Oligonucleotide directed and recorded combinatorial synthesis of encoded probe molecules

A method of forming a molecule of formula (I) comprising:

• providing at least one hybridization array, the at least one hybridization array comprising at least one single stranded anti-codon oligomer immobilized on the at least one hybridization array, wherein the at least one single stranded anti-codon oligomer immobilized on the at least one hybridization array is capable of hybridizing to a coding region of a molecule of formula (II):
• ([(B1)(M−1)-D-L1]Y-H1)O-G-(H2-[L2-E-(B2)(K−1)]W)P (II)
• wherein
• G is an oligonucleotide, the oligonucleotide comprising at least two coding regions and at least one terminal coding region, wherein the at least two coding regions are single stranded and the at least one terminal coding region is single or double stranded;
• H1 is a hairpin structure comprising oligonucleotides, wherein H1 terminates in a 5′ end and is attached to an end of the oligonucleotide G;
• H2 is a hairpin structure comprising oligonucleotides, wherein H2 terminates in a 3′ end and is attached to an end of the oligonucleotide G;
• D is a first building block;
• E is a second building block, wherein D and E are the same or different;
• B1 is a positional building block and M represents an integer from 1 to 20;
• B2 is a positional building block and K represents an integer from 1 to 20, wherein B1 and B2 are the same or different, wherein M and K are the same or different;
• L1 is a linker that operatively links H1 to D;
• L2 is a linker that operatively links H2 to E;
• O is an integer from zero to 1;
• P is an integer from zero to 1;
• provided that at least one of O and P is 1;
• Y is an integer from 1 to 5;
• W is an integer from 1 to 5;
• and
• wherein at least one of each positional building block B1 at position M and B2 at position K is identified by one of the coding regions and wherein at least one of the first building block D and second building block E is identified by the at least one terminal coding region;
• sorting the pool of molecules of formula (II) into sub-pools by hybridizing a coding region of the sub-pool of molecules of formula (II) to the at least one single stranded anti-codon oligomer immobilized on the at least one hybridization array;
• a step of optionally releasing the sub-pool of molecules of formula (II) from the at least one hybridization array into separate containers;
• providing at least one of building block B1 and B2;
• and
• reacting the at least one of building block B1 and B2 with the molecule of formula (II) to form a sub-pool of molecules of formula (I):
• ([(B1)M-D-L1]Y-H1)O-G-(H2-[L2-E-(B2)K]W)P, (I)
• wherein
• G is an oligonucleotide, the oligonucleotide comprising at least two coding regions and at least one terminal coding region, wherein each coding region is single stranded and the at least one terminal coding region is single or double stranded;
• H1 is a hairpin structure comprising oligonucleotides, wherein H1 terminates in a 5′ end and is attached to an end of the oligonucleotide G;
• H2 is a hairpin structure comprising oligonucleotides, wherein H2 terminates in a 3′ end and is attached to an end of the oligonucleotide G;
• D is a first building block;
• E is a second building block, wherein D and E are the same or different;
• B1 is a positional building block and M represents an integer from 1 to 20;
• B2 is a positional building block and K represents an integer from 1 to 20, wherein B1 and B2 are the same or different, wherein M and K are the same or different;
• L1 is a linker that operatively links H1 to D;
• L2 is a linker that operatively links H2 to E;
• O is an integer from zero to 1;
• P is an integer from zero to 1;
• provided that at least one of O and P is 1;
• Y is an integer from 1 to 5;
• W is an integer from 1 to 5;
• and
• wherein at least one of each positional building block B1 at position M and B2 at position K is identified by one of the coding regions, and wherein at least one of the first building block D and second building block E is identified by the at least one terminal coding region.