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On the left is a drawing of the complex formed between alpha-hemolysin and dsDNA with linkage through an oligomer. On the right, movement of this complex in relation to a nanopore channel is shown sequentially in two steps (I) and (II). Once the complex is inserted into the nanopore, the alpha-hemolysin protein will be functional in the newly formed hybrid, biological and solid state, nanopore system.

Nanopore sequencing is a fourth generation[1] approach used in the sequencing of biopolymers- specifically, polynucleotides in the form of DNA or RNA.

Using nanopore sequencing, a single molecule of DNA or RNA can be sequenced without the need for PCR amplification or chemical labeling of the sample. At least one of these aforementioned steps is necessary in the procedure of any previously developed sequencing approach. Nanopore sequencing has the potential to offer relatively low-cost genotyping, high mobility for testing, and rapid processing of samples with the ability to display results in real-time. Publications on the method outline its use in rapid identification of viral pathogens,[2] monitoring ebola,[3] environmental monitoring,[4] food safety monitoring, human genome sequencing,[5] plant genome sequencing,[6] monitoring of antibiotic resistance,[7] haplotyping[8] and other applications.

Background

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Nanopore sequencing uses electrophoresis to transport an unknown sample through an orifice of diameter 10-9 meters, in magnitude. A nanopore system always contains an electrolytic solutions- when a constant electric field is applied, an electric current can be observed in the system. The magnitude of the electric current density across a nanopore surface depends on the nanopore's dimensions and the composition of DNA or RNA occupying the nanopore. Sequencing is made possible because, when close enough to nanopores, samples elicit characteristic changea in electric current density across nanopore unit normal surfaces. For an infinitesimally small length of time, total charge flowing through a nanopore channel equals the surface integral of electric current density flux across the nanopore surface.

Types

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Biological

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alpha-hemolysin pore (made up of 7 identical subunits in 7 colors) and 12-mer single-stranded DNA (in white) on the same scale to illustrate DNA effects on conductance when moving through a nanopore. Below is an orthogonal view of the same molecules.

Biological nanopore sequencing relies on the use of transmembrane proteins, called porins, that are embedded in lipid membranes so as to create size dependent porous surfaces- with nanometer scale "holes" distributed across the membranes. Sufficiently low translocation velocity can be attained through the incorporation of various proteins that facilitate the movement of DNA or RNA through the pores of the lipid membranes.[9]

Alpha hemolysin

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Alpha hemolysin (αHL), a nanopore from bacteria that causes lysis of red blood cells, has been studied for over 15 years.[10] To this point, studies have shown that all four bases can be identified using ionic current measured across the αHL pore.[11][12] The structure of αHL is advantageous to identify specific bases moving through the pore. The αHL pore is ~10 nm long, with two distinct 5 nm sections. The upper section consists of a larger, vestibule-like structure and the lower section consists of three possible recognition sites (R1, R2, R3), and is able to discriminate between each base.[11][12]

Sequencing using αHL has been developed through basic study and structural mutations, moving towards the sequencing of very long reads. Protein mutation of αHL has improved the detection abilities of the pore.[13] The next proposed step is to bind an exonuclease onto the αHL pore. The enzyme would periodically cleave single bases, enabling the pore to identify successive bases. Coupling an exonuclease to the biological pore would slow the translocation of the DNA through the pore, and increase the accuracy of data acquisition.

Notably, theorists have shown that sequencing via exonuclease enzymes as described here is not feasible.[14] This is mainly due to diffusion related effects imposing a limit on the capture probability of each nucleotide as it is cleaved. This results in a significant probability that a nucleotide is either not captured before it diffuses into the bulk or captured out of order, and therefore is not properly sequenced by the nanopore, leading to insertion and deletion errors. Therefore, major changes are needed to this method before it can be considered a viable strategy.

A recent study has pointed to the ability of αHL to detect nucleotides at two separate sites in the lower half of the pore.[15] The R1 and R2 sites enable each base to be monitored twice as it moves through the pore, creating 16 different measurable ionic current values instead of 4. This method improves upon the single read through the nanopore by doubling the sites that the sequence is read per nanopore.

