Polypeptide tagged nucleotides and use thereof in nucleic acid sequencing by nanopore detection

Patent metadata

Field	Value
Publication number	US-10975426-B2
Application number	US-201615770922-A
Country	US
Kind code	B2
Filing date	Aug 26, 2016
Priority date	Sep 10, 2015
Publication date	Apr 13, 2021
Grant date	Apr 13, 2021

Abstract

The present disclosure relates to compositions and methods based on polypeptide-tagged nucleotide, and the use of such polypeptide-tagged nucleotides in nanopore devices and methods.

First claim

The invention claimed is:

1. A compound of structural formula (I)
N-P-L-T   (I)

wherein,
N is a nucleoside;
P is an oligophosphate covalently attached to a 5′-O group of the nucleoside,
wherein the oligophosphate consists of 3 to 12 phosphate groups;
L is a linker covalently attached to a terminal phosphate group of the oligophosphate; and
T is a polypeptide tag covalently attached to the linker, wherein the polypeptide has an overall charge and comprises at least one α-helix comprising at least 2 repeats of a sequence motif, wherein the repeats are not interrupted by an amino acid residue that is non-helix-forming, and the amino acid sequence motif is selected from the group consisting of: EAAA, AEAA, AAEA, AAAE, DAAA, ADAA, AADA, AAAD, RAAA, ARAA, AARA, AAAR, KAAA, AKAA, AAKA, and AAAK.

2. The compound of claim 1 , wherein the compound comprises structural formula (II):

wherein,
Base is selected from adenosine, cytidine, guanosine, thymidine, and uridine;
R is selected from H and OH;
n is from 1 to 4;
Linker is the linker comprising a covalently bonded chain of 2 to 100 atoms; and
Polypeptide is the polypeptide tag.

3. The compound of claim 1 , wherein the length of the polypeptide tag is at least 16 amino acid residues, optionally wherein the length of the polypeptide tag is at least 20 amino acid residues, at least 25 amino acid residues, at least 30 amino acid residues, at least 40 amino acid residues, at least 50 amino acid residues, at least 60 amino acid residues, at least 70 amino acid residues, at least 80 amino acid residues, or at least 90 amino acid residues.

4. The compound of claim 1 , wherein the length of the α-helix is at least 10 amino acid residues, at least 16 amino acid residues, at least 20 amino acid residues, at least 25 amino acid residues, at least 30 amino acid residues, or at least 40 amino acid residues.

5. The compound of claim 4 , wherein said α-helix sequence motif comprises at a least 4 amino acid residues, at least 5 amino acid residues, or at least 6 amino acid residues.

6. The compound of claim 1 , wherein the overall charge of the polypeptide tag is negative, optionally wherein the overall charge of the polypeptide tag is between about −10 and −30.

7. The compound of claim 1 , wherein the 25% of the amino acid residues located at the end of the polypeptide tag distal from the linker have a net charge absolute value greater than the net charge absolute value of the 25% of the amino acid residues located at the end of the polypeptide tag proximal to the linker.

8. The compound of claim 1 , wherein P consists of from 3 to 9 phosphate groups, optionally from 4 to 6 phosphate groups, or optionally 6 phosphate groups.

9. The compound of claim 1 , wherein the linker comprises a chemical group selected from the group consisting of: ester, ether, thioether, amine, amide, imide, carbonate, carbamate, squarate, thiazole, thiazolidine, hydrazone, oxime, triazole, di hydropyridazine, phosphodiester, polyethylene glycol (PEG), and combinations thereof.

10. A method of preparing a polypeptide-tagged nucleotide compound of structural formula (II)

wherein,
Base is selected from adenosine, cytidine, guanosine, thymidine, and uridine;
R is selected from H and OH;
n is from 1 to 4;
Linker is a linker comprising a covalently bonded chain of 2 to 100 atoms; and
Polypeptide is a polypeptide tag comprising an overall charge and at least one α-helix comprising at least 2 repeats of a sequence motif, wherein the repeats are not interrupted by an amino acid residue that is non-helix-forming, and the amino acid sequence motif is selected from the group consisting of: EAAA, AEAA, AAEA, AAAE, DAAA, ADAA, AADA, AAAD, RAAA, ARAA, AARA, AAAR, KAAA, AKAA, AAKA, and AAAK

the method comprising:
(a) providing (i) a nucleotide with from 3 to 12 phosphates attached to its 5′-position, wherein the terminal phosphate is coupled to a first linker forming group; and (ii) a polypeptide tag, wherein the polypeptide tag comprises at least one α-helix comprising at least 2 repeats of a sequence motif, wherein the repeats are not interrupted by an amino acid residue that is non-helix-forming, and the amino acid sequence motif is selected from the group consisting of: EAAA, AEAA, AAEA, AAAE, DAAA, ADAA, AADA, AAAD, RAAA, ARAA, AARA, AAAR, KAAA, AKAA, AAKA, and AAAK, has an overall charge, and is coupled to a second linker forming group, that is capable of reacting with the first linker forming group to form a linker;
wherein
the first linker forming group is selected from the compounds of structural formulas (IVa)-(XVIIa) and the second linker forming group is the corresponding reactive compound of structural formulas (IVb)-(XVIIb); or
the first linker forming group is selected from the compounds of structural formulas (IVb)-(XVIIb) and the second linker forming group is the corresponding reactive compound of structural formulas (IVa)-(XVIIa); and

(b) reacting the first linker forming group with the second linker forming group, thereby forming a covalent linkage between the nucleotide to the polypeptide tag.

11. The method of claim 10 , wherein (1) the first linker forming group is selected from the group consisting of an alkyne and a diene, and the second linker forming group is selected from the group consisting of an azide and a tetrazine; or (2) the first linker forming group is selected from the group consisting of an azide and a tetrazine, and the second linker forming group is selected from the group consisting of an alkyne and a diene.

12. A composition comprising a set of tagged nucleotides each with a different tag, wherein each different tag causes a different blocking current when it is situated in a nanopore, and the set comprises at least one compound of claim 1 .

13. A method for determining the sequence of a nucleic acid comprising:
(a) providing a nanopore sequencing composition comprising: a membrane, an electrode on the cis side and the trans side of the membrane, a nanopore with its pore extending through the membrane, an electrolyte solution in contact with both electrodes, an active polymerase situated adjacent to the nanopore, and a primer strand complexed with the polymerase;
(b) contacting the nanopore sequencing composition with (i) a strand of the nucleic acid; and (ii) a set of tagged nucleotides each with a different tag, wherein each different tag causes a different blocking current and/or blocking current and/or has a different dwell time when it is situated in the nanopore, and the set comprises at least one compound of claim 1 ; and
(c) detecting the different blocking currents and/or blocking voltages and/or different dwell times of the tags over time and correlating to each of the different tagged nucleotides incorporated by the polymerase which are complimentary to the nucleic acid sequence, and thereby determining the nucleic acid sequence.

Assignees

• Roche Molecular Systems Inc
• Roche Sequencing Solutions Inc

Inventors

• Bergmann Frank
• Seidel Christoph
• Trans Andrew
• Gremyachinskiy Dmitriy
• Kuchelmeister Hannes
• Hillringhaus Lars

Classifications

• C12Q2525/113

  incorporating modified backbone · CPC title

• C07H19/10

  with the saccharide radical esterified by phosphoric or polyphosphoric acids · CPC title

• C12Q2525/204

  specific length of the oligonucleotides · CPC title

• C12Q1/6869 Primary

  Methods for sequencing · CPC title

• C12Q2525/203

  incorporating a composite nucleic acid containing a polypeptide sequence other than PNA · CPC title