Methods for synthesis of encoded libraries

A method of synthesizing a molecule in solution comprising a functional moiety which is operatively linked to an encoding oligonucleotide which identifies the structure of the functional moiety, said method comprising the steps of:

• (a) providing an initiator compound in solution comprising an initial functional moiety comprising n building blocks, where n is an integer of 1 or greater, wherein the initial functional moiety comprises at least one reactive group, and is operatively linked to an initial oligonucleotide;
• wherein the initial functional moiety and the initial oligonucleotide are linked by a linking moiety and wherein the initial oligonucleotide is double-stranded and the linking moiety is covalently coupled to the initial functional moiety and to both strands of the initial oligonucleotide;
• wherein the linking moiety comprises the structure
• wherein
• A is a first functional group capable of forming a covalent bond with the building block;
• B is a second functional group capable of forming a covalent bond with the 5′-end of one strand of the initial oligonucleotide;
• C is a third functional group capable of forming a covalent bond with the 3′-end of the other strand of the initial oligonucleotide;
• S is an atom or a scaffold;
• D is a chemical structure that connects A to S;
• E is a chemical structure that connects B to S;
• and
• F is a chemical structure that connects C to S;
• wherein D, E and F are each, independently, an alkylene group or an oligo(ethylene glycol) group;
• (b) reacting the initiator compound with a building block comprising at least one complementary reactive group, wherein the at least one complementary reactive group is complementary to the reactive group of step (a), under conditions suitable for reaction of the complementary reactive group to form a covalent bond using solution phase synthesis methods;
• (c) reacting the initial oligonucleotide with an incoming oligonucleotide corresponding to the building block of step (b) in the presence of an enzyme which catalyzes ligation of the initial oligonucleotide and the incoming oligonucleotide, under conditions suitable for ligation of the incoming oligonucleotide and the initial oligonucleotide to form an encoding oligonucleotide;
• thereby producing a molecule which comprises a functional moiety comprising n+1 building blocks which is operatively linked to an encoding oligonucleotide which identifies the structure of the functional moiety comprising n+1 building blocks.