Nanopore Analysis of Single-Stranded Binding Protein Interactions with DNA.

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.

Detecting DNA depurination with solid-state nanopores.

Among the different types of DNA damage that occur endogenously in the cell, depurination is especially prevalent. These lesions can initiate mutagenesis and have been implicated in a variety of diseases, including cancer. Here, we demonstrate a new approach for the detection of depurination at the single-molecule scale using solid-state nanopores.

Direct and transmission milling of suspended silicon nitride membranes with a focused helium ion beam.

Helium ion milling of suspended silicon nitride thin films is explored. Milled squares patterned by scanning helium ion microscope are subsequently investigated by atomic force microscopy and the relation between ion dose and milling depth is measured for both the direct (side of ion incidence) and transmission (side opposite to ion incidence) regimes. We find that direct-milling depth varies linearly with beam dose while transmission-milling depth varies with the square of the beam dose, resulting in a straightforward method of controlling local film thickness.

Detection of the Dinozoans Pfiesteria piscicida and P. shumwayae: a review of detection methods and geographic distribution.

Molecular methods, including conventional PCR, real-time PCR, denaturing gradient gel electrophoresis, fluorescent fragment detection PCR, and fluorescent in situ hybridization, have all been developed for use in identifying and studying the distribution of the toxic dinoflagellates Pfiesteria piscicida and P. shumwayae. Application of the methods has demonstrated a worldwide distribution of both species and provided insight into their environmental tolerance range and temporal changes in distribution.