Reaction discovery system

• US 8,691,729 B2
• Filed: 01/09/2008
• Issued: 04/08/2014
• Est. Priority Date: 07/15/2005
• Status: Expired due to Fees

• Current Assignee: United States Navy (U.S. Department Of Defense)
• Original Assignee: President and Fellows of Harvard College (Harvard Corporation)
• Inventors: Liu, David R., Kanan, Matthew William, Rozenman, Mary M.
• Primary Examiner(s): BOESEN, CHRISTIAN C
• Application Number:
  US11/971,642
• Publication Number:
  US 20110312507A1
• Time in Patent Office: 2,281 Days
• Field of Search: None
• US Class Current: 506/11
• CPC Class Codes: C12N 15/1068 Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis

Abstract

A novel reaction discovery system that does not depend on DNA duplex formation is provided. The advantages of this system include exploring reactions conditions not possible where DNA hybridization is required. For example, the inventive reaction discovery system allows for reaction conditions using organic solvents, higher temperatures, and water-insoluble reagents, catalysts, and ligands. The invention also provides single-stranded oligonucleotide templates with substrate pairs covalently attached and methods of screening for reaction conditions that result in a direct covalent bond between the substrates. Kits are also provided for practicing this novel reaction discovery system.

Claims

1. A method of identifying new chemical reactions, the method comprising steps of:

providing one or more single-stranded DNA templates,

wherein each template has a unique pair of substrates covalently linked to the template;

wherein each substrate comprises one or more functional groups selected from the group consisting of aliphatic halides, aryl halides, esters, amides, carbonates, carbamates, ureas, alcohols, thiols, amines, alkyls, alkenes, alkynes, aryls, heteroaryls and phosphorus-containing groups;

wherein a portion of the sequence of the single-stranded DNA template encodes the identity of the two substrates covalently linked to the template; and

wherein one of the two substrates and biotin is covalently linked to the template through a cleavable linker;

subjecting the single-stranded DNA templates with the substrates covalently linked to the template to reaction conditions,

whereby a covalent bond is formed directly between each of the two different substrates covalently linked to a single template;

cleaving the cleavable linker;

selecting unique substrate pairs that reacted to form the a covalent bond between the two substrates that form the unique pair of substrates covalently linked to the template using streptavidin; and

identifying the selected unique substrate pairs that reacted using the encoded single-stranded DNA template covalently liked to the unique substrate pairs and reaction conditions.

2. The method of claim 1, wherein the step of identifying comprises:

amplifying the single-stranded DNA template covalently liked to the selected unique substrate pairs that reacted using PCR; and

sequencing the amplified DNA.

3. The method of claim 1, wherein the step of identifying comprises using a microarray to identify the single-stranded DNA template covalently liked to the selected unique substrate pairs that reacted.