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Kudr J, Skalickova S, Nejdl L, Moulick A, Ruttkay-Nedecky B, Adam V, Kizek R. Fabrication of solid-state nanopores and its perspectives. Electrophoresis 2015; 36:2367-79. [DOI: 10.1002/elps.201400612] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 05/13/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Jiri Kudr
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Sylvie Skalickova
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Lukas Nejdl
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Amitava Moulick
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Branislav Ruttkay-Nedecky
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Vojtech Adam
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
| | - Rene Kizek
- Department of Chemistry and Biochemistry, Faculty of Agronomy; Mendel University in Brno; Brno Czech Republic
- Central European Institute of Technology; Brno University of Technology; Brno Czech Republic
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Marshall MM, Ruzicka J, Zahid OK, Henrich VC, Taylor EW, Hall AR. Nanopore Analysis of Single-Stranded Binding Protein Interactions with DNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:4582-4588. [PMID: 25839962 DOI: 10.1021/acs.langmuir.5b00457] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We study the binding of E. coli single-stranded binding protein (SSB) to single-stranded DNA (ssDNA) using a solid-state nanopore assay. We find that saturated nucleoprotein complexes can be distinguished easily from free SSB, ssDNA, or double-stranded DNA individually and demonstrate that the high affinity of SSB for ssDNA can be exploited to achieve high-fidelity differentiation from duplex molecules in a mixture. We then study nucleoprotein filament formation by systematically varying the amount of SSB relative to ssDNA. We observe a concomitant shift in the mean amplitude of electrical events that is consistent with weakly cooperative binding. Finally, we compare circular and linearized ssDNA saturated with SSB and use the results to infer structural details of the nucleoprotein complex.
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Affiliation(s)
- Michael M Marshall
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Jan Ruzicka
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Osama K Zahid
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Vincent C Henrich
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Ethan W Taylor
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
| | - Adam R Hall
- †Joint School of Nanoscience and Nanoengineering and ‡Center for Biotechnology, Genomics, and Health Research, University of North Carolina at Greensboro, Greensboro, North Carolina 27401, United States
- §Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and ∥Comprehensive Cancer Center, Wake Forest University School of Medicine, Winston-Salem, North Carolina 27101, United States
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