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Papers by Chiara Manneschi

Research paper thumbnail of Micro and nanofluidic platforms for advanced diagnostics

ABSTRACT AbstrAct Aims: sensitivity, selectivity and tunability are keywords to develop effective... more ABSTRACT AbstrAct Aims: sensitivity, selectivity and tunability 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

Research paper thumbnail of Modulating DNA Translocation by a Controlled Deformation of a PDMS Nanochannel Device

Scientific Reports, 2012

Several strategies have been developed for the control of DNA translocation in nanopores and nano... more 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. SUBJECT AREAS: NANOBIOTECHNOLOGY NANOFLUIDICS BIOPHYSICS APPLIED PHYSICS

Research paper thumbnail of Stretching of DNA confined in nanochannels with charged walls

Research paper thumbnail of Mechanical squeezing of an elastomeric nanochannel device: numerical simulations and ionic current characterization

Microfluidics and Nanofluidics, 2013

ABSTRACT Peculiar transport phenomena appear at nanoscale, since surface effects strongly affect ... more ABSTRACT Peculiar transport phenomena appear at nanoscale, since surface effects strongly affect the behaviour of fluids. Electrostatic and steric interactions, capillary forces and entropic effects play a key role in the behaviour of fluids and biomolecules. Since these effects strongly depend on the size of the nanofluidic system, a careful characterization of the fluidic environment is necessary. Moreover, the possibility to dynamically modulate the size of nanochannels is very appealing in the field of biomolecule manipulation. Recently, we have developed a lab-on-chip made of poly(dimethylsiloxane) (PDMS). This polymeric device is based on a tuneable nanochannel able to dynamically change its dimension in order to fit the application of interest. In fact, a mechanical compression applied on the top of the elastomeric device squeezes the nanochannel, reducing the channel cross section and allowing a dynamical optimization of the nanostructures. In this paper, this squeezing process is fully characterized both numerically and experimentally. This analysis provides information on the reduction of the nanochannel dimensions induced by compression as a function of the work of adhesion and of the stiffness of the materials composing the device. Moreover, calculations demonstrate the possibility to predict the change of the nanochannel size and shape induced by the compression. The possibility to dynamically tune the channel size opens up new opportunities in biomolecular sensing or sieving and in the study of new hydrodynamics effects.

Research paper thumbnail of Conformations of DNA in Triangular Nanochannels

Macromolecules, 2013

Despite the widespread use of triangular nanochannels for the manipulation and analysis of DNA, s... more Despite the widespread use of triangular nanochannels for the manipulation and analysis of DNA, studies on the confining effects induced by these nanofluidic structures on the molecules are still absent. Here, we perform coarse-grained Monte Carlo simulations to study the conformations of DNA in nanochannels. The influence of the shape of the nanochannel cross section is examined by comparing the elongation of molecules in triangular, rectangular, and square channels. Furthermore, the conformation of λ-DNA under weak confinement is studied both computationally and experimentally. Good agreement between optical measurements and simulations supports the reliability of the numerical model in predicting the molecule conformation, making it a reliable method to obtain information essential in many applications, such as DNA barcoding.

Research paper thumbnail of Modulating DNA Translocation by a Controlled Deformation of a PDMS Nanochannel Device

Scientific Reports, 2012

Several strategies have been developed for the control of DNA translocation in nanopores and nano... more 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. SUBJECT AREAS: NANOBIOTECHNOLOGY NANOFLUIDICS BIOPHYSICS APPLIED PHYSICS

Research paper thumbnail of DNA detection with a polymeric nanochannel device

Lab on a Chip, 2011

We present the development and the electrical characterization of a polymeric nanochannel device.... more We present the development and the electrical characterization of a polymeric nanochannel device. Standard microfabrication coupled to Focused Ion Beam (FIB) nanofabrication is used to fabricate a silicon master, which can be then replicated in a polymeric material by soft lithography. Such an elastomeric nanochannel device is used to study DNA translocation events during electrophoresis experiments. Our results demonstrate that an easy and low cost fabrication technique allows creation of a low noise device for single molecule analysis.

Research paper thumbnail of Micro and nanofluidic platforms for advanced diagnostics

Aims: sensitivity, selectivity and tunability are keywords to develop effective and reliable diag... more Aims: sensitivity, selectivity and tunability 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.

