IP Library › Granted Patent US 12,258,375
Granted Patent B2
US 12,258,375 · App. 18/504,590 · Granted Mar 25, 2025

Mutant lysenin pores

Inventors: Mark John Bruce (Oxford, GB); James Anthony Clarke (Oxford, GB); Andrew John Heron (Oxford, GB); Lakmal Nishantha Jayasinghe (Oxford, GB); Elizabeth Jayne Wallace (Oxford, GB)
Assignee: Oxford Nanopore Technologies PLC
C07K14/43536G01N27/447C07K2319/55C12Q1/6869
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Quick Facts
Patent No.
US 12,258,375
App. No.
18/504,590
Granted
Mar 25, 2025
Kind
B2
Abstract

The invention relates to mutant forms of lysenin. The invention also relates to analyte characterisation using lysenin.

Claims (108)

1. A method of characterising a target analyte, comprising:

(a) contacting the target analyte with a protein pore such that the target analyte moves through the protein pore, wherein the protein pore comprises at least one lysenin monomer that comprises a barrel-forming region comprising the amino acid sequence as set forth in positions 44 to 126 of SEQ ID NO: 2 with one or more amino acid substitutions, wherein at least one of the amino acid substitutions introduces a cysteine, lysine, or non-natural amino acid; and

(b) taking one or more measurements as the target analyte moves through the protein pore, wherein the measurements are indicative of one or more characteristics of the target analyte, thereby characterising the target analyte.

2. The method according to claim 1 , wherein the target analyte is a metal ion, an inorganic salt, a polymer, an amino acid, a peptide, a polypeptide, a protein, a nucleotide, an oligonucleotide, a polynucleotide, a dye, a bleach, a pharmaceutical, a diagnostic agent, a recreational drug, an explosive or an environmental pollutant.

3. The method according to claim 2 , wherein the target analyte is a target polynucleotide.

4. The method according to claim 3 , wherein step (a) comprises contacting the target polynucleotide with the protein pore and a polynucleotide binding protein, wherein the polynucleotide binding protein controls the movement of the target polynucleotide through the protein pore.

5. The method according to claim 3 , wherein characterising the target polynucleotide comprises determining the sequence of the target polynucleotide.

6. The method according to claim 1 , wherein a potential is applied across the protein pore in (b).

7. The method according to claim 6 , wherein the potential is a voltage potential or a chemical potential.

8. The method according to claim 1 , wherein the method further comprises characterising two or more target analytes, wherein (a) comprises contacting the two or more target analytes with the protein pore such that each of the two or more target analytes move through the protein pore and (b) comprises taking measurements as the two or more target analytes move through the protein pore, wherein the measurements are indicative of one or more characteristics of each of the two or more target analytes.

9. The method according to claim 8 , wherein the two or more target analytes are 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 30, 40, 50, or 100 analytes.

10. The method according to claim 1 , wherein the one or more measurements are electrical measurements or optical measurements.

11. The method according to claim 3 , wherein the one or more characteristics are selected from (i) the length of the target polynucleotide, (ii) the identity of the target polynucleotide, (iii) the sequence of the target polynucleotide, (iv) the secondary structure of the target polynucleotide and (v) whether or not the target polynucleotide is modified.

12. The method according to claim 1 , wherein the cysteine, lysine, or non-natural amino acid is further attached to (i) a polyethylene glycol, a nucleic acid, a dye, a fluorophore, or a chromophore; (ii) a molecular adaptor; or (iii) a polynucleotide binding protein.

13. The method according to claim 12 , wherein the cysteine, lysine, or non-natural amino acid is attached to (i), (ii), or (iii) via a linker.

14. The method according to claim 1 , wherein the one or more amino acid substitutions (a) alter the steric effect of the monomer, (b) alter the net charge of the monomer, (c) alter the ability of the monomer to hydrogen bond with a polynucleotide, (d) introduce or remove chemical groups that interact through delocalized electron pi systems, (e) alter the structure of the monomer, and/or (f) increase or decrease net positive charge.

15. The method according to claim 1 , wherein the one or more substitutions comprise substitution at one or more of the following positions of SEQ ID NO: 2: M44, N46, N48, E50, R52, H58, D68, F70, E71, S74, E76, S78, Y79, S80, H81, S82, E84, E85, S86, Q87, S89, M90, E92, E94, E97, E102, H103, T104, T106, R115, Q117, N119, D121 and D126.

16. The method according to claim 15 , wherein the amino acid(s) substituted into the one or more positions are selected from asparagine (N), serine(S), glutamine (Q), arginine (R), glycine (G), tyrosine (Y), aspartic acid (D), leucine (L), lysine (K) or alanine (A).

17. The method according to claim 1 , wherein the one or more substitutions comprise one or more of the following amino acid substitutions:

(a) serine(S) at position 44;

(b) serine(S) at position 46;

(c) serine(S) at position 48;

(d) serine(S) at position 52;

(e) serine(S) at position 58;

(f) serine(S) at position 68;

(g) serine(S) at position 70;

(h) serine(S) at position 71;

(i) serine(S) at position 76;

(j) serine(S) at position 79;

(k) serine(S) at position 81;

(l) serine(S), aspartic acid (D) or glutamine (Q) at position 84;

(m) serine(S) or lysine (K) at position 85;

(n) serine(S) at position 87;

(o) serine(S) at position 90;

(p) asparagine (N) or glutamine (Q) at position 92;

(q) serine(S) or asparagine (N) at position 94;

(r) serine(S) or asparagine (N) at position 97;

(s) serine(S) at position 102;

(t) serine(S) at position 103;

(u) asparagine (N) or serine(S) at position 121;

(v) serine(S) at position 50;

(w) asparagine (N) or serine(S) at position 94;

(x) asparagine (N) or serine(S) at position 97;

(y) serine(S) or asparagine (N) at position 121;

(z) asparagine (N) or glutamine (Q) or glycine (G) at position 126; and

(aa) serine(S) or asparagine (N) at position 128.

