Fixed DNA Molecule Arrays for High-Throughput Single DNA-Protein Interaction Studies.

The DNA Curtains assay is a recently developed experimental platform for protein-DNA interaction studies at the single-molecule level that is based on anchoring and alignment of DNA fragments. The DNA Curtains so far have been made by using chromium barriers and fluid lipid bilayer membranes, which makes such a specialized assay technically challenging and relatively unstable. Herein, we report on an alternative strategy for DNA arraying for analysis of individual DNA-protein interactions. It relies on stable DNA tethering onto nanopatterned protein templates via high affinity molecular recognition. We describe fabrication of streptavidin templates (line features as narrow as 200 nm) onto modified glass coverslips by combining surface chemistry, atomic force microscopy (AFM), and soft lithography techniques with affinity-driven assembly. We have employed such chips for arraying single- and double-tethered DNA strands, and we characterized the obtained molecular architecture: we evaluated the structural characteristics and specific versus nonspecific binding of fluorescence-labeled DNA using AFM and total internal reflection fluorescence microscopy. We demonstrate the feasibility of our DNA molecule arrays for short single-tethered as well as for lambda single- and double-tethered DNA. The latter type of arrays proved very suitable for localization of single DNA-protein interactions employing restriction endonucleases. The presented molecular architecture and facile method of fabrication of our nanoscale platform does not require clean room equipment, and it offers advanced functional studies of DNA machineries and the development of future nanodevices.

Single-molecule microscopy studies of LHCII enriched in Vio or Zea.

Plants have developed multiple self-regulatory mechanisms to efficiently function under varying sunlight conditions. At high light intensities, non-photochemical quenching (NPQ) is activated on a molecular level, safely dissipating an excess excitation as heat. The exact molecular mechanism for NPQ is still under debate, but it is widely agreed that the direct participation of the carotenoid pigments is involved, one of the proposed candidate being the zeaxanthin. In this work, we performed fluorescence measurements of violaxanthin- and zeaxanthin-enriched major light-harvesting complexes (LHCII), in ensemble and at the single pigment-protein complex level, where aggregation is prevented by immobilization of LHCIIs onto a surface. We show that a selective enrichment of LHCII with violaxanthin or zeaxanthin affects neither the ability of LHCII to switch into a dissipative conformation nor the maximal level of induced quenching. However, the kinetics of the fluorescence decrease due to aggregation on the timescale of seconds are different, prompting towards a modulatory effect of zeaxanthin in the dynamics of quenching.