Research paper thumbnail of Mechanical squeezing of an elastomeric nanochannel device: numerical simulations and ionic current characterization

Microfluidics and Nanofluidics, 2013

ABSTRACT Peculiar transport phenomena appear at nanoscale, since surface effects strongly affect ... more ABSTRACT Peculiar transport phenomena appear at nanoscale, since surface effects strongly affect the behaviour of fluids. Electrostatic and steric interactions, capillary forces and entropic effects play a key role in the behaviour of fluids and biomolecules. Since these effects strongly depend on the size of the nanofluidic system, a careful characterization of the fluidic environment is necessary. Moreover, the possibility to dynamically modulate the size of nanochannels is very appealing in the field of biomolecule manipulation. Recently, we have developed a lab-on-chip made of poly(dimethylsiloxane) (PDMS). This polymeric device is based on a tuneable nanochannel able to dynamically change its dimension in order to fit the application of interest. In fact, a mechanical compression applied on the top of the elastomeric device squeezes the nanochannel, reducing the channel cross section and allowing a dynamical optimization of the nanostructures. In this paper, this squeezing process is fully characterized both numerically and experimentally. This analysis provides information on the reduction of the nanochannel dimensions induced by compression as a function of the work of adhesion and of the stiffness of the materials composing the device. Moreover, calculations demonstrate the possibility to predict the change of the nanochannel size and shape induced by the compression. The possibility to dynamically tune the channel size opens up new opportunities in biomolecular sensing or sieving and in the study of new hydrodynamics effects.

Research paper thumbnail of DNA manipulation with elastomeric nanostructures fabricated by soft-moulding of a FIB-patterned stamp

Lab on a Chip, 2011

A Focused Ion Beam (FIB)-patterned silicon mould is used to fabricate elastomeric nanostructures,... more A Focused Ion Beam (FIB)-patterned silicon mould is used to fabricate elastomeric nanostructures, whose cross-section can be dynamically and reversibly tuned by applying a controlled mechanical stress. Direct-write, based on FIB milling, allows the fabrication of nanostructures with a variety of different geometries, aspect ratio, spacing and distribution offering a higher flexibility compared to other nanopatterning approaches. Moreover, a simple double replication process based on poly(dimethylsiloxane) permits a strong reduction of the fabrication costs that makes this approach well-suited for the production of low cost nanofluidic devices. DNA stretching and single molecule manipulation capabilities of these platforms have been successfully demonstrated.

Research paper thumbnail of Fabrication of elastomeric nanofluidic devices for manipulation of long DNA molecules

We propose a method for the separation of long DNA molecules, based on elastomeric nanochannels w... more We propose a method for the separation of long DNA molecules, based on elastomeric nanochannels with tunable cross section. These nanoconfinement structures can be used to stretch DNA molecules and lower their conformational entropy. The sieving mechanism of entropic recoil, proposed by Cabodi et al. [1], will be implemented using an array of elastomeric nanocheannels. Structures of various dimensions are

Research paper thumbnail of Tunable elastomeric nanochannels for separation and manipulation of long DNA molecules

Nanofluidic structures, such as nanochannels have been successfully used to confine and stretch D... more Nanofluidic structures, such as nanochannels have been successfully used to confine and stretch DNA molecules, offering the opportunity of investigating on their conformational changes. Moreover, the integration of these confinement systems on lab-on-chips has shown a great potential for applications such as biomolecule sieving or single molecule manipulation. Arrays of nanochannels are fabricated on silicon substrates using a focused ion

Research paper thumbnail of Device and single-molecule analysis method by means of detection of the collisions of a target molecule on functionalized nanopores

ABSTRACT The present invention concerns a device and a method of single- molecule analysis by det... more ABSTRACT The present invention concerns a device and a method of single- molecule analysis by detection of a target molecule on functionalized nanopores in such a way that it interacts with the target molecule and has an effective diameter smaller than the dimension of the target molecule.

Research paper thumbnail of DNA detection with a polymeric nanochannel device

Lab on a Chip, 2011

We present the development and the electrical characterization of a polymeric nanochannel device.... more We present the development and the electrical characterization of a polymeric nanochannel device. Standard microfabrication coupled to Focused Ion Beam (FIB) nanofabrication is used to fabricate a silicon master, which can be then replicated in a polymeric material by soft lithography. Such an elastomeric nanochannel device is used to study DNA translocation events during electrophoresis experiments. Our results demonstrate that an easy and low cost fabrication technique allows creation of a low noise device for single molecule analysis.

