Franklin Uba - Academia.edu (original) (raw)

Papers by Franklin Uba

Lab on a Chip

Nanofluidic circuit for detecting damage (abasic sites) in single DNA molecules.

A consistent and reproducible degree of stretching of DNA is important for single DNA molecule an... more A consistent and reproducible degree of stretching of DNA is important for single DNA molecule analysis such as DNA mapping and fast sequencing. Micro/nanopost or posts arrays are known to be able to uncoil genomic scale DNAs upon collision on the posts. Here, we built periodical hexagon nanoposts array embedded in a polymeric micro/nanofluidic device at low costs by a novel NanoImprinting process. The electrophoresis of λ-DNA and T4 DNA were studied in the posts array. A periodical stretching/recoiling motion was observed for both DNAs. Experiments showed a stretching to over 90% of its contour length was highly reproducible for both λ-DNA and T4 DNA. This non-gel electrophoresis of DNA also can be useful for the study of fundamental of DNA separation.

We report the use of thermoplastic nanochannels for electrophoresis. Studies concerning the surfa... more We report the use of thermoplastic nanochannels for electrophoresis. Studies concerning the surface charge and electroosmotic flow (EOF) of thermoplastic nanochannels indicated that the EOF can be modified based on O2 plasma treatment and subsequent EDC/EDA chemistry, which can facilitate the electrophoretic separation of different analytes. The separation of solutes using thermoplastic nanochannels was possible, which conventional capillary electrophoresis could not provide due to the unique flow properties associated with nanofluidics

We present a microfluidic chip embedded with gold electrodes for digital counting of bacteria. Mi... more We present a microfluidic chip embedded with gold electrodes for digital counting of bacteria. Microfluidic chip is fabricated to detect single Escherichia coli flowing in a channel which size is comparable to the bacteria. The chip is fabricated by photolithography, dry etching, e-beam evaporation, lift-off process, and focused ion beam (FIB) milling process. We could detect the trace of the individual bacterium passage by measuring the current change using the built-in gold electrodes located in the middle of the fluidic channel.

Nanochannel-based fluidic devices have shown tremendous potential in real-time DNA/RNA analysis, ... more Nanochannel-based fluidic devices have shown tremendous potential in real-time DNA/RNA analysis, DNA mapping, electrochemomechanical battery and other applications. Compared to Si/SiO2 substrates that are normally used for nanochannel fabrication, polymer substrates have the advantages such as versatile surface properties, biocompatible, easy-fabrication, low cost etc. However, one big issue for all polymer-based nanofluidic devices is how to obtain a good bonding of nanochannels without break or block the nanochannel and whether the different bonding methods affect the behavior of biomolecules in the nanochannels.

Lab on a Chip, 2017

This review presents an overview of recent advancements in the fabrication, surface modification ... more This review presents an overview of recent advancements in the fabrication, surface modification and applications of thermoplastic nanofluidic devices.

Analytical Chemistry, 2016

Phenomena associated with microscale electrophoresis separations cannot, in many cases, be applie... more Phenomena associated with microscale electrophoresis separations cannot, in many cases, be applied to the nanoscale. Thus, understanding the electrophoretic characteristics associated with the nanoscale will help formulate relevant strategies that can optimize the performance of separations carried out on columns with at least one dimension below 150 nm. Electric double layer (EDL) overlap, diffusion, and adsorption/desorption properties and/or dielectrophoretic effects giving rise to stick/slip motion are some of the processes that can play a role in determining the Efficiency of nanoscale electrophoretic separations. We investigated the performance characteristics of electrophoretic separations carried out in nanoslits fabricated in poly(methyl methacrylate), PMMA, devices. Silver nanoparticles (AgNPs) were used as the model system with tracking of their transport via dark field microscopy and localized surface plasmon resonance. AgNPs capped with citrate groups and the negatively charged PMMA walls (induced by O 2 plasma modification of the nanoslit walls) enabled separations that were not apparent when these particles were electrophoresed in microscale columns. The separation of AgNPs based on their size without the need for buffer additives using PMMA nanoslit devices is demonstrated herein.

