Translocation of DNA and protein through a sequentially polymerized polyurea nanopore

Single molecule protein sequencing would tremendously impact in proteomics and human biology and it would promote the development of novel diagnostic and therapeutic approaches. However, its technological realization can only be envisioned, and huge challenges need to be overcome. Major difficulties are inherent to the structure of proteins, which are composed by several different amino-acids. Despite long standing efforts, only few complex techniques, such as Edman degradation, liquid chromatography and mass spectroscopy, make protein sequencing possible. Unfortunately, these techniques present significant limitations in terms of amount of sample required and dynamic range of measurement. It is known that proteins can distinguish closely similar molecules. Moreover, several proteins can work as biological nanopores in order to perform single molecule detection and sequencing. Unfortunately, while DNA sequencing by means of nanopores is demonstrated, very few examples of nanopores able to perform reliable protein-sequencing have been reported so far. Here, we investigate, by means of molecular dynamics simulations, how a re-engineered protein, acting as biological nanopore, can be used to recognize the sequence of a translocating peptide by sensing the “shape” of individual amino-acids. In our simulations we demonstrate that it is possible to discriminate with high fidelity, 9 different amino-acids in a short peptide translocating through the engineered construct. The method, here shown for fluorescence-based sequencing, does not require any labelling of the peptidic analyte. These results can pave the way for a new and highly sensitive method of sequencing.

show abstract

“…A residence time of 125 ns per residue is consistent with translocation velocities reported in Refs. [6,7,31,[33][34][35][36][37][38][39].…”

Section: Resultsmentioning

confidence: 99%

Adaptive nanopores: A bioinspired label-free approach for protein sequencing and identification

et al. 2020

View full text Add to dashboard Cite

show abstract

“…New organic components have also been developed for the purely organic MLD processes; the MLD material library already includes, besides the initially introduced polyimides [ 15,17–22,137–143 ] and polyamides, [ 15,23–28,144–149 ] many other polymers: polyurea, [ 29,30,37,38,51,150–164 ] polythiourea, [ 52 ] polyurethane, [ 165,166 ] polyazomethine, [ 167–172 ] poly(3,4‐ethylenedioxy‐thiophene), [ 173–177 ] polyimide–polyamide, [ 141 ] poly(ethylene terephthalate) (PET), [ 50,178–180 ] and others. [ 31,32,39–44,176,181–200 ] In recent years, the organic precursor library has been rapidly expanding.…”

Section: Organic Precursors In Ald/mldmentioning

confidence: 99%

Atomic/Molecular Layer Deposition for Designer's Functional Metal–Organic Materials

Multia

Karppinen

2022

Adv Materials Inter

View full text Add to dashboard Cite

organic ligands act as bridges between the metal centers to form infinite 1D, 2D, or 3D structures. These materials are often referred to as coordination polymer (CP) [1] or metal-organic framework (MOF) [2] materials; the latter term is used when the metal-organic material is crystalline and highly porous. [3] The research field of CP-and MOF-type materials has grown tremendously over the last two decades. The structural and chemical diversity of these materials has served as a continuous source of scientific excitement; the same diversity has also triggered huge technological interest as these materials possess enormous potential to be tailored for a wide variety of applications ranging from gas capture, storage, and separation to sensing, catalysis, optics, electronics, and energy storage. [4][5][6][7] Most of the targeted application breakthroughs of metal-organics require that these materials can be produced as highquality thin films and coatings, which can be integrated with the other components in the actual device configuration. The possibility to deposit such thin films in an industry-feasible manner on the substrate types needed, would be a major step forward in the field. [8] Traditionally, solvent-based processes such as liquid-phase epitaxy, Langmuir-Blodgett, layer-by-layer, and electrochemical deposition techniques have been used for metal-organic thin films. [9][10][11] These are, however, incompatible with the requirements set by the possible integration of the materials in microelectronics. This is due to corrosion and contamination risks, and the problems in patterning and precise deposition on high-aspect-ratio features. Hence, it is vital to develop solventfree thin-film deposition routes for the metal-organic material family. In the optimal case, these deposition methods should allow conformal coatings on large-area and high-aspect-ratio substrates.The currently strongly emerging ALD/MLD technique is uniquely suited to address the challenge in a scientifically elegant yet industrially feasible way. This technique is derived from the two parent gas-phase thin-film techniques: ALD for inorganic materials (mostly binary metal oxides, sulfides, and nitrides), [12][13][14] and its counterpart MLD for purely organic thin films (e.g., polyimides and polyamides). [15] In both cases, the attractive film growth characteristics are derived from the unique way of separating the different precursor gas pulses. Currently, ALD is the standard thin-film technology in many Atomic layer deposition (ALD) for high-quality conformal inorganic thin films is one of the cornerstones of modern microelectronics, while molecular layer deposition (MLD) is its less-exploited counterpart for purely organic thin films. Currently, the hybrid of these two techniques, i.e., ALD/MLD, is strongly emerging as a state-of-the-art gas-phase route for designer's metal-organic thin films, e.g., for the next-generation energy technologies. The ALD/MLD literature comprises nearly 300 original journal papers covering most of the alkali...

show abstract

“…Individual analytes are detected by observing changes in the transients of the ionic current. The magnitude, dwell time, and frequency of these transients reveal information such as size, [ 2b,8 ] charge, [ 9 ] shape, [ 8,10 ] dipole, [ 11 ] concentration, [ 12 ] and in the case of nucleic acids, even the sequence. [ 13 ] However, the detection of proteins adds significant complexity both in terms of sensitivity and selectivity.…”

Section: Introductionmentioning

confidence: 99%

Single‐Molecule Binding Assay Using Nanopores and Dimeric NP Conjugates

et al. 2021

View full text Add to dashboard Cite

The ability to measure biomarkers, both specifically and selectively at the single‐molecule level in biological fluids, has the potential to transform the diagnosis, monitoring, and therapeutic intervention of diseases. The use of nanopores has been gaining prominence in this area, not only for sequencing but more recently in screening applications. The selectivity of nanopore sensing can be substantially improved with the use of labels, but substantial challenges remain, especially when trying to differentiate between bound from unbound targets. Here highly sensitive and selective molecular probes made from nanoparticles (NPs) that self‐assemble and dimerize upon binding to a biological target are designed. It is shown that both single and paired NPs can be successfully resolved and detected at the single‐molecule nanopore sensing and can be used for applications such as antigen/antibody detection and microRNA (miRNA) sequence analysis. It is expected that such technology will contribute significantly to developing highly sensitive and selective strategies for the diagnosis and screening of diseases without the need for sample processing or amplification while requiring minimal sample volume.

show abstract

Translocation of DNA and protein through a sequentially polymerized polyurea nanopore

Abstract: Here, we investigated the translocation of biomolecules, such as DNA and protein, through a sequentially polymerized polyurea nanopore, with a thin (<10 nm) polymer membrane of uniform thickness.

Cited by 19 publications

References 73 publications

Adaptive nanopores: A bioinspired label-free approach for protein sequencing and identification

Adaptive nanopores: A bioinspired label-free approach for protein sequencing and identification

Atomic/Molecular Layer Deposition for Designer's Functional Metal–Organic Materials

Single‐Molecule Binding Assay Using Nanopores and Dimeric NP Conjugates

Contact Info

Product

Resources

About