Solid-state nanopores: a new platform for DNA biomarker discovery

UNCG Author/Contributor (non-UNCG co-authors, if there are any, appear on document)
Michael M. Marshall (Creator)
The University of North Carolina at Greensboro (UNCG )
Web Site:
Marinella Sandros

Abstract: Solid-state (SS) nanopores emerged as a molecular detection platform in 2001, offering many advantages over their biological counterparts, α-hemolysin nanopores (α-HL). These advantages include better chemical, electrical, mechanical, and thermal stability, as well as size tunability and device integration. In addition, the size of α-HL restricts its application to translocations of single-stranded polynucleotides (ssDNA and ssRNA). This research project focused on developing a SS-nanopore platform for biomarker detection, based on differentiating ssDNA and double-stranded DNA (dsDNA) at the single-molecule scale. Reported dsDNA translocation measurements result in an average residence time of ~ 30 ns/bp, so the temporal resolution required for detection of small DNA duplexes can exceed available bandwidth limitations. To address this issue, several system parameters were explored in order to slow down translocation speed, thereby increasing temporal resolution and signal-to-noise ratio. These parameters included: applied voltage, pH, pore geometry, DNA binding agents, salt composition and concentration, and temperature. Experimental findings showed that SS-nanopores can be precisely fabricated using a controlled helium ion milling technique, acidic conditions cause DNA depurination that results in slower translocation durations, and single-stranded binding proteins (SSBs) bind preferentially to ssDNA, forming complexes with distinct translocation characteristics that permit large (> 7 kb) ds- and ssDNA to be effectively distinguished. Together, these data show that SS-nanopores can serve as a tool to electronically detect the presence and relative concentration of target DNA molecules with ultrahigh sensitivity, thus demonstrating their potential utility as a biomarker discovery platform in both biomedical and environmental applications.

Additional Information

Language: English
Date: 2014
Biomarker, DNA, Nanopore, Solid-state, Translocation
Particle size determination
Biochemical markers
DNA $x Analysis

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