Senior Research Scientist at Stanford School of Medicine. Ph.D. in Applied Physics from Cornell. Inventor of the Smart Toilet technology. Precision Health Innovator
The detection and analysis of rare blood biomarkers is necessary for early diagnosis of cancer an... more The detection and analysis of rare blood biomarkers is necessary for early diagnosis of cancer and to facilitate the development of tailored therapies. However, current methods for the isolation of circulating tumour cells (CTCs) or nucleic acids present in a standard clinical sample of only 5-10 ml of blood provide inadequate yields for early cancer detection and comprehensive molecular profiling. Here, we report the development of a flexible magnetic wire that can retrieve rare biomarkers from the subject's blood in vivo at a much higher yield. The wire is inserted and removed through a standard intravenous catheter and captures biomarkers that have been previously labelled with injected magnetic particles. In a proof-of-concept experiment in a live porcine model, we demonstrate the in vivo labelling and single-pass capture of viable model CTCs in less than 10 s. The wire achieves capture efficiencies that correspond to enrichments of 10-80 times the amount of CTCs in a 5-ml b...
Methods in molecular biology (Clifton, N.J.), 2017
Circulating tumor cells (CTCs) are currently widely studied for their potential application as pa... more Circulating tumor cells (CTCs) are currently widely studied for their potential application as part of a liquid biopsy. These cells are shed from the primary tumor into the circulation, and are postulated to provide insight into the molecular makeup of the actual tumor in a minimally invasive manner. However, they are extremely rare in blood, with typical concentrations of 1-100 in a milliliter of blood; hence, a need exists for a rapid and high-purity method for isolating CTCs from whole blood. Here, we describe the application of a microfabricated magnetic sifter toward isolation of CTCs from whole blood at volumetric flow rates of 10 mL/h, along with the use of a PDMS-based nanowell system for single-cell gene expression profiling. This method allows rapid isolation of CTCs and subsequent integration with downstream genetic profiling methods for clinical applications such as targeted therapy, therapy monitoring, or further biological studies.
Cell-free DNA (cfDNA) diagnostics are emerging as a new paradigm of disease monitoring and therap... more Cell-free DNA (cfDNA) diagnostics are emerging as a new paradigm of disease monitoring and therapy management. The clinical utility of these diagnostics is relatively limited by a low signal-to-noise ratio, such as with low allele frequency (AF) mutations in cancer. While enriching for rare alleles to increase their AF before sample analysis is one strategy that can greatly improve detection capability, current methods are limited in their generalizability, ease of use, and applicability to point mutations. Leveraging the robust single-base-pair specificity and generalizability of the CRISPR associated protein 9 (Cas9) system, we developed a deactivated Cas9 (dCas9)-based method of minor-allele enrichment capable of efficient single-target and multiplexed enrichment. The dCas9 protein was complexed with single guide RNAs targeted to mutations of interest and incubated with cfDNA samples containing mutant strands at low abundance. Mutation-bound dCas9 complexes were isolated, dissoci...
Nanoparticles promise to advance the field of cardiovascular theranostics. However, their sustain... more Nanoparticles promise to advance the field of cardiovascular theranostics. However, their sustained and targeted delivery remains an important obstacle. The body synthesizes some "natural" nanoparticles, including high-density lipoprotein (HDL), which may home to the atherosclerotic plaque and promote cholesterol efflux. In a recent article published in , investigators generated modified, radiolabeled HDL nanoparticles and confirmed they accumulated in atherosclerotic lesions from several different species. These approaches hold promise for the noninvasive diagnosis of vulnerable plaque and in the stratification of patients in whom HDL-mimetic therapy may have a clinical benefit.
Numerous techniques for isolating circulating tumor cells (CTCs) have been developed. Concurrentl... more Numerous techniques for isolating circulating tumor cells (CTCs) have been developed. Concurrently, single-cell techniques that can reveal molecular components of CTCs have become widely available. We discuss how the combination of isolation and multigene profiling of single CTCs in our platform can facilitate eventual translation to the clinic.
This presentation will focus on two aspects of the motor design. Firstly the use of self-assembli... more This presentation will focus on two aspects of the motor design. Firstly the use of self-assembling components whose function is to co-localise the necessary motor functions. We demonstrate that a coiled coil template can be adapted in order to program the self-assembly of three different coiled coils from a solution of six peptides. Secondly the role of linkers between components in controlling dynamics and hence both processivity and power strokes within our motor designs will be discussed. The use of cis-trans isomerization of azobenzene as a mechanism for driving conformational change within the motor will be demonstrated. 1. The Tumbleweed: towards a synthetic protein motor, EHC Bromley et al.
