Dan Nicolau | McGill University (original) (raw)

Papers by Dan Nicolau

arXiv (Cornell University), Oct 11, 2018

Biosensors & bioelectronics, Jan 7, 2018

The uniformity of the protein patterns, their shape, and the contrast between the fluorescence si... more The uniformity of the protein patterns, their shape, and the contrast between the fluorescence signal of the pattern and the background, critically modulate the quantitative accuracy of the microarray-derived data. While significant research focused of the identification of the factors that impact the protein microarray patterns, these studies usually have focused on the optimization of one set of these factors, e.g., how the spot uniformity is affected by different additives, or by different surfaces. However, the complex interaction between proteins, carrier fluids, surfaces, and patterning methodologies used would suggest a systematic and more comprehensive study that considers all these parameters, as well as their inter-relationship. The present work compared the patterning of two fluorescently-tagged proteins, i.e., IgG, BSA, on surfaces with different hydrophobicity and chemistry, and printed by inkjet, pin, and microcontact printing (µCP). The quantification of the spot size...

Biomedical Applications of Micro- and Nanoengineering II, 2005

The demand for polymer-based DNA microarrays will increase because of their cost-effectiveness, b... more The demand for polymer-based DNA microarrays will increase because of their cost-effectiveness, biocompatibility and easy processing. However not all polymers are ideal substrates because of different chemical interactions of polymeric substrates with the DNA molecules. Results from AFM analysis of DNA immobilised on polymeric surfaces are evaluated using fractality, Gaussian distribution and lateral force imaging. It has been found that the nanosize defects in the substrate, such as poly-l-lysine, plays an important role in the growth of DNA aggregates in a vertical direction, whereas the covalent binding of DNA molecules on NHS-functionalised cyclo-olefin copolymer leads to the lateral growth of DNA aggregates.

BioMEMS and Smart Nanostructures, 2001

ABSTRACT

Materials Science and Engineering: B, 2006

In a recent trend of micro- and nano-array technologies, polymers are gaining preference over tra... more In a recent trend of micro- and nano-array technologies, polymers are gaining preference over traditional substrates such as glass, silicates, etc. as a model biosurface to immobilize biomolecules. In present paper, we compared model polymeric surfaces such as cyclo olefin copolymer (COC) and polycarbonate (PC), with traditional surfaces such as silicone-wafer and mica. We used a 2D fractal dimension method,

Biosensors and Bioelectronics, 2017

The actin-myosin system, responsible for muscle contraction, is also the force-generating element... more The actin-myosin system, responsible for muscle contraction, is also the force-generating element in dynamic nanodevices operating with surface-immobilized motor proteins. These devices require materials that are amenable to micro-and nano-fabrication, but also preserve the bioactivity of molecular motors. The complexity of the protein-surface systems is greatly amplified by those of the polymer-fluid interface; and of the structure and function of molecular motors, making the study of these interactions critical to the success of molecular motor-based nanodevices. We measured the density of the adsorbed motor protein (heavy meromyosin, HMM) using quartz crystal microbalance; and motor bioactivity with ATPase assay, on a set of model surfaces, i.e., nitrocellulose, polystyrene, poly(methyl methacrylate), and poly(butyl methacrylate), poly(tert-butyl methacrylate). A higher hydrophobicity of the adsorbing material translates in a higher total number of HMM molecules per unit area, but also in a lower uptake of water, and a lower ratio of active per total HMM molecules per unit area. We also measured the motility characteristics of actin filaments on the model surfaces, i.e., velocity, smoothness and deflection of movement, determined via in vitro motility assays. The filament velocities were found to be controlled by the relative number of active HMM per total motors, rather than their absolute surface density. The study allowed the formulation of the general engineering principles for the selection of polymeric materials for the manufacturing of dynamic nanodevices using protein molecular motors.

Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XVII, 2020

SPIE Proceedings, 2005

The understanding and control of cell growth in confined microenvironments has application to a v... more The understanding and control of cell growth in confined microenvironments has application to a variety of fields including cell biosensor development, medical device fabrication, and pathogen control. While the majority of work in these areas has focused on mammalian and bacterial cell growth, this study reports on the growth behavior of fungal cells in three-dimensionally confined PDMS microenvironments of a

SPIE Proceedings, 2002

The absorption of biomolecules on surfaces is a perennial and general problem relevant to fields ... more The absorption of biomolecules on surfaces is a perennial and general problem relevant to fields as different as biomaterials, biosensors, microarrays for proteomics and microfluidics. The 'responsiveness-to-surfaces' character of the proteins augments the difficulty of the general problem of biomolecule adsorption on surfaces. This complexity of protein adsorption generated a large number of contributions over the years, with a rate not showing signs of slowing down. This contribution proposes the use of existent data, as well as data generated in 'programmatic', factorial experiments, to generate scaling relationships regarding protein attachment on polymer surfaces linking protein molecular descriptors, surface descriptors and solution descriptors in a common, quasi-empirical 'engineering' relationships. These relationships can be used for the design of surfaces for proteomics microarrays and microfluidic devices.