MspA

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Mycobacterium smegmatis porin A (MspA) is the second biological nanopore currently being investigated for DNA sequencing. The MspA pore has been identified as a potential improvement over αHL due to a more favorable structure.[16] The pore is described as a goblet with a thick rim and a diameter of 1.2 nm at the bottom of the pore.[17] A natural MspA, while favorable for DNA sequencing because of shape and diameter, has a negative core that prohibited single stranded DNA(ssDNA) translocation. The natural nanopore was modified to improve translocation by replacing three negatively charged aspartic acids with neutral asparagines.[18]

The electric current detection of nucleotides across the membrane has been shown to be tenfold more specific than αHL for identifying bases.[16] Utilizing this improved specificity, a group at the University of Washington has proposed using double stranded DNA (dsDNA) between each single stranded molecule to hold the base in the reading section of the pore.[16][18] The dsDNA would halt the base in the correct section of the pore and enable identification of the nucleotide. A recent grant has been awarded to a collaboration from UC Santa Cruz, the University of Washington, and Northeastern University to improve the base recognition of MspA using phi29 polymerase in conjunction with the pore.[19]

Solid state

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Solid state nanopore sequencing approaches, unlike biological nanopore sequencing, do not incorporate proteins into their systems. Instead, solid state nanopore technology uses various metal or metal alloy substrates with nanometer sized pores that allow DNA or RNA to pass through. Additionally, these substrates most often serve integral roles in the sequence recognition of nucleic acids as they translocate through the channels along the substrates.[20]

Ionic blockade current

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Tunneling current

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Figure showing the theoretical movement of ssDNA through a tunneling current nanopore system. Detection is made possible by the incorporation of electrodes along the nanopore channel walls- perpendicular to the ssDNA's velocity vector.

Measurement of electron tunneling through bases as ssDNA translocates through the nanopore is an improved solid state nanopore sequencing method. Most research has focused on proving bases could be determined using electron tunneling. These studies were conducted using a scanning probe microscope as the sensing electrode, and have proved that bases can be identified by specific tunneling currents.[21] After the proof of principle research, a functional system must be created to couple the solid state pore and sensing devices.

Researchers at the Harvard Nanopore group have engineered solid state pores with single walled carbon nanotubes across the diameter of the pore.[22] Arrays of pores are created and chemical vapor deposition is used to create nanotubes that grow across the array. Once a nanotube has grown across a pore, the diameter of the pore is adjusted to the desired size. Successful creation of a nanotube coupled with a pore is an important step towards identifying bases as the ssDNA translocates through the solid state pore.

Another method is the use of nanoelectrodes on either side of a pore.[23][24] The electrodes are specifically created to enable a solid state nanopore's formation between the two electrodes. This technology could be used to not only sense the bases but to help control base translocation speed and orientation.

Capacitance variation

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Fluorescence

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An effective technique to determine a DNA sequence has been developed using solid state nanopores and fluorescence.[25] This fluorescence sequencing method converts each base into a characteristic representation of multiple nucleotides which bind to a fluorescent probe strand-forming dsDNA. With the two color system proposed, each base is identified by two separate fluorescences, and will therefore be converted into two specific sequences. Probes consist of a fluorophore and quencher at the start and end of each sequence, respectively. Each fluorophore will be extinguished by the quencher at the end of the preceding sequence. When the dsDNA is translocating through a solid state nanopore, the probe strand will be stripped off, and the upstream fluorophore will fluoresce.[25][26]

This sequencing method has a capacity of 50-250 bases per second per pore, and a four color fluorophore system (each base could be converted to one sequence instead of two), will sequence over 500 bases per second.[25] Advantages of this method are based on the clear sequencing readout—using a camera instead of noisy current methods. However, the method does require sample preparation to convert each base into an expanded binary code before sequencing. Instead of one base being identified as it translocates through the pore, ~12 bases are required to find the sequence of one base.[25]