The Analyst, 2015

We report the surface modification of thermoplastic nanochannels and the evaluation of the surfac... more We report the surface modification of thermoplastic nanochannels and the evaluation of the surface charge density, zeta potential and electroosmotic flow (EOF).

Lab on a Chip, 2015

A low temperature hybrid assembly process for the production of functional thermoplastic nanoflui... more A low temperature hybrid assembly process for the production of functional thermoplastic nanofluidic devices with process yield rates >90% and an assembly time of 16 min is reported.

ELECTROPHORESIS, 2014

Microfluidics for the analysis of membrane proteins: How do we get there? The development of full... more Microfluidics for the analysis of membrane proteins: How do we get there? The development of fully automated and high-throughput systems for proteomics is now in demand because of the need to generate new protein-based disease biomarkers. Unfortunately, it is difficult to identify protein biomarkers that are low abundant when in the presence of highly abundant proteins, especially in complex biological samples such as serum, cell lysates, and other biological fluids. Membrane proteins, which are in many cases of low abundance compared to the cytosolic proteins, have various functions and can provide insight into the state of a disease and serve as targets for new drugs making them attractive biomarker candidates. Traditionally, proteins are identified through the use of gel electrophoretic techniques, which are not always suitable for particular protein samples such as membrane proteins. Microfluidics offers the potential as a fully automated platform for the efficient and high-throughput analysis of complex samples, such as membrane proteins, and do so with performance metrics that exceed their bench-top counterparts. In recent years, there have been various improvements to microfluidics and their use for proteomic analysis as reported in the literature. Consequently, this review presents an overview of the traditional proteomic-processing pipelines for membrane proteins and insights into new technological developments with a focus on the applicability of microfluidics for the analysis of membrane proteins. Sample preparation techniques will be discussed in detail and novel interfacing strategies as it relates to MS will be highlighted. Lastly, some general conclusions and future perspectives are presented.

Analytical Chemistry, 2014

The process of immobilizing enzymes onto solid supports for bioreactions has some compelling adva... more The process of immobilizing enzymes onto solid supports for bioreactions has some compelling advantages compared to their solution-based counterpart including the facile separation of enzyme from products, elimination of enzyme autodigestion, and increased enzyme stability and activity. We report the immobilization of λ-exonuclease onto poly(methylmethacrylate) (PMMA) micropillars populated within a microfluidic device for the on-chip digestion of doublestranded DNA. Enzyme immobilization was successfully accomplished using 3-(3dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide (EDC/NHS) coupling to carboxylic acid functionalized PMMA micropillars. Our results suggest that the efficiency for the catalysis of dsDNA digestion using λ-exonuclease, including its processivity and reaction rate, were higher when the enzyme was attached to a solid support compared to the free solution digestion. We obtained a clipping rate of 1.0 × 10 3 nucleotides s −1 for the digestion of λ-DNA (48.5 kbp) by λ-exonuclease. The kinetic behavior of the solid-phase reactor could be described by a fractal Michaelis− Menten model with a catalytic efficiency nearly 17% better than the homogeneous solution-phase reaction. The results from this work will have important ramifications in new single-molecule DNA sequencing strategies that employ free mononucleotide identification.

We are developing techniques for the fabrication of mixed-scale systems (nm to mm) used for the m... more We are developing techniques for the fabrication of mixed-scale systems (nm to mm) used for the molecular-scale sensing of single-molecules (DNAs, RNAs, peptides and proteins). The system consists of microchannels and nanochannels (10-100 nm) with integrated electrodes of similar dimensions for transducing single molecules. The system is applicable for the rapid and efficient sequencing of biopolymers by measuring flight-times of monomer units clipped from a single polymer. Preliminary results from calculations and Molecular Dynamic (MD) simulations have supported the viability of our system.