Integr. Biol., 2009

Protein molecular motors are natural nano-machines that convert the chemical energy from the hydr... more Protein molecular motors are natural nano-machines that convert the chemical energy from the hydrolysis of adenosine triphosphate into mechanical work. These efficient machines are central to many biological processes, including cellular motion, muscle contraction and cell division. The remarkable energetic efficiency of the protein molecular motors coupled with their nano-scale has prompted an increasing number of studies focusing on their integration in hybrid micro- and nanodevices, in particular using linear molecular motors. The translation of these tentative devices into technologically and economically feasible ones requires an engineering, design-orientated approach based on a structured formalism, preferably mathematical. This contribution reviews the present state of the art in the modelling of protein linear molecular motors, as relevant to the future design-orientated development of hybrid dynamic nanodevices.

Microelectronic Engineering, 2010

Bead-based technologies are an attractive alternative to classical microarrays due to the high su... more Bead-based technologies are an attractive alternative to classical microarrays due to the high surface area of the beads which enables the immobilization of large numbers of probe molecules leading to increased kinetics and improved signal/noise ratios. A simple, versatile and inexpensive method for the fabrication of magnetic bead arrays is presented. The beads are first assembled into silicon pyramidal wells that have been fabricated by established microfabrication techniques and then mounted onto the apex of PDMS pyramids that replicate the silicon substrates by replica moulding. The bead arrays were used to detect oligonucleotide target sequences for the pathogenic avian H5N1 flu virus and results indicated that superior signal/noise ratios could be achieved compared to those from a classical microarray format.

Colloid & Polymer Science, 2003

Adsorption of proteins on solid surfaces has been described as 'a common but very complicated phe... more Adsorption of proteins on solid surfaces has been described as 'a common but very complicated phenomenon' [1]. Complications arise, in part, from geometrical complexity, functional heterogeneity and conformational lability. Systems and processes that fall under the general heading of molecular-scale interactions-e.g. protein folding, growth of biofilms, heterogeneous catalysis, and (bio)chemical separation-respond principally to short-range interactions and steric constraints. In the case of colloidal species in solution, mass transport will respond to electrostatic forces arising from net surface charge densities on the colloid and on its destination surface/interface. The properties of the medium then play important roles, e.g. [2]. The DLVO theory [3] takes account of the diffuse double layer causing action over an intermediate range, as well as the ever-present shortrange van der Waals interaction. Recent theoretical modelling has attempted to relate electrostatic interactions to more detailed models of proteins and their confinement [4, 5, 6]. An all-atom calculation of a macromolecule in aqueous solution interacting with a surface is, as yet, not feasible. Thus, it is common practice to consider the molecule as a simplified structure of interconnected subunits, such as amino acids. The advent of scanning force microscopy (SFM) [7] has provided an important new tool for interrogation of

Biosensors and Bioelectronics, 2004

Biomolecules in a confined solution environment may be subject to electrostatic forces with a ran... more Biomolecules in a confined solution environment may be subject to electrostatic forces with a range up to 100 nm, while van der Waals interaction will account for shorter-range forces. The response of two model poly(amino acids)-poly-l-lysine and poly-l-glutamic acid-has been investigated for a silica/Si-oxide surface at pH 6. The model amino acids were adsorbed, or covalently coupled, to colloidal probes consisting of a microsphere attached to a force-sensing lever. The methodology was based on sensing interaction between the probe and a flat surface through carrying out force versus distance analysis with a scanning force microscope. The results were analyzed within the framework of the conventional DLVO theory. The outcomes illustrate both repulsive and attractive long-range interactions that will hinder, or promote, colloidal biospecies in solution entering the region of attractive short-range interactions at the physical interface. Large 'snap-on' distances were observed for some systems and have been ascribed to compression of the 'soft' functionalized layers. Those observations and measurements of adhesion provided insight into conformation of the adsorbed species and strength of attachment. The results have implications for the efficacy of methods and devices that seek to exploit the properties of micro/nano-fluidic systems.

