroselenoate, triphosphate, or triphosphoroselenoate, a 3′ linked nucleotide, a 3′ linked seleno-nucleotide, a 3′ linked oligonucleotide, a 3′ linked seleno-oligonucleotide, a 3′ linked nucleic acid chain, a 3′ linked seleno-nucleic acid chain, or Z3, wherein any phosphorus atom of a bridging phosphate of the 3′ linked seleno-nucleotide, the 3′ linked seleno-oligonucleotide, or the 3′ linked seleno-nucleic acid chain is bonded to non-selenium atoms;
• and
• (e) X is an oxygen atom or a selenium atom;
• wherein at least one of R1, R2, R3, R4, or X comprises at least one selenium atom;
• and wherein Z1, Z2, or Z3 is diselenide, alkyl-Se, or phosphoroselenoamidite;
• wherein alkyl is a saturated or unsaturated, branched or unbranched hydrocarbon group having between 1 and 24 carbon atoms;
• and wherein at least one of R2, R3, or R4 is Z1, Z2, or Z3;
• the process comprising:
• providing a precursor, the precursor having the structure of the compound except that Z1, Z2, or Z3 is a leaving group;
• and reacting the precursor with a selenide ion, a diselenide ion, or an alkyl selenide ion;
• wherein the reaction occurs in a two phase system comprising a water-immiscible organic phase and an aqueous phase in the presence of a phase transfer catalyst, wherein the phase transfer catalyst causes selenide ion or alkyl selenide ion transfer between the water-immiscible organic phase and the aqueous phase;
• or in one phase of an organic solvent, or a mix of solvents.