Pref-1 is an EGF-repeat-containing protein that inhibits adipocyte differentiation. To better und... more Pref-1 is an EGF-repeat-containing protein that inhibits adipocyte differentiation. To better understand the origin and development of white adipose tissue (WAT), we generated transgenic mouse models for transient or permanent fluorescent labeling of cells using the Pref-1 promoter, facilitating inducible ablation. We show that Pref-1-marked cells retain proliferative capacity and are very early adipose precursors, prior to expression of Zfp423 or PPARg. In addition, the Pref-1-marked cells establish that adipose precursors are mesenchymal, but not endothelial or pericytal, in origin. During embryogenesis, Pref-1-marked cells first appear in the dorsal mesenteric region as early as embryonic day 10.5 (E10.5). These cells become lipid-laden adipocytes at E17.5 in the subcutaneous region, whereas visceral WAT develops after birth. Finally, ablation of Pref-1marked cells prevents not only embryonic WAT development but also later adult adipose expansion upon high-fat feeding, demonstrating the requirement of Pref-1 cells for adipogenesis.
Page 1. Microfluidic Encapsulated NEMS Resonators for Sensor Applications Keith L. Aubin*, Seung-... more Page 1. Microfluidic Encapsulated NEMS Resonators for Sensor Applications Keith L. Aubin*, Seung-min Park, Jingqing Huang, Harold G. Craighead School of Applied and Engineering Physcis Cornell University Ithaca, NY USA *[email protected] ...
Biomolecular transport in nanofluidic confinement offers various means to investigate the behavio... more Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.
Proceedings of the National Academy of Sciences, 2009
Nanofluidics represents a promising solution to problems in fields ranging from biomolecular anal... more Nanofluidics represents a promising solution to problems in fields ranging from biomolecular analysis to optical property tuning. Recently a number of simple nanofluidic fabrication techniques have been introduced that exploit the deformability of elastomeric materials like polydimethylsiloxane (PDMS). These techniques are limited by the complexity of the devices that can be fabricated, which can only create straight or irregular channels normal to the direction of an applied strain. Here, we report a technique for nanofluidic fabrication based on the controlled collapse of microchannel structures. As is demonstrated, this method converts the easy to control vertical dimension of a PDMS mold to the lateral dimension of a nanochannel. We demonstrate here the creation of complex nanochannel structures as small as 60 nm and provide simple design rules for determining the conditions under which nanochannel formation will occur. The applicability of the technique to biomolecular analysis...
Discriminating cellular heterogeneity is important for understanding cellular physiology. However... more Discriminating cellular heterogeneity is important for understanding cellular physiology. However, it is limited by the technical difficulties of single-cell measurements. Here, we develop a two-stage system to determine cellular heterogeneity. In the first stage, we perform multiplex single-cell RNA-cytometry in a microwell array containing over 60,000 reaction chambers. In the second stage, we use the RNA-cytometry data to determine cellular heterogeneity by providing a heterogeneity likelihood score. Moreover, we use Monte-Carlo simulation and RNA-cytometry data to calculate the minimum number of cells required for detecting heterogeneity. We applied this system to characterize the RNA distributions of aging related genes in a highly purified mouse hematopoietic stem cell population. We identified genes that reveal novel heterogeneity of these cells. We also show that changes in expression of genes such as Birc6 during aging can be attributed to the shift of relative portions of cells in the high-expressing subgroup versus lowexpressing subgroup.
Hemolysis, involving the rupture of red blood cells (RBCs) and release of their contents into blo... more Hemolysis, involving the rupture of red blood cells (RBCs) and release of their contents into blood plasma, is a major issue of concern in clinical fields. Hemolysis in vitro can occur as a result of errors in clinical trials; in vivo, hemolysis can be caused by a variety of medical conditions. Blood plasma separation is often the first step in blood-based clinical diagnostic procedures. However, inhibitors released from RBCs due to hemolysis during plasma separation can lead to problems in diagnostic tests such as low sensitivity, selectivity and inaccurate results. In particular, a general lack of simple and reliable blood plasma separation methods has been a major obstacle for microfluidic-based point-of-care (POC) diagnostic devices. Here we present a hemolysis-free microfluidic blood plasma separation platform. A membrane filter was positioned on top of a vertical up-flow channel (filter-in-top configuration) to reduce clogging of RBCs by gravity-assisted cells sedimentation. With this device, separated plasma volume was increased approximately 4-fold (2.4 μL plasma after 20 min with 38% hematocrit human whole blood), and hemoglobin concentration in separated plasma was decreased approximately 90% due to the prevention of RBCs hemolysis, when compared to conventional filter-in-bottom configuration blood plasma separation platforms. On-chip plasma contained ~90% of protein and ~100% of nucleic acids found in off-chip centrifuged plasma, confirming comparable target molecule recovery efficiency. This simple and robust on-chip blood plasma separation device integrates with downstream detection modules to ultimately create sample-to-answer microfluidic POC diagnostics devices.
RNA and DNA aptamers that bind to target molecules with high specificity and affinity have been a... more RNA and DNA aptamers that bind to target molecules with high specificity and affinity have been a focus of diagnostics and therapeutic research. These aptamers are obtained by SELEX (Systematic Evolution of Ligands by EXponential enrichment) often requiring more than 10 successive cycles of selection and amplification, where each cycle normally takes 2 days per cycle of SELEX. Here, we have demonstrated the use of sol-gel arrays of proteins in a microfluidic system for efficient selection of RNA aptamers against multiple target molecules. The microfluidic chip incorporates five sol-gel binding droplets, within which specific target proteins are imbedded. The droplets are patterned on top of individually addressable electrical microheaters used for selective elution of aptamers bound to target proteins in the sol-gel droplets. We demonstrate that specific aptamers bind their respective protein targets and can be selectively eluted by micro-heating. Finally, our microfluidic SELEX system greatly improved selection efficiency, reducing the number of selection cycles needed to produce high affinity aptamers. The process is readily scalable to larger arrays of sol-gel-embedded proteins. To our knowledge, this is the first demonstration of a chip-based selection of aptamers using microfluidics, thereby allowing development of a high throughput and efficient SELEX procedures.