Comparison between types

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Comparison of Biological and Solid State Nanopore Sequencing Systems Based on Major Constraints
Biological Solid State
Low Translocation Velocity ✓
Dimensional Reproducibility ✓
Stress Tolerance ✓
Longevity ✓
Ease of Fabrication ✓

Major constraints

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  1. Translocation Velocity:  The speed at which a molecule of DNA passes through a unit's pore
  2. Dimensional Reproducibility:  The likelihood of a unit's pore to be made the proper size
  3. Stress Tolerance:  The sensitivity of a unit to internal environmental conditions
  4. Longevity: The length of time that a unit is expected to remain functioning
  5. Ease of Fabrication: The ability to produce a unit- usually in regards to mass-production

Biological: advantages and disadvantages

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Biological nanopore sequencing systems have several fundamental characteristics that make them advantageous as compared with solid state systems- with each advantageous characteristic of this design approach stemming from the incorporation of proteins into their technology. Uniform pore structure, the precise control of sample translocation through pore channels, and even the detection of individual nucleotides in samples can be facilitated by unique proteins from a variety of organism types.

The use of proteins in biological nanopore sequencing systems, despite the various benefits, also brings with it some negative characteristics. The sensitivity of proteins in these systems has a large impact on the longevity of units as well as the degree to which these units can withstand environmental stress. One examples is that a motor protein may only unzip samples with sufficient speed at a certain pH range. Another example is that a transmembrane porin may only operate reliably for a certain number of runs before it breaks down. Both of these examples would have to be controlled for in the design of any viable biological nanopore system- something that may be difficult to achieve while keeping the costs of such a technology as low and as competitive to other systems as possible.

Solid state: advantages and disadvantages

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Challenges

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One challenge for the 'strand sequencing' method was in refining the method to improve its resolution to be able to detect single bases. In the early papers methods, a nucleotide needed to be repeated in a sequence about 100 times successively in order to produce a measurable characteristic change. This low resolution is because the DNA strand moves rapidly at the rate of 1 to 5μs per base through the nanopore. This makes recording difficult and prone to background noise, failing in obtaining single-nucleotide resolution. The problem is being tackled by either improving the recording technology or by controlling the speed of DNA strand by various protein engineering strategies and Oxford Nanopore employs a 'kmer approach', analyzing more than one base at any one time so that stretches of DNA are subject to repeat interrogation as the strand moves through the nanopore one base at a time.[27] Various techniques including algorithmic have been used to improve the performance of the MinION technology since it was first made available to users. More recently effects of single bases due to secondary structure or released mononucleotides have been shown.[28][29]

Professor Hagan Bayley proposed in 2010 that creating two recognition sites within an alpha hemolysin pore may confer advantages in base recognition.[30]

One challenge for the 'exonuclease approach',[31] where a processive enzyme feeds individual bases, in the correct order, into the nanopore, is to integrate the exonuclease and the nanopore detection systems. In particular,[32] the problem is that when an exonuclease hydrolyzes the phosphodiester bonds between nucleotides in DNA, the subsequently released nucleotide is not necessarily guaranteed to directly move in to, say, a nearby alpha-hemolysin nanopore. One idea[32] is to attach the exonuclease to the nanopore, perhaps through biotinylation to the beta barrel hemolsyin. The central pore of the protein may be lined with charged residues arranged so that the positive and negative charges appear on opposite sides of the pore. However, this mechanism is primarily discriminatory and does not constitute a mechanism to guide nucleotides down some particular path.

Commercialization

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Agilent Laboratories was the first to license and develop nanopores [33] but does not have any current disclosed research in the area.

