OmpG variants
The present disclosure provides variant OmpG polypeptides, compositions comprising the OmpG variant polypeptides, and methods for using the variant OmpG polypeptides as nanopores for determining the sequence of single stranded nucleic acids. The variant OmpG nanopores reduce the ionic current noise versus the parental OmpG polypeptide from which they are derived and thereby enable sequencing of polynucleotides with single nucleotide resolution. The reduced ionic current noise also provides for the use of these OmpG nanopore variants in other single molecule sensing applications, e.g., protein sequencing.
1. A chip for sequencing a nucleic acid molecule, the chip comprising:
a plurality of OmpG nanopores, wherein at least one of the OmpG nanopores is a variant OmpG nanopore that is disposed adjacent or in proximity to an electrode and that is individually addressable;
wherein the variant OmpG nanopore comprises an amino acid sequence at least 95% identical to SEQ ID NO: 2, the amino acid sequence comprising a deletion of one or more of amino acids 216-227, an amino acid substitution of E229A, and at least one of the following modifications of SEQ ID NO: 2:
i. a Y50 substitution;
ii. an R68 substitution;
iii. an R211 substitution;
iv. an E17 substitution;
v. a D215 deletion; or
vi. a D215 deletion and a Y50K substitution.
2. The chip of claim 1 , wherein the modification is a Y50K, R68N, R211N, or E17K modification.
3. The chip of claim 2 , wherein the variant OmpG nanopore comprises a single polymerase attached thereto.
4. The chip of claim 3 , wherein the variant OmpG nanopore is configured to detect a tag associated with a tagged nucleotide when the nucleotide is incorporated into a growing nucleic acid chain by the polymerase.
5. The chip of claim 1 , wherein the plurality of OmpG nanopores is partitioned into separate partitions so that each partition can receive a different sample.
6. The chip of claim 5 , wherein the chip comprises a silicon surface and wherein side walls associated with the silicon surface separate the partitioned OmpG nanopores into the separate partitions.
7. The chip of claim 2 , wherein the variant OmpG nanopore comprises the amino acid sequence set forth as SEQ ID NO: 10 or SEQ ID NO: 11.
8. A chip for sequencing a nucleic acid molecule, the chip comprising:
a plurality of OmpG nanopores, wherein at least one of the OmpG nanopores is a variant OmpG nanopore that is disposed adjacent or in proximity to an electrode and that is individually addressable;
wherein the variant OmpG nanopore comprises an amino acid sequence at least 95% identical to SEQ ID NO: 2, the amino acid sequence comprising a deletion of one or more of amino acids 216-227, an amino acid substitution of E229A, and a D215 deletion, and
wherein the variant OmpG nanopore comprises a single polymerase attached thereto.
9. The chip of claim 8 , wherein the amino acid sequence further comprises an R211, E15, R68, Y50, E152, E174, E17, D215, K114, E174, F66, or E31 modification of SEQ ID NO: 2.
10. The chip of claim 9 , wherein the amino acid sequence comprises an R211N, R68N, Y50K, Y50N, or E17K substitution of SEQ ID NO: 2.
11. The chip of claim 10 , wherein the amino acid sequence comprises a Y50K substitution.
12. The chip of claim 8 , wherein the variant OmpG nanopore is configured to detect a tag associated with a tagged nucleotide when the nucleotide is incorporated into a growing nucleic acid chain by the polymerase.
13. The chip of claim 8 , wherein the plurality of OmpG nanopores is partitioned so that each partition can receive a different sample and wherein side walls associated with a silicon surface of the chip separate the partitioned OmpG nanopores into the separate partitions.
14. The chip of claim 8 , wherein the variant OmpG nanopore comprises the amino acid sequence set forth as SEQ ID NO: 10.
15. A chip for sequencing a nucleic acid molecule, the chip comprising:
a plurality of OmpG nanopores, wherein at least one of the OmpG nanopores is a variant OmpG nanopore that is disposed adjacent or in proximity to an electrode and that is individually addressable;
wherein the variant OmpG nanopore comprises an amino acid sequence at least 95% identical to SEQ ID NO: 2, the amino acid sequence comprising a deletion of one or more of amino acids 216-227, an amino acid substitution of E229A, and an amino acid substitution of Y50K or Y50N, and
wherein the variant OmpG nanopore comprises a single polymerase attached thereto.
16. The chip of claim 15 , wherein the amino acid sequence further comprises an amino acid substitution at R211, E15, R68, E152, E174, E17, D215, K114, E174, F66, or E31 modification of SEQ ID NO: 2.
17. The chip of claim 16 , wherein the amino acid sequence comprises a D215 deletion.
18. The chip of claim 15 , wherein the variant OmpG nanopore is configured to detect a tag associated with a tagged nucleotide when the nucleotide is incorporated into a growing nucleic acid chain by the polymerase.
19. The chip of claim 15 , wherein the plurality of OmpG nanopores is partitioned so that each partition can receive a different sample and wherein side walls associated with a silicon surface of the chip separate the partitioned OmpG nanopores into the separate partitions.
20. The chip of claim 15 , wherein the variant OmpG nanopore comprises the amino acid sequence set forth as SEQ ID NO: 11.