Biosensors and Bioelectronics, 2004

The immobilisation efficiency of the complexes of oligonucleotide/poly(l-lysine) on two polymeric... more The immobilisation efficiency of the complexes of oligonucleotide/poly(l-lysine) on two polymeric carboxy-rich surfaces, i.e. poly(styrene/ maleic acid) (PSMA) and poly(styrene/maleic anhydride) (PSMAA), has been investigated using X-ray photoelectron spectroscopy, atomic force microscopy (AFM) and fluorescence-based measurements of DNA attachment. A molecularly thin layer of either electrostatically or covalently (via amide bond) bound poly(l-lysine) allows the 'switching' from COOH-based to NH 2-based surface functionality. The results indicate that approximately 54-57% and 55-62% of the applied oligonucleotides bind to polymeric surfaces via the route of electrostatic adsorption of poly(l-lysine) and covalent bonding of poly(l-lysine), respectively. This system can be applied conveniently for the detection of nucleic acids in both disposable and reusable biosensors.

Biosensors and Bioelectronics, 2005

We explored the potential of contractile proteins, actin and myosin, as biosensors of solutions c... more We explored the potential of contractile proteins, actin and myosin, as biosensors of solutions containing mercuric ions. We demonstrate that the reaction of HgCl 2 with myosin rapidly inhibits actin-activated myosin ATPase activity. Mercuric ions inhibit the in vitro analog of contraction, namely the ATP-initiated superprecipitation of the reconstituted actomyosin complex. Hg reduces both the rate and extent of this reaction. Direct observation of the propulsive movement of actin filaments (10 nm in diameter and 1 m long) in a motility assay driven by a proteolytic fragment of myosin (heavy meromyosin or HMM) is also inhibited by mercuric ions. Thus, we have demonstrated the biochemical, biophysical and nanotechnological basis of what may prove to be a useful nano-device.

Society of Photo- …, Dec 1, 2007

SPIE is an international society advancing an interdisciplinary approach to the science and appli... more SPIE is an international society advancing an interdisciplinary approach to the science and application of light. ... Dan V. Nicolau Derek Abbott Kourosh Kalantar-Zadeh Tiziana Di Matteo Sergey M. Bezrukov Editors ... Cosponsored by The Australian National University (Australia) Australian Research Council Nanotechnology Network (Australia) COSNet-ARC Complex Open Systems Research Network (Australia) CUDOS (Australia) RPO (Australia) Bandwidth Foundry (Australia) ... Cooperating Organizations Research School of Physical Sciences and ...

arXiv (Cornell University), Oct 11, 2018

Biosensors & bioelectronics, Jan 7, 2018

The uniformity of the protein patterns, their shape, and the contrast between the fluorescence si... more The uniformity of the protein patterns, their shape, and the contrast between the fluorescence signal of the pattern and the background, critically modulate the quantitative accuracy of the microarray-derived data. While significant research focused of the identification of the factors that impact the protein microarray patterns, these studies usually have focused on the optimization of one set of these factors, e.g., how the spot uniformity is affected by different additives, or by different surfaces. However, the complex interaction between proteins, carrier fluids, surfaces, and patterning methodologies used would suggest a systematic and more comprehensive study that considers all these parameters, as well as their inter-relationship. The present work compared the patterning of two fluorescently-tagged proteins, i.e., IgG, BSA, on surfaces with different hydrophobicity and chemistry, and printed by inkjet, pin, and microcontact printing (µCP). The quantification of the spot size...

Biomedical Applications of Micro- and Nanoengineering II, 2005

The demand for polymer-based DNA microarrays will increase because of their cost-effectiveness, b... more The demand for polymer-based DNA microarrays will increase because of their cost-effectiveness, biocompatibility and easy processing. However not all polymers are ideal substrates because of different chemical interactions of polymeric substrates with the DNA molecules. Results from AFM analysis of DNA immobilised on polymeric surfaces are evaluated using fractality, Gaussian distribution and lateral force imaging. It has been found that the nanosize defects in the substrate, such as poly-l-lysine, plays an important role in the growth of DNA aggregates in a vertical direction, whereas the covalent binding of DNA molecules on NHS-functionalised cyclo-olefin copolymer leads to the lateral growth of DNA aggregates.

