IP Library › Granted Patent US 12,320,796
Granted Patent B2
US 12,320,796 · App. 18/429,862 · Granted Jun 3, 2025

Lipid-free anchoring of thermophilic bacteriophage G20c portal adapter into solid-state nanopores

Inventors: Meni Wanunu (Sharon, MA); Alfred Antson (York, GB); Sandra Greive (York, GB); Benjamin Cressiot (Montlignon, FR)
Assignees: Northeastern University; University of York
G01N33/48721B81B1/002C07K14/005C12Q1/6869B82Y15/00C12N2795/00022Y10S930/22
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Quick Facts
Patent No.
US 12,320,796
App. No.
18/429,862
Granted
Jun 3, 2025
Kind
B2
Abstract

Hybrid nanopores, comprising a protein pore supported within a solid-state membrane, which combine the robust nature of solid-state membranes with the easily tunable and precise engineering of protein nanopores. In an embodiment, a lipid-free hybrid nanopore comprises a water soluble and stable, modified portal protein of the Thermus thermophilus bacteriophage G20c, electrokinetically inserted into a larger nanopore in a solid-state membrane. The hybrid pore is stable and easy to fabricate, and exhibits low peripheral leakage, allowing sensing and discrimination among different types of biomolecules.

Claims (34)

1. A nucleic acid molecule comprising a modification of a nucleic acid sequence of SEQ ID NO: 2, the modification comprising one or more of:

(i) a modification in a portion of the nucleic acid sequence that encodes an upper internal surface residue or a lower internal surface residue of a protein encoded by the nucleic acid sequence, the modification producing an alteration of an electrostatic surface potential of an upper internal surface or a lower internal surface of the protein encoded by the nucleic acid sequence;

(ii) a modification comprising an insertion of a cysteine residue into a protein encoded by the nucleic acid sequence or a replacement of an amino acid residue of a protein encoded by the nucleic acid sequence with a cysteine residue;

(iii) a modification to produce a modification of a tunnel loop residue of a protein encoded by the nucleic acid sequence, the modification in the tunnel loop residue comprising an expansion of a narrowest constriction of a tunnel loop of the protein encoded by the nucleic acid sequence, a restriction of the narrowest constriction of the tunnel loop of the protein encoded by the nucleic acid sequence, or a removal of the narrowest constriction of the tunnel loop of the protein encoded by the nucleic acid sequence;

(iv) a modification to produce a modification of a tunnel loop residue of a protein encoded by the nucleic acid sequence, the modification resulting in an alteration of an electrostatic charge property of a tunnel loop of the protein encoded by the nucleic acid sequence;

(v) a modification which alters an external charge of a protein encoded by the nucleic acid sequence;

(vi) a modification which promotes binding of a protein encoded by the nucleic acid sequence to a solid-state matrix;

(vii) a modification which extends an N-terminus or a C-terminus of a protein encoded by the nucleic acid sequence or an N-terminus or a C-terminus of a cleaved portion of the protein encoded by the nucleic acid sequence; and

(viii) a deletion of an amino acid residue of at least one of a C-terminal region and an N-terminal region of a protein encoded by the nucleic acid sequence.

2. The nucleic acid molecule of claim 1 , wherein the modification of SEQ ID NO: 2 comprises a modification in the portion of the nucleic acid sequence that encodes the lower internal surface residue of the protein encoded by the nucleic acid sequence, the modification producing the alteration of the electrostatic surface potential of the lower internal surface of the protein encoded by the nucleic acid sequence, and wherein the nucleic acid molecule comprises SEQ ID NO: 28.

3. The nucleic acid molecule of claim 1 , wherein the modification of SEQ ID NO: 2 comprises the modification comprising an insertion of a cysteine residue into a protein encoded by the nucleic acid sequence or a replacement of an amino acid residue of a protein encoded by the nucleic acid sequence with a cysteine residue, and wherein the nucleic acid molecule comprises SEQ ID NO: 12 or SEQ ID NO: 38.

