This research project aims to combine the unique and powerful capabilities of two exciting, rapidly evolving fields, plasmonics and nanopores, for the analysis of single DNA molecules. More specifically, recent advances in nanoplasmonics will be utilized to enable label-free, single-molecule trapping and sequencing of DNA using nanopores. A novel type of synthetic nanostructure will be developed to strongly focus light to very high intensity in a nanometer-dimension spot where a solid-state nanopore is created. Through that spot, a DNA molecule will be translocated in a controlled way, allowing the detection of the sequence of the DNA fragments that are sequentially exposed to the intense optical fields of the plasmonic hot spot. The unique aspect of the program is the use of plasmonic tweezers to control DNA in solid-state nanopores. This novel approach to advancing DNA through the nanopore simultaneously enables DNA sequence detection through surface-enhanced Raman spectroscopy. Because locally confined plasmonic fields enhance Raman scattering many orders of magnitude and because of the direct relationship of Raman spectra to the underlying molecular structure, sequence detection will be possible directly, without any labeling. The project's team is a synergetic combination of experts in biomolecular modeling (UIUC), nanopore experiments (TU Delft) and plasmonic sensing (TU Delft).
The specific aims of the projects are to (i) use a plasmonic field to trap DNA in solid-state nanopores, (ii) develop a method to transport DNA through plasmonic nanopores in discrete, ultimately single-nucleotide steps, and (iii) detect the nucleotide sequence of trapped and moving DNA molecules by means of Raman spectroscopy.
This project aims to develop a novel method to sequence human DNA to make it an affordable and rapid medical procedure. The method can, ultimately, enable accurate medical diagnostics of genetic and multifactorial diseases, early detection of cancer, development of drugs tailored to individual genetic makeup and will facilitate the use of DNA sequencing in biomedical research.
| Shi, Xin; Verschueren, Daniel; Pud, Sergii et al. (2018) Integrating Sub-3 nm Plasmonic Gaps into Solid-State Nanopores. Small 14:e1703307 |
| Heerema, Stephanie J; Vicarelli, Leonardo; Pud, Sergii et al. (2018) Probing DNA Translocations with Inplane Current Signals in a Graphene Nanoribbon with a Nanopore. ACS Nano 12:2623-2633 |
| Verschueren, Daniel V; Yang, Wayne; Dekker, Cees (2018) Lithography-based fabrication of nanopore arrays in freestanding SiN and graphene membranes. Nanotechnology 29:145302 |
| Hemmig, Elisa A; Fitzgerald, Clare; Maffeo, Christopher et al. (2018) Optical Voltage Sensing Using DNA Origami. Nano Lett 18:1962-1971 |
| Shi, Xin; Li, Qiao; Gao, Rui et al. (2018) Dynamics of a Molecular Plug Docked onto a Solid-State Nanopore. J Phys Chem Lett 9:4686-4694 |
| Wilson, James; Aksimentiev, Aleksei (2018) Water-Compression Gating of Nanopore Transport. Phys Rev Lett 120:268101 |
| Shi, Xin; Verschueren, Daniel V; Dekker, Cees (2018) Active Delivery of Single DNA Molecules into a Plasmonic Nanopore for Label-Free Optical Sensing. Nano Lett : |
| Restrepo-Pérez, Laura; John, Shalini; Aksimentiev, Aleksei et al. (2017) SDS-assisted protein transport through solid-state nanopores. Nanoscale 9:11685-11693 |
| Cressiot, Benjamin; Greive, Sandra J; Si, Wei et al. (2017) Porphyrin-Assisted Docking of a Thermophage Portal Protein into Lipid Bilayers: Nanopore Engineering and Characterization. ACS Nano 11:11931-11945 |
| Shankla, Manish; Aksimentiev, Aleksei (2017) Modulation of Molecular Flux Using a Graphene Nanopore Capacitor. J Phys Chem B 121:3724-3733 |
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