DNA-templated combinatorial library chemistry
First Claim
Patent Images
1. A method of tag-directed synthesis of a plurality of compounds wherein a nucleic acid tag directs and encodes the synthesis of a compound to which it is covalently attached, comprising:
- (a) providing a pool of subsets of nucleic acid tags, wherein each nucleic acid tag comprises a single stranded DNA sequence having a 5′
terminus and a first variable hybridization sequence linked to a second variable hybridization sequence, wherein said 5′
terminus is covalently attached to a chemical reaction site, and wherein each of said first and second variable hybridization sequences is different for each subset of nucleic acid tags;
(b) splitting the pool of nucleic acid tags of step (a) to form a first group of subsets of nucleic acid tags for participating in a first synthetic reaction, by contacting said nucleic acid tags with a plurality of first immobilized nucleotide sequences, each designed to capture a subset of said nucleic acid tags by specific hybridization between one of said first variable hybridization sequences and one of said first immobilized sequences, and physically separating the subsets of said pool of nucleic acid tags on the basis of said first variable hybridization sequence of each nucleic acid tag and removing said first immobilized sequence;
(c) carrying out the first synthetic reaction by reacting the chemical reaction sites of the nucleic acid tags in each of the subsets formed in step (b) with a selected one of a plurality of first reagents that couples a different chemical subunit to the chemical reaction site of each subset of nucleic acid tags under conditions effective to form a reagent-specific compound intermediate to produce a first group of subsets of reacted nucleic acid tags;
(d) pooling the first group of subsets of reacted nucleic acid tags of step (c) to form a first pool of reacted nucleic acid tags;
(e) splitting the first pool of reacted nucleic acid tags of step (d) to form a second group of subsets of reacted nucleic acid tags for participation in a second synthetic reaction, by contacting said first pool of reacted nucleic acid tags with a plurality of second immobilized nucleotide sequences, each designed to capture a subset of said first pool of reacted nucleic acid tags by specific hybridization between one of said second variable hybridization sequences and the second immobilized sequence, and physically separating the subsets of said first pool of reacted nucleic acid tags on the basis of said second variable hybridization sequence of each nucleic acid tag and removing said second immobilized sequence; and
(f) carrying out the second synthetic reaction by reacting the reagent-specific compound intermediate of the reacted nucleic acid tag in each of the subsets formed in step (e) with a selected one of a plurality of second reagents that couples a different chemical subunit to the reagent-specific compound intermediate of each subset of reacted nucleic acid tags formed in step (e) under conditions effective to form a different sequence oligomer or different sequence small-molecule compound attached to a nucleic acid tag to produce a second group of subsets of reacted nucleic acid tags, whereby a plurality of compounds is produced.
0 Assignments
0 Petitions
Accused Products
Abstract
The present invention describes templated combinatorial chemical libraries comprised of a plurality of bifunctional molecules having both a chemical compound and a nucleic acid tag that defines the structure of the chemical compound and directs its synthesis. Also described are methods for producing, enriching and in vitro evolution of the bifunctional molecules of such libraries based on the nucleic acid tags and methods for selecting for library compounds having a desired activity.
64 Citations
25 Claims
-
1. A method of tag-directed synthesis of a plurality of compounds wherein a nucleic acid tag directs and encodes the synthesis of a compound to which it is covalently attached, comprising:
-
(a) providing a pool of subsets of nucleic acid tags, wherein each nucleic acid tag comprises a single stranded DNA sequence having a 5′
terminus and a first variable hybridization sequence linked to a second variable hybridization sequence, wherein said 5′
terminus is covalently attached to a chemical reaction site, and wherein each of said first and second variable hybridization sequences is different for each subset of nucleic acid tags;(b) splitting the pool of nucleic acid tags of step (a) to form a first group of subsets of nucleic acid tags for participating in a first synthetic reaction, by contacting said nucleic acid tags with a plurality of first immobilized nucleotide sequences, each designed to capture a subset of said nucleic acid tags by specific hybridization between one of said first variable hybridization sequences and one of said first immobilized sequences, and physically separating the subsets of said pool of nucleic acid tags on the basis of said first variable hybridization sequence of each nucleic acid tag and removing said first immobilized sequence; (c) carrying out the first synthetic reaction by reacting the chemical reaction sites of the nucleic acid tags in each of the subsets formed in step (b) with a selected one of a plurality of first reagents that couples a different chemical subunit to the chemical reaction site of each subset of nucleic acid tags under conditions effective to form a reagent-specific compound intermediate to produce a first group of subsets of reacted nucleic acid tags; (d) pooling the first group of subsets of reacted nucleic acid tags of step (c) to form a first pool of reacted nucleic acid tags; (e) splitting the first pool of reacted nucleic acid tags of step (d) to form a second group of subsets of reacted nucleic acid tags for participation in a second synthetic reaction, by contacting said first pool of reacted nucleic acid tags with a plurality of second immobilized nucleotide sequences, each designed to capture a subset of said first pool of reacted nucleic acid tags by specific hybridization between one of said second variable hybridization sequences and the second immobilized sequence, and physically separating the subsets of said first pool of reacted nucleic acid tags on the basis of said second variable hybridization sequence of each nucleic acid tag and removing said second immobilized sequence; and (f) carrying out the second synthetic reaction by reacting the reagent-specific compound intermediate of the reacted nucleic acid tag in each of the subsets formed in step (e) with a selected one of a plurality of second reagents that couples a different chemical subunit to the reagent-specific compound intermediate of each subset of reacted nucleic acid tags formed in step (e) under conditions effective to form a different sequence oligomer or different sequence small-molecule compound attached to a nucleic acid tag to produce a second group of subsets of reacted nucleic acid tags, whereby a plurality of compounds is produced. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
