Polymerase variants and uses thereof

Patent metadata

Field	Value
Publication number	US-10968438-B2
Application number	US-201916694985-A
Country	US
Kind code	B2
Filing date	Nov 25, 2019
Priority date	May 14, 2015
Publication date	Apr 6, 2021
Grant date	Apr 6, 2021

Abstract

Described herein is a variant pol6 polymerase having at least one mutation selected from H223, N224, Y225, H227, I295, Y342, T343, I357, S360, L361, I363, S365, S366, Y367, P368, D417, E475, Y476, F478, K518, H527, T529, M531, N535, G539, P542, N545, Q546, A547, L549, I550, N552, G553, F558, A596, G603, A610, V615, Y622, C623, D624, I628, Y629, R632, N635, M641, A643, I644, T647, I648, T651, I652, K655, W656, D657, V658, H660, F662, L690 and combinations thereof.

First claim

What is claimed is:

1. A modified deoxyribonucleic acid (DNA) polymerase having a DNA polymerase activity, said modified DNA polymerase comprising an amino acid sequence having at least 95% sequence identity to SEQ ID NO:2, which amino acid sequence includes an amino acid substitution at position N224, wherein the substitution is selected from the group consisting of N224Q, N224M, N224R, and N224K.

2. The modified DNA polymerase of claim 1 , wherein modified DNA polymerase is capable of incorporating a tagged deoxyribonucleotide tetraphosphate, a tagged deoxyribonucleotide pentaphosphate, a tagged deoxyribonucleotide hexaphosphate, a tagged deoxyribonucleotide heptaphosphate, and/or a tagged deoxyribonucleotide octophosphate into a growing DNA strand.

3. The modified DNA polymerase of claim 2 , wherein the tag is attached to a terminal phosphate of the polyphosphate deoxyribonucleotide.

4. The modified DNA polymerase of claim 1 , wherein the modified DNA polymerase has an altered characteristic as compared to a DNA polymerase consisting of SEQ ID NO:2.

5. The modified DNA polymerase of claim 1 , wherein the amino acid sequence further includes T529M, S366A, A547F, N545L, Y225L, and D657R substitutions.

6. The modified DNA polymerase of claim 1 , wherein the substitution at position N224 is N224R.

7. A composition comprising the modified DNA polymerase of claim 1 attached to a nanopore.

8. The composition of claim 7 , wherein the nanopore is an alpha-hemolysin nanopore comprising 7 alpha-hemolysin monomers.

9. The composition of claim 8 , wherein 1 of the alpha-hemolysin monomers is attached to the modified DNA polymerase and 6 of the alpha-hemolysin monomers are not attached to a DNA polymerase.

10. The composition of claim 9 , wherein the alpha-hemolysin nanopore is inserted into a membrane adjacent to a sensing electrode, such that the sensing electrode is capable of detecting a current flowing through the nanopore.

11. The composition of claim 10 , wherein the membrane is a lipid bilayer.

12. The composition of claim 7 , wherein the amino acid sequence further includes T529M, S366A, A547F, N545L, Y225L, and D657R substitutions.

13. The composition of claim 12 , wherein the substitution at position N224 is N224R.

14. A method of sequencing a target deoxyribonucleic acid (DNA) molecule, the method comprising:
(a) binding the target DNA molecule to the modified DNA polymerase of claim 1 , wherein the modified DNA polymerase is attached to a nanopore;
(b) incorporating a tagged polyphosphate deoxyribonucleotide into a growing DNA strand by a template-dependent polymerization catalyzed by the modified DNA polymerase, wherein a tag of the tagged polyphosphate deoxyribonucleotide is inserted into the nanopore during the polymerization,
(c) detecting a change in a current flowing through the nanopore caused by insertion of the tag into the nanopore; and
(d) correlating the change in the current to the identity of the tagged polyphosphate deoxyribonucleotide incorporated into the growing DNA strand, thereby sequencing the target DNA molecule.

15. The method of claim 14 , wherein the nanopore is an alpha-hemolysin heptamer.

16. The method of claim 15 , wherein the polyphosphate deoxyribonucleotide is selected from the group consisting of a tetraphosphate, a pentaphosphate, a hexaphosphate, a heptaphosphate, and an octophosphate.

17. The method of claim 14 , wherein the tag is attached to a phosphate of the polyphosphate deoxyribonucleotide.

18. The method of claim 14 , wherein the tag is attached to a terminal phosphate of the polyphosphate deoxyribonucleotide.

19. The method of claim 14 , wherein the amino acid sequence further includes T529M, S366A, A547F, N545L, Y225L, and D657R substitutions.

20. The method of claim 19 , wherein the substitution at position N224 is N224R.

Assignees

• Roche Sequencing Solutions Inc

Inventors

• AYER Aruna
• Arnold Cleoma
• Schwab Charles Wayan
• Thai Eileen
• Lederman Ilya
• Mcgaw Colin Alexander
• SHULTZ Tyler O'Brien

Classifications

• C12N9/1252 Primary

  DNA-directed DNA polymerase (2.7.7.7), i.e. DNA replicase · CPC title

• C12Y207/07007

  DNA-directed DNA polymerase (2.7.7.7), i.e. DNA replicase · CPC title

• C12N9/1241 Primary

  Nucleotidyltransferases (2.7.7) · CPC title

• C12Y207/07

  Nucleotidyltransferases (2.7.7) · CPC title