Mutant aerolysin and uses thereof

Patent metadata

Field	Value
Publication number	US-11845779-B2
Application number	US-202017082682-A
Country	US
Kind code	B2
Filing date	Oct 28, 2020
Priority date	Oct 28, 2020
Publication date	Dec 19, 2023
Grant date	Dec 19, 2023

Abstract

Aerolysin polypeptides and/or mutant aerolysin monomers include modified amino acid sequences that could have improved substrate analyte, such as (poly)nucleotide and peptide, improved reading properties such as enhanced substrate analyte capture and improved substrate analyte recognition and/or discrimination. Also, aerolysin pores may be derived from the mutant monomers as well as apparatuses and devices may include modified aerolysin polypeptides. Further, methods of using modified aerolysin proteins and pores derive therefrom may be used in characterizing and/or sequencing a polymeric molecule or may be for use as molecular sensors.

First claim

The invention claimed is:

1. A mutant aerolysin pore comprising at least one variant polypeptide of SEQ ID NO: 8 having one or more amino acid substitutions at one or more positions corresponding to positions 220, 238, 242, 282, 209, 216, 222, 244, 246, 252, 254 and 258 with the proviso that said one or more amino acid substitutions are not Q212R, R282G, N226Q, K238F, K238G, K238Y, K238C, T232K, Q212R, R282G, D209R, N226Q.

2. A method of sensing and/or characterising a target substrate comprising:
(a) contacting the target substrate with the mutant aerolysin pore of claim 1 so to allow the movement of the target substrate through said pore and a portion of the target substrate interacts with said pore; and
(b) measuring a current passing through said pore, thereby sensing and/or characterising the target substrate.

3. The method of claim 2 , wherein steps (a) and (b) are carried out with a voltage applied across the pore.

4. The method of claim 3 , wherein the target substrate is a nucleic acid, and wherein said contacting is controlled by a handling enzyme so that the movement of the nucleic acid through the pore and a proportion of the nucleotides in the target sequence interacts with the pore.

5. The method of claim 3 , wherein the target substrate 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.

6. The method of claim 2 , wherein the target substrate is a nucleic acid, and wherein said contacting is controlled by a handling enzyme so that the movement of the nucleic acid through the pore and a proportion of the nucleotides in the target sequence interacts with the pore.

7. The method of claim 2 , wherein the target substrate 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.

8. An apparatus for sensing a target substrate in a sample, comprising the mutant aerolysin pore of claim 4 .

9. The apparatus of claim 8 , wherein the target substrate is a nucleic acid sequence, the apparatus further comprising a nucleic acid handling enzyme.

10. A system comprising a membrane having at least one mutant aerolysin pore of claim 4 spanning across the membrane thickness.

11. A construct comprising:
two or more covalently attached monomers derived from a mutant aerolysin monomer;
a homo-oligomeric pore derived from a mutant aerolysin monomer comprising identical mutant monomers; or
a hetero-oligomeric pore derived from a mutant aerolysin monomer, wherein at least one of the monomers differs from the others,
wherein the mutant aerolysin monomer has a modified aerolysin amino acid sequence comprising one or more amino acid substitutions at one or more of the following positions of SEQ ID NO: 8:
R220, wherein the amino acid substituted into the mutant aerolysin monomer at position R220 is selected from the group consisting of asparagine (N), glutamine (O), leucine (L), lysine (K), tryptophan (W), histidine (H) and alanine (A),
R282, wherein the amino acid substituted into the mutant aerolysin monomer at position R282 is selected from the group consisting of asparagine (N), glutamine (O), glutamic acid (E), leucine (L), lysine (K), tryptophan (W), histidine (H) and alanine (A),
K238, wherein the amino acid substituted into the mutant aerolysin monomer at position K238 is selected from the group consisting of asparagine (N), arginine (R), leucine (L), tryptophan (W), histidine (H) and alanine (A),
K242, wherein the amino acid substituted into the mutant aerolysin monomer at position K242 is selected from the group consisting of asparagine (N), glutamine (O), arginine (R), glutamic acid (E), leucine (L), tryptophan (W), histidine (H) and alanine (A),
D216, wherein the amino acid substituted into the mutant aerolysin monomer at position D216 is selected from the group consisting of asparagine (N), serine (S), glutamine (O), arginine (R), glycine (G), tyrosine (Y), glutamic acid (E), leucine (L), lysine (K), cysteine (C) and alanine (A),
D222, wherein the amino acid substituted into the mutant aerolysin monomer at position D222 is selected from the group consisting of asparagine (N), serine (S), glutamine (O), arginine (R), glycine (G), tyrosine (Y), glutamic acid (E), leucine (L), lysine (K), cysteine (C) and alanine (A),
K244, wherein the amino acid substituted into the mutant aerolysin monomer at position K244 is selected from the group consisting of asparagine (N), serine (S), glutamine (O), arginine (R), glycine (G), tyrosine (Y), aspartic acid (D), glutamic acid (E), leucine (L), cysteine (C) and alanine (A),
K246, wherein the amino acid substituted into the mutant aerolysin monomer at position K246 is selected from the group consisting of asparagine (N), serine (S), glutamine (O), arginine (R), glycine (G), tyrosine (Y), aspartic acid (D), glutamic acid (E), leucine (L), cysteine (C) and alanine (A),
E252, wherein the amino acid substituted into the mutant aerolysin monomer at position E252 is selected from the group consisting of asparagine (N), serine (S), glutamine (O), arginine (R), glycine (G), tyrosine (Y), aspartic acid (D), leucine (L), lysine (K), cysteine (C) and alanine (A),
E254, wherein the amino acid substituted into the mutant aerolysin monomer at position E254 is selected from the group consisting of asparagine (N), serine (S), arginine (R), glycine (G), tyrosine (Y), aspartic acid (D), leucine (L), lysine (K), cysteine (C) and alanine (A),
E258, wherein the amino acid substituted into the mutant aerolysin monomer at position E258 is selected from the group consisting of asparagine (N), serine (S), glutamine (O), arginine (R), glycine (G), tyrosine (Y), aspartic acid (D), leucine (L), lysine (K), cysteine (C) and alanine (A), and
D209, wherein the amino acid substituted into the mutant aerolysin monomer at position D209 is selected from the group consisting of asparagine (N), serine (S), glutamine (o), glycine (G), tyrosine (Y), glutamic acid (E), leucine (L), lysine (K), cysteine (C) and alanine (A).

12. The construct of claim 11 , wherein the mutant aerolysin monomer comprises at least one of the following mutations:
R220A/W/K/Q,
R282A/W,
K238A/N/R/W/H,
K242A/W,
D216A/N/R/Q,
D222A/N/R/Q,
K244A/N/R/Q/D,
K246A/N/R/Q/D,
E252A/N/R/Q,
E254A/N/R,
E258A/N/R/Q,
D209K/A/N/Q/E/C/S/G/Y/L

as well as any combination thereof.

13. The construct of claim 11 , wherein the mutant aerolysin monomer comprises at least one of the following mutations:
R220A/W/K/Q,
R282A/W,
K238A/N/R/W,
K242A/W

as well as any combination thereof.

Assignees

• Ecole Polytechnique Fed Lausanne Epfl

Inventors

• Dal Peraro Matteo
• Cao chan

Classifications

• C07K14/195 Primary

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• G01N27/44791

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• G01N33/48721

  Investigating individual macromolecules, e.g. by translocation through nanopores (Coulter counters in general G01N15/12; fabrication methods for nanoscale apertures B81B1/00; sequencing of nucleic acids C12Q1/68) · CPC title