BioMEMS and Smart Nanostructures, 2001

ABSTRACT

Materials Science and Engineering: B, 2006

In a recent trend of micro- and nano-array technologies, polymers are gaining preference over tra... more In a recent trend of micro- and nano-array technologies, polymers are gaining preference over traditional substrates such as glass, silicates, etc. as a model biosurface to immobilize biomolecules. In present paper, we compared model polymeric surfaces such as cyclo olefin copolymer (COC) and polycarbonate (PC), with traditional surfaces such as silicone-wafer and mica. We used a 2D fractal dimension method,

Biosensors and Bioelectronics, 2017

The actin-myosin system, responsible for muscle contraction, is also the force-generating element... more The actin-myosin system, responsible for muscle contraction, is also the force-generating element in dynamic nanodevices operating with surface-immobilized motor proteins. These devices require materials that are amenable to micro-and nano-fabrication, but also preserve the bioactivity of molecular motors. The complexity of the protein-surface systems is greatly amplified by those of the polymer-fluid interface; and of the structure and function of molecular motors, making the study of these interactions critical to the success of molecular motor-based nanodevices. We measured the density of the adsorbed motor protein (heavy meromyosin, HMM) using quartz crystal microbalance; and motor bioactivity with ATPase assay, on a set of model surfaces, i.e., nitrocellulose, polystyrene, poly(methyl methacrylate), and poly(butyl methacrylate), poly(tert-butyl methacrylate). A higher hydrophobicity of the adsorbing material translates in a higher total number of HMM molecules per unit area, but also in a lower uptake of water, and a lower ratio of active per total HMM molecules per unit area. We also measured the motility characteristics of actin filaments on the model surfaces, i.e., velocity, smoothness and deflection of movement, determined via in vitro motility assays. The filament velocities were found to be controlled by the relative number of active HMM per total motors, rather than their absolute surface density. The study allowed the formulation of the general engineering principles for the selection of polymeric materials for the manufacturing of dynamic nanodevices using protein molecular motors.

Nanoscale Imaging, Sensing, and Actuation for Biomedical Applications XVII, 2020

SPIE Proceedings, 2005

The understanding and control of cell growth in confined microenvironments has application to a v... more The understanding and control of cell growth in confined microenvironments has application to a variety of fields including cell biosensor development, medical device fabrication, and pathogen control. While the majority of work in these areas has focused on mammalian and bacterial cell growth, this study reports on the growth behavior of fungal cells in three-dimensionally confined PDMS microenvironments of a

SPIE Proceedings, 2002

The absorption of biomolecules on surfaces is a perennial and general problem relevant to fields ... more The absorption of biomolecules on surfaces is a perennial and general problem relevant to fields as different as biomaterials, biosensors, microarrays for proteomics and microfluidics. The 'responsiveness-to-surfaces' character of the proteins augments the difficulty of the general problem of biomolecule adsorption on surfaces. This complexity of protein adsorption generated a large number of contributions over the years, with a rate not showing signs of slowing down. This contribution proposes the use of existent data, as well as data generated in 'programmatic', factorial experiments, to generate scaling relationships regarding protein attachment on polymer surfaces linking protein molecular descriptors, surface descriptors and solution descriptors in a common, quasi-empirical 'engineering' relationships. These relationships can be used for the design of surfaces for proteomics microarrays and microfluidic devices.

Integr. Biol., 2009

Protein molecular motors are natural nano-machines that convert the chemical energy from the hydr... more Protein molecular motors are natural nano-machines that convert the chemical energy from the hydrolysis of adenosine triphosphate into mechanical work. These efficient machines are central to many biological processes, including cellular motion, muscle contraction and cell division. The remarkable energetic efficiency of the protein molecular motors coupled with their nano-scale has prompted an increasing number of studies focusing on their integration in hybrid micro- and nanodevices, in particular using linear molecular motors. The translation of these tentative devices into technologically and economically feasible ones requires an engineering, design-orientated approach based on a structured formalism, preferably mathematical. This contribution reviews the present state of the art in the modelling of protein linear molecular motors, as relevant to the future design-orientated development of hybrid dynamic nanodevices.

Microelectronic Engineering, 2010

Bead-based technologies are an attractive alternative to classical microarrays due to the high su... more Bead-based technologies are an attractive alternative to classical microarrays due to the high surface area of the beads which enables the immobilization of large numbers of probe molecules leading to increased kinetics and improved signal/noise ratios. A simple, versatile and inexpensive method for the fabrication of magnetic bead arrays is presented. The beads are first assembled into silicon pyramidal wells that have been fabricated by established microfabrication techniques and then mounted onto the apex of PDMS pyramids that replicate the silicon substrates by replica moulding. The bead arrays were used to detect oligonucleotide target sequences for the pathogenic avian H5N1 flu virus and results indicated that superior signal/noise ratios could be achieved compared to those from a classical microarray format.