Research paper thumbnail of Micro and nanofluidic platforms for advanced diagnostics

ABSTRACT AbstrAct Aims: sensitivity, selectivity and tunability are keywords to develop effective... more ABSTRACT AbstrAct Aims: sensitivity, selectivity and tunability 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

Research paper thumbnail of Modulating DNA Translocation by a Controlled Deformation of a PDMS Nanochannel Device

Scientific Reports, 2012

Several strategies have been developed for the control of DNA translocation in nanopores and nano... more 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. SUBJECT AREAS: NANOBIOTECHNOLOGY NANOFLUIDICS BIOPHYSICS APPLIED PHYSICS

Research paper thumbnail of Stretching of DNA confined in nanochannels with charged walls

Research paper thumbnail of Mechanical squeezing of an elastomeric nanochannel device: numerical simulations and ionic current characterization

Microfluidics and Nanofluidics, 2013

ABSTRACT Peculiar transport phenomena appear at nanoscale, since surface effects strongly affect ... more ABSTRACT Peculiar transport phenomena appear at nanoscale, since surface effects strongly affect the behaviour of fluids. Electrostatic and steric interactions, capillary forces and entropic effects play a key role in the behaviour of fluids and biomolecules. Since these effects strongly depend on the size of the nanofluidic system, a careful characterization of the fluidic environment is necessary. Moreover, the possibility to dynamically modulate the size of nanochannels is very appealing in the field of biomolecule manipulation. Recently, we have developed a lab-on-chip made of poly(dimethylsiloxane) (PDMS). This polymeric device is based on a tuneable nanochannel able to dynamically change its dimension in order to fit the application of interest. In fact, a mechanical compression applied on the top of the elastomeric device squeezes the nanochannel, reducing the channel cross section and allowing a dynamical optimization of the nanostructures. In this paper, this squeezing process is fully characterized both numerically and experimentally. This analysis provides information on the reduction of the nanochannel dimensions induced by compression as a function of the work of adhesion and of the stiffness of the materials composing the device. Moreover, calculations demonstrate the possibility to predict the change of the nanochannel size and shape induced by the compression. The possibility to dynamically tune the channel size opens up new opportunities in biomolecular sensing or sieving and in the study of new hydrodynamics effects.

Research paper thumbnail of Conformations of DNA in Triangular Nanochannels

Macromolecules, 2013

Despite the widespread use of triangular nanochannels for the manipulation and analysis of DNA, s... more Despite the widespread use of triangular nanochannels for the manipulation and analysis of DNA, studies on the confining effects induced by these nanofluidic structures on the molecules are still absent. Here, we perform coarse-grained Monte Carlo simulations to study the conformations of DNA in nanochannels. The influence of the shape of the nanochannel cross section is examined by comparing the elongation of molecules in triangular, rectangular, and square channels. Furthermore, the conformation of λ-DNA under weak confinement is studied both computationally and experimentally. Good agreement between optical measurements and simulations supports the reliability of the numerical model in predicting the molecule conformation, making it a reliable method to obtain information essential in many applications, such as DNA barcoding.

Research paper thumbnail of Modulating DNA Translocation by a Controlled Deformation of a PDMS Nanochannel Device

Scientific Reports, 2012

Several strategies have been developed for the control of DNA translocation in nanopores and nano... more 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. SUBJECT AREAS: NANOBIOTECHNOLOGY NANOFLUIDICS BIOPHYSICS APPLIED PHYSICS

Research paper thumbnail of DNA detection with a polymeric nanochannel device

Lab on a Chip, 2011

We present the development and the electrical characterization of a polymeric nanochannel device.... more We present the development and the electrical characterization of a polymeric nanochannel device. Standard microfabrication coupled to Focused Ion Beam (FIB) nanofabrication is used to fabricate a silicon master, which can be then replicated in a polymeric material by soft lithography. Such an elastomeric nanochannel device is used to study DNA translocation events during electrophoresis experiments. Our results demonstrate that an easy and low cost fabrication technique allows creation of a low noise device for single molecule analysis.

Research paper thumbnail of Micro and nanofluidic platforms for advanced diagnostics

Aims: sensitivity, selectivity and tunability are keywords to develop effective and reliable diag... more Aims: sensitivity, selectivity and tunability 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.