4. The nucleic acid molecule of claim 1 , wherein the modification of SEQ ID NO: 2 comprises the modification to produce a modification of a tunnel loop residue of the protein encoded by the nucleic acid sequence, the modification in the tunnel loop residue comprising the expansion of the narrowest constriction of the tunnel loop of the protein encoded by the nucleic acid sequence, the restriction of the narrowest constriction of the tunnel loop of the protein encoded by the nucleic acid sequence, or the removal of the narrowest constriction of the tunnel loop of the protein encoded by the nucleic acid sequence, and wherein the nucleic acid molecule comprises one of: SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 24 and SEQ ID NO: 26.

5. The nucleic acid molecule of claim 1 , wherein the modification of SEQ ID NO: 2 comprises a modification to produce a modification of a tunnel loop residue of the protein encoded by the nucleic acid sequence, the modification resulting in the alteration of the electrostatic charge property of the tunnel loop of the protein encoded by the nucleic acid sequence, and wherein the nucleic acid molecule comprises SEQ ID NO: 20.

6. The nucleic acid molecule of claim 1 , wherein the modification of SEQ ID NO: 2 comprises the modification which alters the external charge of the protein encoded by the nucleic acid sequence, and wherein the nucleic acid molecule comprises one of: SEQ ID NO: 10 and SEQ ID NO: 14.

7. The nucleic acid molecule of claim 1 , wherein the modification of SEQ ID NO: 2 comprises the modification which promotes binding of the protein encoded by the nucleic acid sequence to the solid-state matrix, and wherein the nucleic acid molecule comprises one of: SEQ ID NO: 30, SEQ ID NO: 32 and SEQ ID NO: 36.

8. The nucleic acid molecule of claim 1 , wherein the modification of SEQ ID NO: 2 comprises the modification which extends the N-terminus of the cleaved portion of the protein encoded by the nucleic acid sequence, and wherein the nucleic acid molecule comprises SEQ ID NO: 34.

9. The nucleic acid molecule of claim 1 , wherein the modification of SEQ ID NO: 2 comprises a deletion of an amino acid residue of at least one of the C-terminal region and the N-terminal region of the protein encoded by the nucleic acid sequence, and wherein the nucleic acid molecule comprises one of: SEQ ID NO: 4, SEQ ID NO: 6 and SEQ ID NO: 8.

10. The nucleic acid molecule of claim 1 , wherein the modification of SEQ ID NO: 2 comprises a modification to produce a modification in one or more of: a wing loop residue, a tunnel loop residue, an upper internal surface residue, a lower internal surface residue, an external surface residue, a C-terminal end residue, and an N-terminal end residue; of a protein encoded by the nucleic acid sequence.

11. A nucleic acid molecule comprising a modification of a nucleic acid sequence of SEQ ID NO: 2, the nucleic acid molecule comprising one of: SEQ ID NO: 28; SEQ ID NO: 12; SEQ ID NO: 38; SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 20, SEQ ID NO: 10, SEQ ID NO: 14, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 36, SEQ ID NO: 34, SEQ ID NO: 4, SEQ ID NO: 6, and SEQ ID NO: 8.

12. A nucleic acid molecule comprising a modification of a nucleic acid sequence of SEQ ID NO: 2, the nucleic acid molecule comprising one of: SEQ ID NO: 28; SEQ ID NO: 38; SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 20, SEQ ID NO: 10, SEQ ID NO: 14, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 36, SEQ ID NO: 34, SEQ ID NO: 4, SEQ ID NO: 6, and SEQ ID NO: 8.

