METHODS AND KITS FOR DYNAMIC TARGETED HYPERMUTATION

• US 20190309284A1
• Filed: 03/19/2019
• Published: 10/10/2019
• Est. Priority Date: 03/19/2018
• Status: Active Application

• Current Assignee: Massachusetts Institute of Technology
• Original Assignee: Massachusetts Institute of Technology
• Inventors: Shoulders, Matthew D., Papa, Louis John, Moore, Christopher Lawrence
• Application Number:
  US16/357,790
• Publication Number:
  US 20190309284A1
• Time in Patent Office: Days
• CPC Class Codes: C07K 14/245 Escherichia (G)
• CPC Class Codes: C07K 2319/00 Fusion polypeptide
• CPC Class Codes: C07K 2319/80 containing a DNA binding domain, e.g. Lacl or Tet-repressor
• CPC Class Codes: C12N 15/102 Mutagenizing nucleic acids
• CPC Class Codes: C12N 15/907 in mammalian cells
• CPC Class Codes: C12N 9/22 Ribonucleases RNAses, DNAses catalytic nucleic acids C12N15/113
• CPC Class Codes: C12N 9/78 acting on carbon to nitrogen bonds other than peptide bonds (3.5)
• CPC Class Codes: C12Y 305/04001 Cytosine deaminase (3.5.4.1)
• CPC Class Codes: C12Y 305/04002 Adenine deaminase (3.5.4.2)
• CPC Class Codes: C12Y 305/04003 Guanine deaminase (3.5.4.3)
• CPC Class Codes: C12Y 305/04004 Adenosine deaminase (3.5.4.4)
• CPC Class Codes: C12Y 305/04005 Cytidine deaminase (3.5.4.5)
• CPC Class Codes: C12Y 305/04006 AMP deaminase (3.5.4.6)
• CPC Class Codes: C12Y 305/04007 ADP deaminase (3.5.4.7)

Abstract

Disclosed herein are methodologies and kits for dynamic targeted hypermutation that harness the enzymatic activity of a polynucleic acid-binding protein fused to a nucleobase-editing enzyme to specifically target mutations across a region of interest. These methodologies and kits facilitate the rapid creation of diverse DNA libraries in vivo or in vitro.

Claims

1. A nucleobase-editing fusion protein comprising a processive polynucleic acid-binding protein fused to a nucleobase-editing enzyme which is capable of altering nucleobases in a pre-existing polynucleic acid sequence.

2. The nucleobase-editing fusion protein of claim 1, wherein:

the processive polynucleic acid-binding protein of the nucleobase-editing fusion protein comprises the amino acid sequence of an RNA polymerase, a DNA polymerase, a DNA methyltransferase, a DNA glycosylase, or a DNA helicase;

the nucleobase-editing enzyme comprises the amino acid sequence of an Apobec protein, a TadA protein, an AMPD protein, a CDA protein, an ADAT protein, an ADAR protein, or a GDA protein;

or

a combination thereof.

3. The nucleobase-editing fusion protein of claim 1, wherein the processive polynucleic acid-binding protein of the nucleobase-editing fusion protein comprises the amino acid sequence of T7 RNA polymerase or a functional variant thereof.

5. The nucleobase-editing fusion protein of claim 1, wherein the nucleobase-editing enzyme comprises the amino acid sequence of an Apobec protein, optionally wherein the Apobec protein is rApobec1 or a functional variant thereof.

7. The nucleobase-editing fusion protein of claim 1, wherein the nucleobase-editing enzyme comprises the amino acid sequence of a TadA protein, optionally wherein the TadA protein is E. coli TadA comprising an A106V mutation and/or a D108N mutation or a protein homolog comprising a homologous mutation(s).

4. (canceled)

6. (canceled)

8. (canceled)

9. A method of performing dynamic targeted hypermutation comprising contacting at least one polynucleic acid with at least one non-naturally occurring nucleobase-editing fusion protein, wherein:

a. each of the at least one non-naturally occurring nucleobase-editing fusion proteins comprises a processive polynucleic acid-binding protein fused to a nucleobase-editing enzyme;

b. each of the at least one polynucleic acid comprises a target region; and

c. the contacting of the at least one polynucleic acid with the at least one non-naturally occurring nucleobase-editing fusion protein generates mutations at a rate exceeding background mutation rates only in the target region of the at least one polynucleic acid of (b), wherein the background mutation rate of the at least one polynucleic acid of (b) is determined in the absence of the non-naturally occurring nucleobase-editing fusion protein.

10. The method of claim 9, wherein:

the processive polynucleic acid-binding protein of the nucleobase-editing fusion protein comprises the amino acid sequence of an RNA polymerase, a DNA polymerase, a DNA methyltransferase, a DNA glycosylase, or a DNA helicase;

the nucleobase-editing enzyme comprises the amino acid sequence of an Apobec protein, a TadA protein, an AMPD protein, a CDA protein, an ADAT protein, an ADAR protein, or a GDA protein;

or

a combination thereof.

11. The method of claim 9, wherein the processive polynucleic acid-binding protein of at least one of the at least one non-naturally occurring nucleobase-editing fusion proteins comprises the amino acid sequence of T7 RNA polymerase or a functional variant thereof.

