A nanofluidic device for single molecule studies with in situ control of environmental solution conditions

Abstract

We report an approach to study the in-situ conformational response of single biomolecules such as DNA to a change in environmental solution conditions. These conditions are, for instance, the composition of the buffer or the presence of protein. For this purpose, we designed and fabricated a nanofluidic device featuring two arrays of parallel nanochannels in a perpendicular configuration. The cross-sections of the channels are rectangular with a diameter down to 175 nm. The lab-on-chip devices were made of polydimethylsiloxane (PDMS) cast on a high quality master stamp, obtained by proton beam writing and UV lithography. Biomolecules can be inserted into the device through the array of channels in one direction, whereas the buffer can be exchanged through the intersecting array of channels in the other direction. A buffer exchange time inside the grid of nanochannels of less than one second is measured by monitoring the conductivity of solutions of salt. The exchange time of protein is typically a few seconds, as determined by imaging of the influx of fluorescence labelled protamine. We demonstrate the functionality of the device by investigating the compaction of DNA by protamine and unpacking of pre-compacted DNA through an increase in concentration of salt.

Nanoconfined Circular and Linear DNA: Equilibrium Conformations and Unfolding Kinetics

“…Comparing Eqs. (12) and (14) yields a ratio of extensions in the interval R lin /R circ = 1.92 -2 at D = l p , approaching 2 as D tends to zero. Comparing instead Eqs.…”

“…Recently, several groups have used nanofluidic channels to investigate the physical properties of nanoconfined DNA-protein complexes [12][13][14][15][16] and for optical mapping of single DNA molecules [17][18][19][20][21] .…”

Single Particle Nanoplasmonic Sensing in Individual Nanofluidic Channels

“…This highlights the importance of the new information that can be obtained by our sensing concept inside nanochannels because as, our measurements show, predicting accurately the resulting local concentrations is nearly impossible even in the case of our relatively simple device with straight channels. In more complex fluidic systems comprising crossings or constrictions, 42 concentration distributions of reagents will be even more complicated to predict. Thus, in such systems integrated local plasmonic readout can constitute a powerful tool for measuring and verifying targeted specific conditions in situ, to derive correct correlations between (bio)molecule properties and local environment.…”

Superhydrophobic Devices Molecular Detection

“…Microfabrication techniques are largely contributing to design and fabricate nano-and micropatterned devices for singlemolecule manipulation, probing, and sensing. For instance, nanopores [9], nanochannels [10][11][12], nanomechanical sensors [13], nanoantennas [14,15], and more generally laboratory-on-chips [16,17] are the ultimate developments of micronanotechnology aimed at single-molecule detection. In this paper, we describe how our micro-and nanofabricated superhydrophobic surfaces can be used to concentrate and vehiculate to specific detection points the analyte to achieve single-molecule detection with a high signal-to-noise ratio, allowing X-ray diffraction, Raman spectroscopy, and electron microscopy characterizations.…”