Stimulus response of polymer-decorated nanopores/nanochannels is a fascinating topic both in polymer science and modern nanotechnology; however, it is still challenging for standard analytical methods to characterize these switchable nanopores/nanochannels. In this study, based on the physics of polymer translocation we developed an analytic method and thus for the first time were able to quantitatively measure the effective thickness of the polymer layer around the rim of nanopores. As an application example of this method, we studied the translocation dynamics of fluorescence DNA through poly(N-isopropylacrylamide) decorated switchable nanopores in aqueous environments. By adding small amounts of ethanol to the aqueous buffer solution a switch-like response of the DNA-translocation can be observed. It is also observed that a pronounced switching effect can be only realized in a window of moderate grafting densities of poly(N-isopropylacrylamide) layer. These are attributed to the cononsolvency effect which causes a collapse of the polymer layer and thus a transition between "closed" and "open" states of the nanopores for DNA translocation. Our study clearly transpired that cononsolvency effect of polymers can be used as a novel trigger to change the size of nanopores, in analogy to the opening and closure of the gates of cell-membrane channels. We envisage that our study will spawn further developments for the design of switchable nano-gates and nanopores.

Three-stranded R-loop structures have been associated with genomic instability phenotypes. What underlies their wide-ranging effects on genome stability remains poorly understood. Here we combined biochemical and atomic force microscopy approaches with single molecule R-loop footprinting to demonstrate that R-loops formed at the model Airn locus in vitro adopt a defined set of three-dimensional conformations characterized by distinct shapes and volumes, which we call R-loop objects. Interestingly, we show that these R-loop objects impose specific physical constraints on the DNA, as revealed by the presence of stereotypical angles in the surrounding DNA. Biochemical probing and mutagenesis experiments revealed that the formation of R-loop objects at Airn is dictated by the extruded non-template strand, suggesting that R-loops possess intrinsic sequence-driven properties. Consistent with this, we show that R-loops formed at the fission yeast gene sum3 do not form detectable R-loop objects. Our results reveal that R-loops differ by their architectures and that the organization of the non-template strand is a fundamental characteristic of R-loops, which could explain that only a subset of R-loops is associated with replication-dependent DNA breaks.

Nanopores combined with optical approaches can be used to detect viral particles.In this work, we demonstrate the ability of hydrodynamical driving and optical sensing to identify and quantify viral particles in a biological sample. We have developed a simple and rapid method which requires only fluorescent labelling of the particles and can therefore be applied to a wide range of virus type. The system operates in real time and at the single particle level while providing a low error on concentration (4%) and a low limit of detection of 10 5 particles/mL for an acquisition time of 60 seconds, with the ability to increase the acquisition time to achieve a lower limit.