Colloid & Polymer Science, 2003

Adsorption of proteins on solid surfaces has been described as 'a common but very complicated phe... more Adsorption of proteins on solid surfaces has been described as 'a common but very complicated phenomenon' [1]. Complications arise, in part, from geometrical complexity, functional heterogeneity and conformational lability. Systems and processes that fall under the general heading of molecular-scale interactions-e.g. protein folding, growth of biofilms, heterogeneous catalysis, and (bio)chemical separation-respond principally to short-range interactions and steric constraints. In the case of colloidal species in solution, mass transport will respond to electrostatic forces arising from net surface charge densities on the colloid and on its destination surface/interface. The properties of the medium then play important roles, e.g. [2]. The DLVO theory [3] takes account of the diffuse double layer causing action over an intermediate range, as well as the ever-present shortrange van der Waals interaction. Recent theoretical modelling has attempted to relate electrostatic interactions to more detailed models of proteins and their confinement [4, 5, 6]. An all-atom calculation of a macromolecule in aqueous solution interacting with a surface is, as yet, not feasible. Thus, it is common practice to consider the molecule as a simplified structure of interconnected subunits, such as amino acids. The advent of scanning force microscopy (SFM) [7] has provided an important new tool for interrogation of

Biosensors and Bioelectronics, 2004

Biomolecules in a confined solution environment may be subject to electrostatic forces with a ran... more Biomolecules in a confined solution environment may be subject to electrostatic forces with a range up to 100 nm, while van der Waals interaction will account for shorter-range forces. The response of two model poly(amino acids)-poly-l-lysine and poly-l-glutamic acid-has been investigated for a silica/Si-oxide surface at pH 6. The model amino acids were adsorbed, or covalently coupled, to colloidal probes consisting of a microsphere attached to a force-sensing lever. The methodology was based on sensing interaction between the probe and a flat surface through carrying out force versus distance analysis with a scanning force microscope. The results were analyzed within the framework of the conventional DLVO theory. The outcomes illustrate both repulsive and attractive long-range interactions that will hinder, or promote, colloidal biospecies in solution entering the region of attractive short-range interactions at the physical interface. Large 'snap-on' distances were observed for some systems and have been ascribed to compression of the 'soft' functionalized layers. Those observations and measurements of adhesion provided insight into conformation of the adsorbed species and strength of attachment. The results have implications for the efficacy of methods and devices that seek to exploit the properties of micro/nano-fluidic systems.

Biosensors and Bioelectronics, 2004

The immobilisation efficiency of the complexes of oligonucleotide/poly(l-lysine) on two polymeric... more The immobilisation efficiency of the complexes of oligonucleotide/poly(l-lysine) on two polymeric carboxy-rich surfaces, i.e. poly(styrene/ maleic acid) (PSMA) and poly(styrene/maleic anhydride) (PSMAA), has been investigated using X-ray photoelectron spectroscopy, atomic force microscopy (AFM) and fluorescence-based measurements of DNA attachment. A molecularly thin layer of either electrostatically or covalently (via amide bond) bound poly(l-lysine) allows the 'switching' from COOH-based to NH 2-based surface functionality. The results indicate that approximately 54-57% and 55-62% of the applied oligonucleotides bind to polymeric surfaces via the route of electrostatic adsorption of poly(l-lysine) and covalent bonding of poly(l-lysine), respectively. This system can be applied conveniently for the detection of nucleic acids in both disposable and reusable biosensors.

Biosensors and Bioelectronics, 2005

We explored the potential of contractile proteins, actin and myosin, as biosensors of solutions c... more We explored the potential of contractile proteins, actin and myosin, as biosensors of solutions containing mercuric ions. We demonstrate that the reaction of HgCl 2 with myosin rapidly inhibits actin-activated myosin ATPase activity. Mercuric ions inhibit the in vitro analog of contraction, namely the ATP-initiated superprecipitation of the reconstituted actomyosin complex. Hg reduces both the rate and extent of this reaction. Direct observation of the propulsive movement of actin filaments (10 nm in diameter and 1 m long) in a motility assay driven by a proteolytic fragment of myosin (heavy meromyosin or HMM) is also inhibited by mercuric ions. Thus, we have demonstrated the biochemical, biophysical and nanotechnological basis of what may prove to be a useful nano-device.

Society of Photo- …, Dec 1, 2007

SPIE is an international society advancing an interdisciplinary approach to the science and appli... more SPIE is an international society advancing an interdisciplinary approach to the science and application of light. ... Dan V. Nicolau Derek Abbott Kourosh Kalantar-Zadeh Tiziana Di Matteo Sergey M. Bezrukov Editors ... Cosponsored by The Australian National University (Australia) Australian Research Council Nanotechnology Network (Australia) COSNet-ARC Complex Open Systems Research Network (Australia) CUDOS (Australia) RPO (Australia) Bandwidth Foundry (Australia) ... Cooperating Organizations Research School of Physical Sciences and ...