Solid-state nanopore has been widely studied as an effective tool to detect and analyze small biomolecules, such as DNA, RNA, and proteins, at a single molecule level. In this study, we demonstrate a rapid identification of the location of zinc finger protein (ZFP), which is bound to a specific locus along the length of a double-stranded DNA (dsDNA) to a single protein resolution using a low noise solid-state nanopore. When ZFP labeled DNAs were driven through a nanopore by an externally applied electric field, characteristic ionic current signals arising from the passage of the DNA/ZFP complex and bare DNA were detected, which enabled us to identify the locations of ZFP binding site. We examined two DNAs with ZFP binding sites at different positions and found that the location of the additional current drop derived from the DNA/ZFP complex is well-matched with a theoretical one along the length of the DNA molecule. These results suggest that the protein binding site on DNA can be mapped or that genetic information can be read at a single molecule level using solid-state nanopores.

No abstract

K. pneumoniae is an opportunistic pathogen that causes nosocomial infections, such as, pneumonia, urinary tract infections, septic shock, and gastro intestinal disease. Lipopolysaccharide (LPS), capsular polysaccharide, and fimbriae are recognized major virulence factors of K. pneumoniae and play key roles during early stages of infections. In this study, we functionalized the surface of gold electrode with mannose and mucin to monitor the adhesion-associated virulence factors of K. pneumoniae. The binding characteristics of K. pneumoniae 2242 wild type and of its isogenic mutants lacking outer-core LPS (∆wabG) or fimbriae (∆fimA) were investigated using Faradaic impedance spectra. The results obtained showed fimbriae are responsible for K. pneumoniae adhesion to the mannose of glycoprotein on the surfaces of epithelial cells, whereas outer-core LPS and capsular polysaccharide are associated with specific binding to mucous. These results concurred with those of a conventional in vitro assay using human ileocecal epithelial cell (HCT-8 cells) and a human bladder epithelial cell (T-24), indicating that the devised method could be useful for investigating virulence-associated interactions of pathogenic bacteria with specific host cells and organs.

Magnetic separation and purification of MBP-tagged protein using AMB.

The microbiological production of 2,3-butanediol (2,3-BDO) has attracted considerable attention as an alternative way to produce high-value chemicals from renewable sources. Among the number of 2,3-BDO-producing microorganisms, Klebsiella pneumoniae has been studied most extensively and is known to produce large quantity of 2,3-BDO from a range of substrates. On the other hand, the pathogenic characteristics of the bacteria have limited its industrial applications. In this study, two major virulence traits, outer core LPS and fimbriae, were removed through homologous recombination from 2,3-BDO-producing K. pneumoniae 2242 to expand its uses to the industrial scale. The K. pneumoniae 2242 ∆wabG mutant strain was found to have an impaired capsule, which significantly reduced its ability to bind to the mucous layer and evade the phagocytic activity of macrophage. The association with the human ileocecal epithelial cell, HCT-8, and the bladder epithelial cell, T-24, was also reduced dramatically in the K. pneumoniae 2242 ∆fimA mutant strain that was devoid of fimbriae. However, the growth rate and production yield for 2,3-BDO were unaffected. The K. pneumoniae strains developed in this study, which are devoid of the major virulence factors, have a high potential for the efficient and sustainable production of 2,3-BDO.