13. A vector comprising a modification of a nucleic acid sequence of SEQ ID NO: 2, the modification comprising one or more of:

(i) a modification in a portion of the nucleic acid sequence that encodes an upper internal surface residue or a lower internal surface residue of a protein encoded by the nucleic acid sequence, the modification producing an alteration of an electrostatic surface potential of an upper internal surface or a lower internal surface of the protein encoded by the nucleic acid sequence;

(ii) a modification comprising an insertion of a cysteine residue into a protein encoded by the nucleic acid sequence or a replacement of an amino acid residue of a protein encoded by the nucleic acid sequence with a cysteine residue;

(iii) a modification to produce a modification of a tunnel loop residue of a protein encoded by the nucleic acid sequence, the modification of the tunnel loop residue comprising an expansion of a narrowest constriction of a tunnel loop of the protein encoded by the nucleic acid sequence, a restriction of the narrowest constriction of the tunnel loop of the protein encoded by the nucleic acid sequence, or a removal of the narrowest constriction of the tunnel loop of the protein encoded by the nucleic acid sequence;

(iv) a modification to produce a modification of a tunnel loop residue of a protein encoded by the nucleic acid sequence, the modification resulting in an alteration of an electrostatic charge property of a tunnel loop of the protein encoded by the nucleic acid sequence;

(v) a modification which alters an external charge of a protein encoded by the nucleic acid sequence;

(vi) a modification which promotes binding of a protein encoded by the nucleic acid sequence to a solid-state matrix;

(vii) a modification which extends an N-terminus or a C-terminus of a protein encoded by the nucleic acid sequence or an N-terminus or a C-terminus of a cleaved portion of the protein encoded by the nucleic acid sequence; and

(viii) a deletion of an amino acid residue of at least one of a C-terminal region and an N-terminal region of a protein encoded by the nucleic acid sequence.

14. A cell comprising the vector of claim 13 .

15. The cell of claim 14 , wherein the vector comprises a modification of a nucleic acid sequence of SEQ ID NO: 2, the modification comprising one or more of: SEQ ID NO: 28: SEQ ID NO: 12; SEQ ID NO: 38; SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 20, SEQ ID NO: 10, SEQ ID NO: 14, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 36, SEQ ID NO: 34, SEQ ID NO: 4, SEQ ID NO: 6, and SEQ ID NO: 8.

16. The cell of claim 14 , wherein the vector comprises a modification of a nucleic acid sequence of SEQ ID NO: 2, the modification comprising one or more of: SEQ ID NO: 28; SEQ ID NO: 38; SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 20, SEQ ID NO: 10, SEQ ID NO: 14, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 36, SEQ ID NO: 34, SEQ ID NO: 4, SEQ ID NO: 6, and SEQ ID NO: 8.

17. A vector comprising a modification of a nucleic acid sequence of SEQ ID NO: 2, the modification comprising one or more of: SEQ ID NO: 28; SEQ ID NO: 12; SEQ ID NO: 38; SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 22, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 20, SEQ ID NO: 10, SEQ ID NO: 14, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 36, SEQ ID NO: 34, SEQ ID NO: 4, SEQ ID NO: 6, and SEQ ID NO: 8.

18. A vector comprising a modification of a nucleic acid sequence of SEQ ID NO: 2, the modification comprising one or more of: SEQ ID NO: 28; SEQ ID NO: 38; SEQ ID NO: 16, SEQ ID NO: 18, SEQ ID NO: 24, SEQ ID NO: 26, SEQ ID NO: 20, SEQ ID NO: 10, SEQ ID NO: 14, SEQ ID NO: 30, SEQ ID NO: 32, SEQ ID NO: 36, SEQ ID NO: 34, SEQ ID NO: 4, SEQ ID NO: 6, and SEQ ID NO: 8.

Assignments (2)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 1, 2024
From: WANUNU, MENI; CRESSIOT, BENJAMIN
To: NORTHEASTERN UNIVERSITY
Reel/Frame 066327/0179 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 1, 2024
From: ANTSON, ALFRED; GREIVE, SANDRA
To: UNIVERSITY OF YORK
Reel/Frame 066327/0194 →
Continuity (4)
Continuation 17809705 · Jun 29, 2022
Continuation 16416139 · May 17, 2019
Provisional Application 62673118 · May 17, 2018
Related Publication 20240361296A1 · Oct 31, 2024
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