Multinomial encoding for oligonucleotide-directed combinatorial chemistry

A molecule according to formula (I),

• [(B1)M-L1]O-G-[(L2-(B2)K]P
• wherein
• G includes an oligonucleotide, the oligonucleotide comprising at least two coding regions, wherein the at least two coding regions are single stranded;
• 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 B1 to G;
• L2 is a linker that operatively links B2 to G;
• O is zero or 1;
• P is zero or 1;
• provided that at least one of O and P is 1;
• and
• wherein each positional building block B1 at position M and/or B2 at position K is identified by from 1 to 5 coding regions, and from about 10% to 100% of the positional building blocks B1 at position M and/or B2 at position K, based on a total number of positional building blocks, are identified by a combination of from 2 to 5 independent coding regions.

A method of identifying probe molecules capable of binding or selecting for a target molecule comprising:

• exposing the target molecule to a pool of probe molecules, wherein the probe molecules are according to claim 1,
• removing at least one probe molecule that does not bind the target molecule,
• amplifying the oligonucleotide of G from the at least one probe molecule that was not removed from the target molecule to form a copy sequence,
• sequencing the copy sequence to identify each coding region and combination of coding regions of the probe molecule to further identify each positional building block B1 at position M and/or B2 at position K.

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

• providing at least one first hybridization array, the at least one first hybridization array comprising at least one first single stranded anti-codon oligomer immobilized on the at least one first hybridization array, wherein the at least one first single stranded anti-codon oligomer immobilized on the at least one first hybridization array is capable of hybridizing to a first coding region of a molecule of formula (II):
• [(B1)(M-1)-L1]O-G-[(L2-(B2)(K-1))P (II)
• wherein
• G includes an oligonucleotide, the oligonucleotide comprising at least two coding regions, wherein the at least two coding regions are single stranded;
• 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 B1 to G;
• L2 is a linker that operatively links B2 to G;
• O is zero or 1;
• P is zero or 1;
• provided that at least one of O and P is 1;
• and
• wherein each positional building block B1 at position M and/or B2 at position K is identified by from 1 to 5 coding regions, and from about 10% to 100% of the positional building blocks B1 at position M and/or B2 at position K, based on a total number of positional building blocks, are identified by a combination of from 2 to 5 independent coding regions;
• sorting the pool of molecules of formula (II) into a first set of sub-pools by hybridizing the first coding region of the molecules of formula (II) to the at least one first single stranded anti-codon oligomer immobilized on the at least one first hybridization array;
• releasing the first set of sub-pools of molecules of formula (II) from the at least one first hybridization array into separate containers;
• providing at least one second hybridization array, the at least one second hybridization array comprising at least one second single stranded anti-codon oligomer immobilized on the at least one second hybridization array, wherein the at least one second single stranded anti-codon oligomer immobilized on the at least one second hybridization array is capable of hybridizing to a second coding region of a molecule of formula (II):
• independently sorting each, or at least one, of the first set of sub-pools of molecules of formula (II) into a second set of sub-pools by hybridizing the second coding region of the molecules of formula (II) to the at least one second single-stranded anti-codon oligomer immobilized on the at least one second hybridization array;
• 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-L1]O-G-[(L2-(B2)K)P
• wherein
• G includes an oligonucleotide, the oligonucleotide comprising at least two coding regions,
• wherein the at least two coding regions are single stranded;
• 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 B1 to G;
• L2 is a linker that operatively links B2 to G;
• O is zero or 1;
• P is zero or 1;
• provided that at least one of O and P is 1;
• and
• wherein each positional building block B1 at position M and/or B2 at position K is identified by from 1 to 5 coding regions, and from about 10% to 100% of the positional building blocks B1 at position M and/or B2 at position K, based on a total number of positional building blocks, are identified by a combination of from 2 to 5 independent coding regions.

A method of forming an oligonucleotide-encoded molecule comprising:

• providing at least one first hybridization array, the at least one first hybridization array comprising at least one first single stranded anti-codon oligomer immobilized on the at least one first hybridization array, wherein the at least one first single stranded anti-codon oligomer immobilized on the at least one first hybridization array is capable of hybridizing to a first coding region of an oligonucleotide molecule G comprising:
• at least a first coding region and a second coding region, wherein the first and second coding regions are single-stranded and wherein the first and second coding regions are different;
• and
• a reactive site either on the 3′ terminus of G, or an internal nucleotide 5′ to the at least a first and second coding region, or an internal nucleotide 3′ to the at least a first and second coding region;
• (b) sorting a pool of oligonucleotides G into a first set of sub-pools by hybridizing the first coding region of the oligonucleotide to the at least one first single stranded anti-codon oligomer immobilized on the at least one first hybridization array;
• (c) providing at least one second hybridization array, the at least one second hybridization array comprising at least one second single stranded anti-codon oligomer immobilized on the at least one second hybridization array, wherein the at least one second single stranded anti-codon oligomer immobilized on the at least one second hybridization array is capable of hybridizing to the second coding region of the oligonucleotide;
• (d) independently sorting at least one of the first set of sub-pools of the oligonucleotide into a second set of sub-pools by hybridizing the second coding region of the oligonucleotide to the at least one second single-stranded anti-codon oligomer immobilized on the at least one second hybridization array.