A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm wide nanopore reveals a strong bias favoring the capture of molecules near their ends. A theoretical model shows that bias to be a consequence of configurational entropy, rather than a search by the polymer for an energetically favorable configuration. We also quantified the fluctuations and length-dependence of the speed of simultaneously translocating polymer segments from our study of folded DNA configurations.

Abstract-We report on our progress towards an Ocean Appliance -envisioned as a complete, pre-built "server-in-abox" equipped with an ocean observation database, a forecast engine, a web server publishing an extensible web interface, a suite of web services establishing interoperability, and a library of data ingest and processing functions. Collectively, these services allow efficient ingest, organization, analysis, and distribution of observations and model results with minimal onsite configuration. By packaging the hardware as well as the software, the effort required to install and adapt the tools to the environment of the local data provider is minimized, streamlining the adoption of interoperability standards and simplifying environmental data management. We report results from a pilot project using the appliance to support cruise operations and describe preparations for an upcoming multi-ship experiment involving real-time telemetry and coordinated, simultaneous analysis of forecasts and observations.

BtuB is a TonB-dependent outer membrane transporter of vitamin B12 in E. coli. In this work, we investigated the interaction between BtuB and the inner membrane protein TonB using site-directed spin labeling (SDSL). In CHAPS/ POPC mixed micelles, the Ton box of BtuB undergoes an order-to-disorder transition upon addition of vitamin B12 which appears to be identical to that seen in POPC bilayers. Under these conditions, addition of a C-terminal fragment of TonB broadens the EPR lineshapes, indicating that there is an ordering of the Ton box and an interaction between the transporter Ton box and this C-terminal fragment. Residues N-terminal to the Ton box do not appear to interact with TonB. These changes appear to be independent of the addition of the substrate, vitamin B12. The EPR data obtained are generally consistent with the crystal structure that has been obtained for this complex (Shultis et al. Science 312, (2006)); however, preliminary distance measurements using DEER indicate that there may be multiple states of TonB when it is bound to BtuB. Spin labels incorporated into TonB also become ordered upon interaction with BtuB, and the EPR lineshapes indicate that there is a decrease in backbone dynamics of TonB upon association with BtuB. An EPR based equilibrium binding assay was carried out to determine the affinity between this C-terminal TonB fragment and BtuB, and was performed using either labels on BtuB or labels on TonB. Both labels indicate that there is an affinity of approximately 50 mM between BtuB and TonB, which is, unexpectedly, independent of substrate addition.