Long lifetime alpha-hemolysin nanopores

a nanopore and alpha-hemolysin technology, applied in the field of alpha-hemolysin variants of staphylococcus aureaus, can solve the problems of difficult task, short time-consuming and laborious nanopores using wild-type alpha-hemolysins, and often serve as rate-limiting features of alpha-hemolysin nanopores during sequencing reactions, etc., to achieve more sequencing data than the effect of improving the lifetime of the nanopor

Inactive Publication Date: 2018-01-04
ROCHE SEQUENCING SOLUTIONS INC
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0008]Provided herein are mutant staphylococcal alpha hemolysin (αHL) polypeptides that, when incorporated into a nanopore, improve the lifetime of the nanopore during a DNA sequencing reaction. For example, a nanopore including one or more of the variants described herein lasts longer—and hence provides more sequencing data—than a nanopore that consists of wild-type alpha hemolysin.

Problems solved by technology

Previous work on DNA detection in the a-HL pore has focused on analyzing the ionic current signature as DNA translocates through the pore (Kasianowicz et al., 1996, Akeson et al., 1999, Meller et al., 2001), a very difficult task given the translocation rate (˜1 nt / μs at 100 mV) and the inherent noise in the ionic current signal.
While the use of nanopores has revolutionized DNA sequencing, nanopores using wild-type alpha-hemolysins are only able to generate sequence data for a short amount of time.
Hence, the lifetime of the alpha-hemolysin nanopore during the sequencing reaction often serves as the rate-limiting feature of the sequencing reaction.
Further, use of wild-type alpha hemolysin often results in a significant number of deletion errors, i.e., bases that are not measured.

Method used

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Examples

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example 1

Expression and Recovery

[0136]This example illustrates the expression and recovery of protein from bacterial host cells, e.g., E. coli.

[0137]DNA encoding the wild-type a-HL was purchased from a commercial source. The sequence was verified by sequencing.

[0138]Plasmid Construction.

[0139]The gene encoding either a wild-type or variant α-hemolysin was inserted into a pPR-IBA2 plasmid (IBA Life Sciences, Germany) under the control of T7 promoter.

[0140]Transformation.

[0141]E. coli BL21 DE3 (from Life Technologies) cells were transformed with the expression vector comprising the DNA encoding the wild-type or variant α-hemolysin using techniques well-known in the art. Briefly, the cells were thawed on ice (if frozen). Next, the desired DNA (in a suitable vector / plasmid) was added directly into the competent cells (should not exceed 5% of that of the competent cells) and mixed by flicking the tube. The tubes were placed on ice for 20 minutes. Next, the cells were placed in a 42° C. water bat...

example 2

Alpha-Hemolysin Variants

[0147]The following example details the introduction of a mutation at a desired residue.

[0148]Mutations.

[0149]Site-directed mutagenesis is carried out using a QuikChange Multi Site-Directed Mutagenesis kit (Stratagene, La Jolla, Calif.) to prepare the example H35G+V149K+H144A (SEQ ID NO: 4) and H35G+E111N+M113A+126−131G+H144A+K147N (SEQ ID NO: 19), with the sequences including a C-terminal linker / TEV / HisTag for purification. QuikChange Multi Site-Directed Mutagenesis kit (Stratagene, La Jolla, Calif.) is also carried out to prepare a variant (E111N+M113A+126−131G+K147N, SEQ ID NO: 20) for Polymerase attachment, with the variant including a C-terminal SpyTag, KG linker, and HisTag. The variants were expressed and purified as in Example 1.

example 3

Assembly of Nanopore Including Variants

[0150]This example describes the assembly of a 1:6 heptameric nanopore including one subunit having a SpyTag sequence for subsequent polymerase attachment (the “α-HL-variant-SpyTag” subunit) and six α-HL-variant subunits with no SpyTag (the “α-HL-variant” subunits).

[0151]The α-HL-variant-SpyTag (E111N+M113A+126−131G+K147N, SEQ ID NO: 20)) was prepared and expressed as described in Examples 1 and 2 with a C-terminal SpyTag, KG linker, and HisTag. The α-HL-variant-SpyTag protein was then then purified on a cobalt affinity column using a cobalt elution buffer (200 mM NaCl, 300 mM imidazole, 50 mM tris, pH 8). The protein was stored at 4° C. if used within 5 days, otherwise 8% trehalose was added and stored at −80° C.

[0152]For the α-HL-variant subunits, variants of H35G+E111N+M113A+126-131G+H144A+K147N (SEQ ID NO: 19) were prepared and expressed as described in Examples 1 and 2 with a linker / TEV / HisTag and purified on a cobalt affinity column using...

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Abstract

Described herein are variants of alpha-hemolysin having at least one amino acid substitution at H35G, E111N, M113A, and/or K147N in the mature, wild-type alpha-hemolysin amino acid sequence. In certain examples, the variant may have a substitution at E111S, M113S, T145S, K147S, or L135I in the mature alpha-hemolysin amino acid sequence. The α-hemolysin variants may also include a substitution at H144A and/or a series of glycine residues spanning residues 127 to 131 of the mature, wild-type alpha hemolysin. Also provided are nanopore assemblies including the alpha-hemolysin variants, the assembly having an increased nanopore lifetime. Further, provided are variants that, in addition to providing increased lifetime, provide a decreased time-to-thread. Hence, the variants provided herein both increase nanopore lifetime and improve efficiency and accuracy of DNA sequencing reactions using nanopores comprising the variants.

Description

RELATED APPLICATIONS[0001]This application claims the benefit of U.S. Provisional Application Ser. No. 62 / 357,230, filed on Jun. 30, 2016, the contents of which are hereby incorporated in their entirety.SEQUENCE LISTING INCORPORATION BY REFERENCE[0002]This application hereby incorporates-by-reference a sequence listing submitted herewith in a computer-readable format, having a file name of 33725_WO_seqlist_ST25, created on Jun. 29, 2017, which is 56,233 bytes in size.TECHNICAL FIELD[0003]Disclosed are methods and compositions relating to Staphylococcus aureaus alpha-hemolysin variants that, when assembled into a multi-subunit nanopore, increase the sequencing lifetime of the nanopore during a nucleic acid sequencing reaction. Also disclosed are variants that, when assembled into a multi-subunit nanopore, improve sequencing efficiency and accuracy.BACKGROUND[0004]Hemolysins are members of a family of protein toxins that are produced by a wide variety of organisms. Some hemolysins, fo...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/68A61K38/02C12N15/01C07K14/00
CPCC12Q1/6869C07K14/00C12N15/01A61K38/02C07K14/31
Inventor AMBROSO, MARKCRAIG, TIMOTHYDIPIETRO, MATTHEWHARRIS, CORISSAPORTER, MARSHALL
Owner ROCHE SEQUENCING SOLUTIONS INC
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