Methods for screening proteins using DNA encoded chemical libraries as templates for enzyme catalysis

• US 9,150,853 B2
• Filed: 03/13/2013
• Issued: 10/06/2015
• Est. Priority Date: 03/21/2012
• Status: Active Grant

• Current Assignee: Gen9, Inc. (Ginkgo Bioworks Holdings, Inc.)
• Original Assignee: Gen9, Inc. (Ginkgo Bioworks Holdings, Inc.)
• Inventors: Hudson, Michael E., Jacobson, Joseph
• Primary Examiner(s): Riggs, Larry
• Assistant Examiner(s): DINES, KARLA A
• Application Number:
  US13/799,039
• Publication Number:
  US 20130252849A1
• Time in Patent Office: 937 Days
• Field of Search: 506/11
• US Class Current: 1/1
• CPC Class Codes: C12N 15/1034 Isolating an individual clone by screening libraries
• CPC Class Codes: C12N 15/1037 Screening libraries presented on the surface of microorganisms, e.g. phage display, E. coli display
• CPC Class Codes: C12N 15/1086 Preparation or screening of expression libraries, e.g. reporter assays

Abstract

Disclosed are methods, compositions and devices for screening a protein library for proteins having a desired activity, such as capable of catalyzing the formation of a bond between two reactants. In an exemplary embodiments, a plurality of proteins are expressed in vitro from a plurality of nucleic acids, the plurality of proteins are exposed with two single stranded oligonucleotides having complementary sequences, each oligonucleotide having a reactant and a fluorophore, the fluorescence of the protein-reactant-oligonucleotide-fluorophore complexes is detected and the complexes showing detectable fluorescence energy transfer are isolated, thereby isolating proteins having the desired enzymatic activity.

Claims

1. A method for screening a protein library for a protein having a desired activity, the method comprising:

a) providing a solid surface having a plurality of distinct features, each distinct feature comprising a plurality of single-stranded anchor oligonucleotides hybridized to a plurality of double-stranded nucleic acids, wherein the plurality of double-stranded nucleic acids encode a plurality of proteins;

b) hybridizing a single-stranded oligonucleotide having a first reactant to a free end of the plurality of double stranded nucleic acids;

c) expressing in vitro a plurality of proteins from the plurality of double-stranded nucleic acids in the presence of a second reactant having a detectable label; and

d) determining the presence of the detectable label on at least one of the distinct features, wherein the presence of the label is correlated to the presence of at least one protein that catalyzes the formation of a bond between the first and second reactants, thereby identifying at least one nucleic acid encoding the at least one protein having the desired activity.

2. The method of claim 1 wherein the plurality of double-stranded oligonucleotides encodes for a library of proteins.

3. The method of claim 2 wherein the library of proteins is a library of protein variants.

4. The method of claim 1 wherein the step of expressing is in the presence of a library of reactants.

5. The method of claim 1 wherein the at least one protein having a desired activity catalyzes a condensation reaction.

6. The method of claim 1 wherein the solid surface is an array.

7. The method of claim 1 wherein, in the expressing step, each of the plurality of the proteins and the double-stranded nucleic acids encoding the plurality of proteins are linked with puromycin.

8. The method of claim 1 wherein, in the expressing step, the second reactant is fluorescently labeled.

9. A method for screening a protein library, the method comprising:

a) providing a solid surface having a plurality of distinct features, each distinct feature comprising a plurality of anchor oligonucleotides hybridized to a plurality of double-stranded nucleic acids encoding a plurality of proteins;

b) providing a library first reactants, each first reactant being linked to an oligonucleotide;

c) ligating the oligonucleotide linked to the first reactant to the free end of the plurality of double-stranded nucleic acids;

d) expressing in vitro a plurality of proteins from the plurality of double-stranded nucleic acids in the presence of a library of second reactants having a detectable label; and

e) determining the presence of the detectable label on at least one of the distinct features, wherein the presence of the label is correlated to the presence of at least one protein that catalyzes the formation of a bond between the first and second reactants, thereby identifying at least one nucleic acid encoding the at least one protein having the desired activity.

10. The method of claim 9 wherein each first reactant is linked to a single-stranded oligonucleotide.

11. The method of claim 9 wherein each first reactant is linked to a double-stranded oligonucleotide.

12. The method of claim 9 wherein the plurality of double-stranded oligonucleotides have an extending 5′

or 3′

end and wherein in the step (b), the reactant is linked to an oligonucleotide having a sequence complementary to the extending 5′

or 3′

end of the double-stranded oligonucleotide.

13. The method of claim 9 wherein the solid surface is an array.