References

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  1. ^ Niedringhaus, Thomas P.; Milanova, Denitsa; Kerby, Matthew B.; Snyder, Michael P.; Barron, Annelise E. (2011-06-15). "Landscape of Next-Generation Sequencing Technologies". Analytical Chemistry. 83 (12): 4327–4341. doi:10.1021/ac2010857. ISSN 0003-2700. PMC 3437308. PMID 21612267.
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  19. ^ "Advanced Sequencing Technology Awards 2011".
  20. ^ Carson, Spencer; Wanunu, Meni (2015). "Challenges in DNA motion control and sequence readout using nanopore devices". Nanotechnology. 26 (7): 074004. doi:10.1088/0957-4484/26/7/074004. PMC 4710574. PMID 25642629.
  21. ^ Chang, S; Huang, S; He, J; Liang, F; Zhang, P; Li, S; Chen, X; Sankey, O; Lindsay, S (2010). "Electronic signatures of all four DNA nucleosides in a tunneling gap". Nano Lett. 10 (3): 1070–1075. doi:10.1021/nl1001185. PMC 2836180. PMID 20141183.
  22. ^ Sadki, ES; Garaj, S; Vlassarev, D; Golovchenko, JA; Branton, D (2011). "Embedding a carbon nanotube across the diameter of a solid state nanopore". J. Vac. Sci. Technol. 29: 5.
  23. ^ Ivanov, A; Instuli, E; McGilvery, C; Baldwin, G; McComb, D; Albrecht, T; Edel, J (2011). "DNA tunneling detector embedded in a nanopore". Nano Lett. 11 (1): 279–285. doi:10.1021/nl103873a. PMC 3020087. PMID 21133389.
  24. ^ "Archived copy". Archived from the original on November 29, 2011. Retrieved December 17, 2011.{{cite web}}: CS1 maint: archived copy as title (link)
  25. ^ a b c d McNally, B; Singer, A; Yu, Z; Sun, Y; Weng, Z; Meller, A (2010). "Optical recognition of converted DNA nucleotides for single molecule DNA sequencing using nanopore arrays". Nano Lett. 10 (6): 2237–2244. doi:10.1021/nl1012147. PMC 2883017. PMID 20459065.
  26. ^ Soni, G; Singer, A; Yu, Z; Sun, Y; McNally, B; Meller, A (2010). "Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores". Rev. Sci. Instrum. 81 (1): 014301. doi:10.1063/1.3277116. PMC 2821415. PMID 20113116.
  27. ^ Bayley, Hagan (2006). "Sequencing single molecules of DNA". Current Opinion in Chemical Biology. 10 (6): 628–637. doi:10.1016/j.cbpa.2006.10.040. PMID 17113816.
  28. ^ Ashkenas, N; Sánchez-Quesada J; Bayley H; Ghadiri MR (2005-02-18). "Recognizing a single base in an individual DNA strand: a step toward DNA sequencing in nanopores". Angew Chem Int Ed Engl. 44 (9): 1401–4. doi:10.1002/anie.200462114. PMC 1828035. PMID 15666419.
  29. ^ Winters-Hilt, S; Vercoutere W; DeGuzman VS; Deamer D; Akeson M; Haussler D (February 2003). "Highly accurate classification of Watson-Crick basepairs on termini of single DNA molecules". Biophys J. 84 (2 Pt 1): 967–76. doi:10.1016/S0006-3495(03)74913-3. PMC 1302674. PMID 12547778.
  30. ^ Stoddart D; Maglia G; Mikhailova E; Heron A; Bayley H (2010). "Multiple Base-Recognition Sites in a Biological Nanopore: Two Heads are Better than One". Angew Chem Int Ed Engl. 49 (3): 556–9. doi:10.1002/anie.200905483. PMC 3128935. PMID 20014084.
  31. ^ Astier, Y; Braha O; Bayley H (2006-02-08). "Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5'-monophosphates by using an engineered protein nanopore equipped with a molecular adapter". J Am Chem Soc. 128 (5): 1705–10. doi:10.1021/ja057123+. PMID 16448145.
  32. ^ a b Rusk, Nicole (2009-04-01). "Cheap Third-Generation Sequencing". Nature Methods. 6 (4): 244–245. doi:10.1038/nmeth0409-244a. S2CID 18893754.
  33. ^ "Agilent Laboratories, Harvard University Collaborate On Development of Breakthrough Technology for the Analysis of Nucleic Acids". Business Wire. 2001-05-21.

Reviews

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