Chiara Manneschi

Modulating DNA Translocation by a Controlled Deformation of a PDMS Nanochannel Device

Several strategies have been developed for the control of DNA translocation in nanopores and nanochannels. However, the possibility to reduce the molecule speed is still challenging for applications in the field of single molecule analysis, such as ultra-rapid sequencing. This paper demonstrates the possibility to alter the DNA translocation process through an elastomeric nanochannel device by dynamically changing its cross section. More in detail, nanochannel deformation is induced by a macroscopic mechanical compression of the polymeric device. This nanochannel squeezing allows slowing down the DNA molecule passage inside it. This simple and low cost method is based on the exploitation of the elastomeric nature of the device, can be coupled with different sensing techniques, is applicable in many research fields, such as DNA detection and manipulation, and is promising for further development in sequencing technology.

Stretching of DNA confined in nanochannels with charged walls

There is currently a growing interest in control of stretching of DNA inside nanoconfined regions due to the possibility to analyze and manipulate single biomolecules for applications such as DNA mapping and barcoding, which are based on stretching the DNA in a linear fashion. In the present work, we couple Finite Element Methods and Monte Carlo simulations in order to study the conformation of DNA molecules confined in nanofluidic channels with neutral and charged walls. We find that the electrostatic forces become more and more important when lowering the ionic strength of the solution. The influence of the nanochannel cross section geometry is also studied by evaluating the DNA elongation in square, rectangular, and triangular channels. We demonstrate that coupling electrostatically interacting walls with a triangular geometry is an efficient way to stretch DNA molecules at the scale of hundreds of nanometers. The paper reports experimental observations of λ-DNA molecules in poly(dimethylsiloxane) nanochannels filled with solutions of different ionic strength. The results are in good agreement with the theoretical predictions, confirming the crucial role of the electrostatic repulsion of the constraining walls on the molecule stretching.

Micro and nanofluidic platforms for advanced diagnostics

Aims: Sensitivity, selectivity and tenability are keywords to develop effective and reliable diagnostic and bioanalytical tools. In this context, micro and nanofluidic devices constitute a powerful and versatile answer to the growing and urgent demand for innovative solutions. Nevertheless, a precise control of size and functionality of such structures is necessary for ensuring advanced manipulation and sensing capabilities, up to single molecule level. Methods: We report here on different strategies for the development of micro and nanofluidic platforms for advanced diagnostics based on the exploitation of the elastic properties of deformable materials, and on surface chemical functionalization processes. Results: We demonstrated that applying a macroscopic mechanical compression to elastomeric nanostructures it is possible to increase their confining power and vary the dynamics of DNA translocation process, while the use of the chemical functionalization allows to tune both the size and the functionality of the biosensor. Conclusion: We believe that a smart integration of these two approaches would allow a significant step forward for the fabrication of next-generation lab-on-chip devices for biomedical diagnostic applications.