-
-
18. A method for the iterative synthesis and screening of a plurality of compounds to produce a subpopulation of compounds having a desired activity, wherein a nucleic acid tag directs and encodes the synthesis of the compound to which it is covalently attached, said method comprising:
-
(a) providing a pool of subsets of the nucleic acid tags in which each nucleic acid tag comprises a single stranded DNA sequence having a 5′
terminus and a first variable hybridization sequence linked to a second variable hybridization sequence, wherein said 5′
terminus is covalently attached to a chemical reaction site, and wherein each of said first and second variable hybridization sequences is different for each subset of nucleic acid tags;(b) splitting the pool of nucleic acid tags of step (a) to form a first group of subsets of nucleic acid tags for participating in a first synthetic reaction, by contacting said nucleic acid tags with a plurality of first immobilized nucleotide sequences, each designed to capture a subset of said nucleic acid tags by specific hybridization between one of said first variable hybridization sequences and one of said first immobilized sequences, and physically separating the subsets of said pool of nucleic acid tags on the basis of said first variable hybridization sequence of each nucleic acid tag and removing said first immobilized hybridization sequence; (c) carrying out the first synthetic reaction by reacting the chemical reaction sites of the nucleic acid tags in each of the subsets formed in step (b) with a selected one of a plurality of first reagents that couples a different chemical subunit to the chemical reaction site of each subset of nucleic acid tags under conditions effective to form a reagent-specific compound intermediate to produce a first group of subsets of reacted nucleic acid tags; (d) pooling the first group of subsets of reacted nucleic acid tags of step (c) to form a first pool of reacted nucleic acid tags; (e) splitting the pool of the first group of reacted nucleic acid tags of step (d) to form a second group of subsets of reacted nucleic acid tags for participation in a second synthetic reaction, by contacting said first pool of reacted nucleic acid tags with a plurality of second immobilized nucleotide sequences, each designed to capture a subset of said first pool of reacted nucleic acid tags by specific hybridization between one of said second variable hybridization sequences and the second immobilized sequence, and physically separating the subsets of said first pool on the basis of said second variable hybridization sequence of each nucleic acid tag and removing said second immobilized sequence; (f) carrying out the second synthetic reaction by reacting the reagent-specific compound intermediate of the reacted nucleic acid tag in each of the subsets formed in step (e) with a selected one of a plurality of second reagents that couples a different chemical subunit to the reagent-specific compound intermediate of each subset of reacted nucleic acid tags formed in step (e) under conditions effective to form a different sequence oligomer or different sequence small-molecule compound to produce a second group of subsets of reacted nucleic acid tags; (g) subjecting the second group of subsets of reacted nucleic acid tags produced in step (f) to one or more additional rounds of (i) pooling to form an Nth pool of reacted nucleic acid tags, (ii) splitting to form and Nth group of subsets of reacted nucleic acid tags, and (iii) synthesis to produce subsets of Nth reacted nucleic acid tags, wherein each round includes an additional step-specific subset of Nth variable hybridization sequences and Nth immobilized nucleotide sequences, and wherein each additional round comprises; (h) forming an Nth pool of reacted nucleic acid tags, wherein each of said nucleic acid tags of step (a) comprises said Nth variable hybridization sequence linked to said second variable hybridization sequence, wherein each of said first, second and Nth variable hybridization sequences is different for each subset of nucleic acid tags; (i) splitting the Nth pool of reacted nucleic acid tags of step (h) to form an Nth group of subsets of reacted nucleic acid tags for participating in an Nth reaction step, by contacting said Nth pool of reacted nucleic acid tags with a plurality of said Nth immobilized nucleotide sequences, each designed to capture a subset of said reacted nucleic acid tags by specific hybridization between one of said Nth variable hybridization sequences and the Nth immobilized sequence, and physically separating the subsets of said Nth pool on the basis of said Nth variable hybridization sequence of each reacted nucleic acid tag and removing said Nth immobilized sequence; (j) carrying out the Nth reaction step by reacting the reacted nucleic acid tags in each of the subsets formed in step (i) with a selected one of a plurality of Nth-reaction reagents that couples a different chemical subunit to the different sequence oligomer or different sequence small-molecule compound of each subset formed in step (i) under conditions effective to produce subsets of Nth reacted nucleic acid tags; (k) repeating steps (h)-(j) if necessary, until synthesis of a plurality of compounds is complete; (l) identifying from said plurality of compounds of step (k), one or more compounds having a desired activity to yield a subpopulation of nucleic acid tags; and (m) producing a pool of nucleic acid tags based on the subpopulation of nucleic acid tags from step (l) and repeating steps (a)-(l) if necessary, until synthesis of a plurality of compounds having the desired activity is complete. - View Dependent Claims (19, 20, 21, 22, 23, 24, 25)
-
Specification