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Karawdeniya BI, Bandara YMNDY, Nichols JW, Chevalier RB, Hagan JT, Dwyer JR. Challenging Nanopores with Analyte Scope and Environment. JOURNAL OF ANALYSIS AND TESTING 2019. [DOI: 10.1007/s41664-019-00092-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Fanzio P, Mussi V, Menotta M, Firpo G, Repetto L, Guida P, Angeli E, Magnani M, Valbusa U. Selective protein detection with a dsLNA-functionalized nanopore. Biosens Bioelectron 2014; 64:219-26. [PMID: 25218776 DOI: 10.1016/j.bios.2014.08.081] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 08/10/2014] [Accepted: 08/27/2014] [Indexed: 12/19/2022]
Abstract
In the last years, nanopore technology has been increasingly exploited for biomolecule detection and analysis. Recently, the main focus of the research has moved from the study of nucleic acids to the analysis of proteins and DNA-protein complexes. In this paper, chemically functionalized solid-state nanopore has been used to recognize Nuclear Factor-kappa B proteins (NF-κB), that are involved in several disorders and inflammation processes, so that their identification is of crucial importance for prognostic applications. In particular, we show that it is possible to electrically detect the specific interaction between p50, a protein belonging to the NF-κB family, and dsLNA probe molecules covalently attached to the surface of a FIB fabricated SiN pore. The obtained results have been compared with those related to BSA protein, which does not interact with the used probes. Finally, the potential of the device has been further tested by analyzing a whole cell extract. In this case, three principal peaks in the distribution of electrical event duration can be identified, corresponding to different interacting NF-κB complexes, so that the methodology appears to be effective also to study biological samples of considerable complexity. Ultimately, the presented data emphasize the selectivity and versatility of the functionalized nanopore device, demonstrating its applicability in bioanalytics and advanced diagnostics.
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Affiliation(s)
- Paola Fanzio
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genova, Italy
| | - Valentina Mussi
- National Research Council, Institute for Complex Systems ISC-CNR, Via del Fosso del Cavaliere 100, 00133 Roma, Italy
| | - Michele Menotta
- Department of Biomolecular Sciences, University of Urbino 'Carlo Bo', Via Saffi 2, 61029 Urbino, PU, Italy
| | - Giuseppe Firpo
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genova, Italy
| | - Luca Repetto
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genova, Italy
| | - Patrizia Guida
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genova, Italy
| | - Elena Angeli
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genova, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino 'Carlo Bo', Via Saffi 2, 61029 Urbino, PU, Italy
| | - Ugo Valbusa
- Department of Physics, University of Genoa, via Dodecaneso 33, 16146 Genova, Italy
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Modulating DNA translocation by a controlled deformation of a PDMS nanochannel device. Sci Rep 2012; 2:791. [PMID: 23145315 PMCID: PMC3494361 DOI: 10.1038/srep00791] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 09/28/2012] [Indexed: 11/21/2022] Open
Abstract
Several strategies have been developed for the control of DNA translocation in nanopores and nanochannels. However, the possibility to reduce the molecule speed is still challenging for applications in the field of single molecule analysis, such as ultra-rapid sequencing. This paper demonstrates the possibility to alter the DNA translocation process through an elastomeric nanochannel device by dynamically changing its cross section. More in detail, nanochannel deformation is induced by a macroscopic mechanical compression of the polymeric device. This nanochannel squeezing allows slowing down the DNA molecule passage inside it. This simple and low cost method is based on the exploitation of the elastomeric nature of the device, can be coupled with different sensing techniques, is applicable in many research fields, such as DNA detection and manipulation, and is promising for further development in sequencing technology.
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Mussi V, Fanzio P, Firpo G, Repetto L, Valbusa U. Size and functional tuning of solid state nanopores by chemical functionalization. NANOTECHNOLOGY 2012; 23:435301. [PMID: 23060606 DOI: 10.1088/0957-4484/23/43/435301] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We demonstrate the possibility of using a simple functionalization procedure, based on an initial vapour-phase silanization, to control the size and functionality of solid state nanopores. The presented results show that, by varying the silanization time, it is possible to modify the efficiency of probe molecule attachment, thus shrinking the pore to the chosen size, while introducing a specific sensing selectivity. The proposed method allows us to tune the nanopore biosensor adapting it to the specific final application, and it can be efficiently applied when the pore initial diameter does not exceed a limit dimension related to the mean free path of the silane molecules at the working pressure.
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Affiliation(s)
- Valentina Mussi
- Nanomed Labs, Physics Department, University of Genova, Via Dodecaneso, 33 Genova, I-16146, Italy.
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Rai V, Hapuarachchi HC, Ng LC, Soh SH, Leo YS, Toh CS. Ultrasensitive cDNA detection of dengue virus RNA using electrochemical nanoporous membrane-based biosensor. PLoS One 2012; 7:e42346. [PMID: 22927927 PMCID: PMC3426509 DOI: 10.1371/journal.pone.0042346] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 07/03/2012] [Indexed: 11/21/2022] Open
Abstract
A nanoporous alumina membrane-based ultrasensitive DNA biosensor is constructed using 5′-aminated DNA probes immobilized onto the alumina channel walls. Alumina nanoporous membrane-like structure is carved over platinum wire electrode of 76 µm diameter dimension by electrochemical anodization. The hybridization of complementary target DNA with probe DNA molecules attached inside the pores influences the pore size and ionic conductivity. The biosensor demonstrates linear range over 6 order of magnitude with ultrasensitive detection limit of 9.55×10−12 M for the quantification of ss-31 mer DNA sequence. Its applicability is challenged against real time cDNA PCR sample of dengue virus serotype1 derived from asymmetric PCR. Excellent specificity down to one nucleotide mismatch in target DNA sample of DENV3 is also demonstrated.
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Affiliation(s)
- Varun Rai
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Lee Ching Ng
- Environmental Health Institute, National Environmental Agency, Singapore, Singapore
| | - Siew Hwa Soh
- Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Yee Sin Leo
- Communicable Disease Centre, Tan Tock Seng Hospital, Singapore, Singapore
| | - Chee-Seng Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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Rai V, Deng J, Toh CS. Electrochemical nanoporous alumina membrane-based label-free DNA biosensor for the detection of Legionella sp. Talanta 2012; 98:112-7. [DOI: 10.1016/j.talanta.2012.06.055] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 06/22/2012] [Accepted: 06/22/2012] [Indexed: 11/26/2022]
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