Two color DNA barcode detection in photoluminescence suppressed silicon nitride nanopores.

Optical sensing of solid-state nanopores is a relatively new approach that can enable high-throughput, multicolor readout from a collection of nanopores. It is therefore highly attractive for applications such as nanopore-based DNA sequencing and genotyping using DNA barcodes. However, to date optical readout has been plagued by the need to achieve sufficiently high signal-to-noise ratio (SNR) for single fluorophore sensing, while still maintaining millisecond resolution.

Optoelectronic control of surface charge and translocation dynamics in solid-state nanopores.

Nanopores can be used to detect and analyse biomolecules. However, controlling the translocation speed of molecules through a pore is difficult, which limits the wider application of these sensors. Here, we show that low-power visible light can be used to control surface charge in solid-state nanopores and can influence the translocation dynamics of DNA and proteins.

The Effect of dye-dye interactions on the spatial resolution of single-molecule FRET measurements in nucleic acids.

We study the effect of dye-dye interactions in labeled double-stranded DNA molecules on the Förster resonance energy transfer (FRET) efficiency at the single-molecule level. An extensive analysis of internally labeled double-stranded DNA molecules in bulk and at the single-molecule level reveals that donor-acceptor absolute distances can be reliably extracted down to approximately 3-nm separation, provided that dye-dye quenching is accounted for. At these short separations, we find significant long-lived fluorescence fluctuations among discrete levels originating from the simultaneous and synchronous quenching of both dyes.

Automated system for single molecule fluorescence measurements of surface-immobilized biomolecules.

Fluorescence Resonance Energy Transfer (FRET) microscopy has been widely used to study the structure and dynamics of molecules of biological interest, such as nucleic acids and proteins. Single molecule FRET (sm-FRET) measurements on immobilized molecules permit long observations of the system -effectively until both dyes photobleach- resulting in time-traces that report on biomolecular dynamics with a broad range of timescales from milliseconds to minutes. To facilitate the acquisition of large number of traces for statistical analyses, the process must be automated and the sample environment should be tightly controlled over the entire measurement time (approximately 12 hours).

Modeling solid-state effects on NMR chemical shifts using electrostatic models.

This paper presents a comparison of the embedded ion method (EIM) and the surface charge representation of the electrostatic embedding potential (SCREEP) method, two methods which can be used to calculate solid-state effects on NMR chemical shifts. The results in a selected group of compounds with known single-crystal solid-state NMR data and neutron diffraction structures, confirm that these effects are important in both (13)C and (15)N chemical shifts. The solid-state effects calculated by both methods are similar and of equal statistical quality when compared with the experimental data.