Research paper thumbnail of Mechanical squeezing of an elastomeric nanochannel device: numerical simulations and ionic current characterization

Microfluidics and Nanofluidics, 2013

ABSTRACT Peculiar transport phenomena appear at nanoscale, since surface effects strongly affect ... more ABSTRACT Peculiar transport phenomena appear at nanoscale, since surface effects strongly affect the behaviour of fluids. Electrostatic and steric interactions, capillary forces and entropic effects play a key role in the behaviour of fluids and biomolecules. Since these effects strongly depend on the size of the nanofluidic system, a careful characterization of the fluidic environment is necessary. Moreover, the possibility to dynamically modulate the size of nanochannels is very appealing in the field of biomolecule manipulation. Recently, we have developed a lab-on-chip made of poly(dimethylsiloxane) (PDMS). This polymeric device is based on a tuneable nanochannel able to dynamically change its dimension in order to fit the application of interest. In fact, a mechanical compression applied on the top of the elastomeric device squeezes the nanochannel, reducing the channel cross section and allowing a dynamical optimization of the nanostructures. In this paper, this squeezing process is fully characterized both numerically and experimentally. This analysis provides information on the reduction of the nanochannel dimensions induced by compression as a function of the work of adhesion and of the stiffness of the materials composing the device. Moreover, calculations demonstrate the possibility to predict the change of the nanochannel size and shape induced by the compression. The possibility to dynamically tune the channel size opens up new opportunities in biomolecular sensing or sieving and in the study of new hydrodynamics effects.

Research paper thumbnail of DNA manipulation with elastomeric nanostructures fabricated by soft-moulding of a FIB-patterned stamp

Lab on a Chip, 2011

A Focused Ion Beam (FIB)-patterned silicon mould is used to fabricate elastomeric nanostructures,... more A Focused Ion Beam (FIB)-patterned silicon mould is used to fabricate elastomeric nanostructures, whose cross-section can be dynamically and reversibly tuned by applying a controlled mechanical stress. Direct-write, based on FIB milling, allows the fabrication of nanostructures with a variety of different geometries, aspect ratio, spacing and distribution offering a higher flexibility compared to other nanopatterning approaches. Moreover, a simple double replication process based on poly(dimethylsiloxane) permits a strong reduction of the fabrication costs that makes this approach well-suited for the production of low cost nanofluidic devices. DNA stretching and single molecule manipulation capabilities of these platforms have been successfully demonstrated.

Research paper thumbnail of Fabrication of elastomeric nanofluidic devices for manipulation of long DNA molecules

We propose a method for the separation of long DNA molecules, based on elastomeric nanochannels w... more We propose a method for the separation of long DNA molecules, based on elastomeric nanochannels with tunable cross section. These nanoconfinement structures can be used to stretch DNA molecules and lower their conformational entropy. The sieving mechanism of entropic recoil, proposed by Cabodi et al. [1], will be implemented using an array of elastomeric nanocheannels. Structures of various dimensions are

Research paper thumbnail of Tunable elastomeric nanochannels for separation and manipulation of long DNA molecules

Nanofluidic structures, such as nanochannels have been successfully used to confine and stretch D... more Nanofluidic structures, such as nanochannels have been successfully used to confine and stretch DNA molecules, offering the opportunity of investigating on their conformational changes. Moreover, the integration of these confinement systems on lab-on-chips has shown a great potential for applications such as biomolecule sieving or single molecule manipulation. Arrays of nanochannels are fabricated on silicon substrates using a focused ion

Research paper thumbnail of Device and single-molecule analysis method by means of detection of the collisions of a target molecule on functionalized nanopores

ABSTRACT The present invention concerns a device and a method of single- molecule analysis by det... more ABSTRACT The present invention concerns a device and a method of single- molecule analysis by detection of a target molecule on functionalized nanopores in such a way that it interacts with the target molecule and has an effective diameter smaller than the dimension of the target molecule.

Research paper thumbnail of DNA detection with a polymeric nanochannel device

Lab on a Chip, 2011

We present the development and the electrical characterization of a polymeric nanochannel device.... more We present the development and the electrical characterization of a polymeric nanochannel device. Standard microfabrication coupled to Focused Ion Beam (FIB) nanofabrication is used to fabricate a silicon master, which can be then replicated in a polymeric material by soft lithography. Such an elastomeric nanochannel device is used to study DNA translocation events during electrophoresis experiments. Our results demonstrate that an easy and low cost fabrication technique allows creation of a low noise device for single molecule analysis.