Detergent‐Assisted Braking of Peptide Translocation through a Single‐Layer Molybdenum Disulfide Nanopore

Abstract

of the compositive amino acids. In other words, if the sequence of a protein is known, then a protein's crystal structure can be predicted by a devised algorithm assisted by computer science, which was proven to be feasible by Moult et al. [2] In addition, knowledge of accurate protein sequence is a key point for revealing the biological mechanisms of protein functions and is also beneficial for discovering potential drugs that can effectively activate or inhibit a certain protein. Researchers have provided and attempted many possible methods of sequencing a protein string. Unfortunately, only Edman degradation [3] and mass spectrometry [4] can satisfy the demand of protein sequencing. A combination of both methods can achieve protein sequencing even at the attomole level. [5] However, the proposed methods have fundamental disadvantages, such as limited dynamic range and restricted detection environment. The fluorescence technique, [6] which is similar to DNA sequencing, was suggested to be used in protein fingerprinting. However, it is challenging because of the lack of fluorophores that can label up to ≈20 amino acids, and the differentiation among the optical signals cannot be guaranteed. Tunneling current measurement, which was initially proposed by Aviram and Ratner, [7] has been successfully used to study various biomolecules [8] and even to discriminate single nucleotides in a DNA strand. [9] The success of tunneling current in DNA sequencing has inspired researchers to perform protein sequencing. Preliminary results from Lindsay's group validate the feasibility of protein sequencing by measuring the tunneling current. However, they reported an accuracy of only 80% for the discrimination of three sets of amino acids; [10] this result is far from the target of accurate protein sequencing. Nanopore, which is a nanoconfinement [11-13] with great versatility, has been widely used for sensing single molecules, such as nanoparticles, [14] DNAs, [15] RNAs, [16] proteins, [17,18] and viruses. [19] Besides of single molecule detection, nanopores are also able to quantify analyte-protein binding complexes. [20,21] With the approximately 20-year development of nanoporebased single molecule technology, DNA sequencing by using a tiny nanoscale biological nanopore has been achieved in recent years. A commercialized miniaturized device called MinION, Protein sequencing holds the key to unveiling protein dynamics, which is significant for molecular diagnostics and drug design. Single-molecule sensing based on 2D nanopores is a versatile technique for realizing low-cost and high-throughput protein sequencing targets. However, the remaining challenge is that protein translocates rapidly through nanopores, where few current signals can be gathered for accurate protein sequencing. It is theoretically found that adding nonionic detergents to a solution can slow protein molecules by almost one order when they permeate through a 1.4 nm MoS 2 nanopore that is slightly larger than the diameter of the peptide but smaller than the d...

Navigated Delivery of Peptide to the Nanopore Using In-Plane Heterostructures of MoS2 and SnS2 for Protein Sequencing

“…It should be noted that the ionic current trace was a little bit noisier due to a relatively high sampling frequency which was about three orders higher than the 10 MHz measurement bandwidth reported recently. Also the current fluctuations were observed; these were induced by the conformation change of the peptide and orientation change of the residues inside the nanopores, which have been validated in our previous works. , Due to the strong interaction between the peptide and SnS 2 , the peptide took up to 300 ns to fully translocate through the nanopore, which was much slower compared to protein translocation through pristine MoS 2 nanopores reported in our previous simulations performed with the similar conditions. , To study whether the nanopore in the heterostructure could identify and differentiate the compositions of the peptides, the peptide with sequence of (FK) 7 F was obtained by modify methionines in (MK) 7 M to phenylalanines, and then it was electrophoretically driven through the same nanopore. For both peptides, I 0 and Δ I were found to be linearly increased with the applied electric field, Figure c,d.…”

“…In order to investigate whether the flexible constraint is effective to maintain the adsorption of peptide on the nanostripe or not, an electric field of 0.06 V/Å was applied to the system along the direction of the nanopore axis. Because the peptide is within the capture radius of the nanopore, , when an applied bias was applied, the peptide would be captured by the nanopore, which has already been found in our previous simulations ,,− of biomolecules translocation through 2D membranes such as graphene and MoS 2 nanopores. Interestingly, with up to ∼50 ns simulations under the action of the electric field force, the peptide did not detach from the SnS 2 nanostripe and was stably bound to the nanostripe, SI Figure S19.…”

“…49,50 Due to the strong interaction between the peptide and SnS 2 , the peptide took up to 300 ns to fully translocate through the nanopore, which was much slower compared to protein translocation through pristine MoS 2 nanopores reported in our previous simulations performed with the similar conditions. 42,46 To study whether the nanopore in the hetero-structure could identify and differentiate the compositions of the peptides, the peptide with sequence of (FK) 7 F was obtained by modify methionines in (MK) 7 M to phenylalanines, and then it was electrophoretically driven through the same nanopore. For both peptides, I 0 and ΔI were found to be linearly increased with the applied electric field, Figure 5c,d.…”

Simultaneous Sensing of Force and Current Signals to Recognize Proteinogenic Amino Acids at a Single-Molecule Level

“…Sequencing protein can provide vital information in some biological processes and disease diagnostics. − Benefiting from the rapid development of third-generation sequencing techniques, − the nanopore sensing technique inspires protein sequencing. , Nanopore current sensing achieves sequencing by detecting the real-time ionic current change when a protein thread permeates a nanopore. , This technique has advantages of the single-molecule-level resolution, long-readability, and high-fidelity over the classical sequencing methods, Edman degradation and mass spectrometry . Two-dimensional (2D) materials − are favored as nanopore sensors because the thinness guarantees a theoretically atom-level resolution and enables single-residue detection, compared with their counterparts, solid-state and biological nanopores . Sequencing using 2D materials is first achieved and confirmed in experiments to sense DNA chains by graphene nanopore. − Among all 2D materials, graphene and its derivatives stand out for their excellent physical and chemical properties. − Graphene is one of the most promising 2D material nanopore sensors in sequencing. − …”

Oligonucleotide Discrimination Enabled by Tannic Acid-Coordinated Film-Coated Solid-State Nanopores

“…Surface coatings have been commonly used to endow functionalities to solid-state substrate-based biosensors . The primary motivation for nanopore coatings is to avoid the adhesion of biomolecules to the pore wall, and intensive efforts have been devoted to avoiding nanopore clogging through various surface coating methods, such as coatings by physisorption of chemicals (Tween 20, polyethylene glycol), − atomic layer deposited metal oxide layers (Al 2 O 3 , HfO 2 ), , fluid lipid bilayers, salinization, , and other covalent surface modifications. , However, investigations on the interaction between the coated molecules and the target analytes, and how to further use this interaction to slow down the translocation of analytes, remain a significant issue and need more efforts. − …”