13. The method of claim 9, wherein the nucleobase-editing enzyme of at least one of the at least one non-naturally occurring nucleobase-editing fusion proteins comprises:

the amino acid sequence of an Apobec protein, optionally wherein the Apobec protein is rApobec1 or a functional variant thereof;

the amino acid sequence of a TadA protein, optionally wherein the TadA protein is E. coli TadA comprising an A106V mutation and/or a D108N mutation or a protein homolog comprising a homologous mutation(s);

or

a combination thereof.

17. The method of claim 9, wherein each of the at least one polynucleic acid comprises, from 5′

to 3′

;

a promoter region that is bound by at least one of the at least one non-naturally occurring nucleobase-editing fusion proteins in a sequence-specific manner;

the target region; and

a terminator region comprising a terminator array.

18. The method of claim 17, wherein:

the terminator array comprises four or more terminators, optionally four or more T7 UUCG terminators;

the promoter region of at least one of the at least one polynucleic acids comprises the sequence of SEQ ID NO;

21, and/or SEQ ID NO;

22, SEQ ID NO;

23;

the contacting of the at least one polynucleic acid with the at least one non-naturally occurring nucleobase-editing fusion protein occurs in a living cell;

or

a combination thereof.

21. The method of claim 18, wherein:

at least one of the at least one non-naturally occurring nucleobase-editing fusion proteins is encoded on a plasmid, wherein the plasmid has copy number of less than 10;

at least one of the at least one non-naturally occurring nucleobase-editing fusion proteins is conditionally expressed in the living cell;

or

a combination thereof.

23. The method of claim 18, wherein the living cell contains a modified genome comprising:

a. an integration of a polynucleic acid sequence encoding for and driving the expression of at least one non-naturally occurring nucleobase-editing fusion protein; and

/or

b. an integration of a polynucleic sequence comprising, from 5′

to 3′

;

a promoter region that is bound by at least one of the at least one non-naturally occurring nucleobase-editing fusion proteins in a sequence-specific manner;

the target region; and

a terminator region comprising a terminator array.

24. The method of claim 18, wherein the living cell contains a modified genome and a plasmid that facilitates expression of a T7 inhibitor, optionally wherein the T7 inhibitor is T7 lysozyme, wherein the modified genome of the living cell comprises:

a. an integration of a polynucleic acid sequence encoding for and driving the expression of the non-naturally occurring nucleobase-editing fusion protein, wherein the sequence driving the expression of the fusion protein comprises a sequence bound by LacI repressor that inhibits transcription of the fusion protein when LacI is bound; and

/or

b. a deletion of genomic sequence encoding for uracil deglycosylase.

26. The method of claim 21, wherein the living cell is treated to increase the expression and/or activity of the uracil deglycoslyase inhibitor, ugi.

12. (canceled)

14-16. -16. (canceled)

19-20. -20. (canceled)

22. (canceled)

25. (canceled)

27. A kit for performing dynamic targeted hypermutation comprising:

a. a polypeptide comprising the amino acid sequence of a non-naturally occurring nucleobase-editing fusion protein comprising a processive polynucleic acid-binding protein fused to a nucleobase-editing enzyme or a polynucleic acid sequence encoding for and driving the expression of said polypeptide; and

b. a polynucleic acid sequence comprising, from 5′

to 3′

;

a promoter region that is bound by the non-naturally occurring nucleobase-editing fusion protein of (a) in a sequence-specific manner;

a cloning site; and

a terminator region comprising a terminator array.

29. The kit of claim 27, wherein:

the processive polynucleic acid-binding protein of the nucleobase-editing fusion protein comprises the amino acid sequence of an RNA polymerase, a DNA polymerase, a DNA methyltransferase, a DNA glycosylase, or a DNA helicase;

the nucleobase-editing enzyme comprises the amino acid sequence of an Apobec protein, a TadA protein, an AMPD protein, a CDA protein, an ADAT protein, an ADAR protein, or a GDA protein;

or

a combination thereof.

30. The kit of claim 27, wherein the processive polynucleic acid-binding protein of the non-naturally occurring nucleobase-editing fusion protein comprises the amino acid sequence of T7 RNA polymerase or a functional variant thereof.

32. The kit of claim 27, wherein the nucleobase-editing enzyme of the nucleobase-editing fusion protein comprises:

the amino acid sequence of an Apobec protein, optionally wherein the Apobec protein is rApobec1 or a functional variant thereof;

the amino acid sequence of a TadA protein, optionally wherein the TadA protein is E. coli TadA comprising an A106V mutation and/or a D108N mutation or a protein homolog comprising a homologous mutation(s);

or

a combination thereof.

36. The kit of claim 27, wherein;

the terminator array comprises four or more terminators, optionally four or more T7 UUCG terminators;

the promoter region comprises the sequence of SEQ ID NO;

21, SEQ ID NO;

22, and/or SEQ ID NO;

23;

or

a combination thereof.

28. (canceled)

31. (canceled)

33-35. -35. (canceled)

37. (canceled)