18. The method according to claim 17 , wherein the one or more substitutions comprises amino acid substitutions selected from the group consisting of:

i. one or more of E84D and E85K;

ii. one or more of E84Q, E85K, E92Q, E97S, D126G and E167A;

iii. one or more of E92N, E94N, E97N, D121N and D126N;

iv. one or more of E92N, E94N, E97N, D121N, D126N and E128N;

v. one or more of E76S, E84Q, E85K, E92Q, E97S, D126G and E167A;

vi. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E50S;

vii. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E71S;

viii. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E94S;

ix. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E102S;

x. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E128S;

xi. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E135S;

xii. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and D68S;

xiii. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and D121S;

xiv. one or more of E84Q, E85K, E92Q, E97S, D126G, E167 A and D134S; or

xv. one or more of E84D, E85K and E92Q;

xvi. one or more of E84Q, E85K, E92Q, E97S, D126G and E135S;

xvii. one or more of E85K, E92Q, E94S, E97S and D126G;

xviii. one or more of E76S, E85K, E92Q, E97S and D126G;

xix. one or more of E71S, E85K, E92Q, E97S and D126G;

xx. one or more of D68S, E85K, E92Q, E97S and D126G;

xxi. one or more of E85K, E92Q, E97S and D126G;

xxii. one or more of E84Q, E85K, E92Q, E97S, H103S and D126G;

xxiii. one or more of E84Q, E85K, M90S, E92Q, E97S and D126G;

xxiv. one or more of E84Q, Q87S, E85K, E92Q, E97S and D126G;

xxv. one or more of E84Q, E85S, E92Q, E97S and D126G;

xxvi. one or more of E84S, E85K, E92Q, E97S and D126G;

xxvii. one or more of H81S, E84Q, E85K, E92Q, E97S and D126G;

xxviii. one or more of Y79S, E84Q, E85K, E92Q, E97S and D126G;

xxix. one or more of F70S, E84Q, E85K, E92Q, E97S and D126G;

xxx. one or more of H58S, E84Q, E85K, E92Q, E97S and D126G;

xxxi. one or more of R52S, E84Q, E85K, E92Q, E97S and D126G;

xxxii. one or more of N48S, E84Q, E85K, E92Q, E97S and D126G;

xxxiii. one or more of N46S, E84Q, E85K, E92Q, E97S and D126G;

xxxiv. one or more of M44S, E84Q, E85K, E92Q, E97S and D126G;

xxxv. one or more of E92Q and E97S;

xxxvi. one or more of E84Q, E85K, E92Q and E97S;

xxxvii. one or more of E84Q and E85K;

xxxviii. one or more of E84Q, E85K and D126G;

xxxix. one or more of E84Q, E85K, D126G and E167A;

xl. one or more of E92Q, E97S and D126G;

xli. one or more of E84Q, E85K, E92Q, E97S and D126G;

xlii. one or more of E84Q, E85K, E92Q, E97S and E167A;

xliii. one or more of E84Q, E85K, E92Q, D126G and E167A;

xliv. one or more of E84Q, E85K, E97S, D126G and E167A;

xlv. one or more of E84Q, E92Q, E97S, D126G and E167A;

xlvi. one or more of E85K, E92Q, E97S, D126G and E167A;

xlvii. one or more of E84D, E85K and E92Q;

xlviii. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and D121S;

xlix. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and D68S;

l. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E135S;

li. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E128S;

lii. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E102S;

liii. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E94S;

liv. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E71S;

lv. one or more of E84Q, E85K, E92Q, E97S, D126G, E167A and E50S;

lvi. one or more of E76S, E84Q, E85K, E92Q, E97S, D126G and E167 A;

lvii. one or more of E92N, E94N, E97N, D121N, D126N and E128N;

lviii. one or more of E92N, E94N, E97N, D121N and D126N; or

lix. one or more of E84Q, E85K, E92Q, E97S, D126G and E167A.

19. The method according to claim 1 , wherein the protein pore is a homo-oligomeric protein pore.

20. The method according to claim 1 , wherein the protein pore is a hetero-oligomeric protein pore.

Assignments (2)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Nov 13, 2023
From: BRUCE, MARK JOHN; CLARKE, JAMES A; HERON, ANDREW JOHN; JAYASINGHE, LAKMAL NISHANTHA; WALLACE, ELIZABETH JANE
To: OXFORD NANOPORE TECHNOLOGIES LIMITED
Reel/Frame 065536/0659 →
CHANGE OF NAME Recorded Nov 13, 2023
From: OXFORD NANOPORE TECHNOLOGIES LIMITED
To: OXFORD NANOPORE TECHNOLOGIES PLC
Reel/Frame 065549/0028 →
Continuity (5)
Continuation 17108536 · Dec 1, 2020
Continuation 15692498 · Aug 31, 2017
Continuation 14391660
Provisional Application 61622174 · Apr 10, 2012
Related Publication 20240199711A1 · Jun 20, 2024
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