Biological systems continuously acquire and use energy sources to perform various functions. This... more Biological systems continuously acquire and use energy sources to perform various functions. This energy is, in part, transduced to generate the forces that control the mechanical behavior of the cell (e.g. cell shape and motion). In this case, the system is in the non-equilibrium state and the material may be called ''Active Soft Matter''. To investigate the mechanical properties of soft, active systems, we have synthesized an active gel with a well-known semi-flexible biopolymer, DNA, and DNA-associated motor proteins. We study the mechanics of this system using two kinds of microrheological techniques. First, we use a passive measurement in which the intrinsic fluctuation of embedded particles gives information on gel mechanics. Second, we use an active measurement utilizing the forced oscillating motion of embedded particles by an external magnetic field. We discuss these results in comparison to cytoskeletal systems, and seek to establish universal principles of motor-driven active gels.
We present the integration of a cyclo olefin copolymer microfluidic chip with electrochemical pum... more We present the integration of a cyclo olefin copolymer microfluidic chip with electrochemical pumps and an SU-8 tip for electrospray ionization mass spectrometry. The electrochemical pump, using electrolysis as an internal pressure source, was fabricated directly on the surface of the polymer chip. The triangular SU-8 emitter tip was fabricated on a glass wafer using standard photolithography. After release from the glass wafer, this tip was aligned to the microchannel and bonded between two polymer plates. The electrochemical pump and the electrospray tip were tested with electrospray ionization mass spectrometry. Mass spectrometry confirmed the stability of the electrochemical pump and the electrospray tip.
Aptamers are well-known protein capture reagents that bind to specific proteins and can be effect... more Aptamers are well-known protein capture reagents that bind to specific proteins and can be effective in inhibiting the protein's normal interactions. Here, we have described a process for selective binding and elution of aptimers from the nanoporous silicate sol-gel droplets within which target proteins are immobilized. These silicate sol-gel droplets are incorporated with polydimethylsiloxane (PDMS) microfluidic systems and individually addressable
ABSTRACT The Al nanoapertures surrounded by periodic patterns on the pyramid were fabricated. The... more ABSTRACT The Al nanoapertures surrounded by periodic patterns on the pyramid were fabricated. The nanosize aperture surrounded by equidistant elliptic groove patterns presented greater transmission than the aperture with circular groove patterns. The translocation of λ-DNA through these fabricated nanostructures was examined.
Biomolecular transport in nanofluidic confinement offers various means to investigate the behavio... more Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.
The detection and analysis of rare blood biomarkers is necessary for early diagnosis of cancer an... more The detection and analysis of rare blood biomarkers is necessary for early diagnosis of cancer and to facilitate the development of tailored therapies. However, current methods for the isolation of circulating tumour cells (CTCs) or nucleic acids present in a standard clinical sample of only 5-10 ml of blood provide inadequate yields for early cancer detection and comprehensive molecular profiling. Here, we report the development of a flexible magnetic wire that can retrieve rare biomarkers from the subject's blood in vivo at a much higher yield. The wire is inserted and removed through a standard intravenous catheter and captures biomarkers that have been previously labelled with injected magnetic particles. In a proof-of-concept experiment in a live porcine model, we demonstrate the in vivo labelling and single-pass capture of viable model CTCs in less than 10 s. The wire achieves capture efficiencies that correspond to enrichments of 10-80 times the amount of CTCs in a 5-ml b...
Methods in molecular biology (Clifton, N.J.), 2017
Circulating tumor cells (CTCs) are currently widely studied for their potential application as pa... more Circulating tumor cells (CTCs) are currently widely studied for their potential application as part of a liquid biopsy. These cells are shed from the primary tumor into the circulation, and are postulated to provide insight into the molecular makeup of the actual tumor in a minimally invasive manner. However, they are extremely rare in blood, with typical concentrations of 1-100 in a milliliter of blood; hence, a need exists for a rapid and high-purity method for isolating CTCs from whole blood. Here, we describe the application of a microfabricated magnetic sifter toward isolation of CTCs from whole blood at volumetric flow rates of 10 mL/h, along with the use of a PDMS-based nanowell system for single-cell gene expression profiling. This method allows rapid isolation of CTCs and subsequent integration with downstream genetic profiling methods for clinical applications such as targeted therapy, therapy monitoring, or further biological studies.
Cell-free DNA (cfDNA) diagnostics are emerging as a new paradigm of disease monitoring and therap... more Cell-free DNA (cfDNA) diagnostics are emerging as a new paradigm of disease monitoring and therapy management. The clinical utility of these diagnostics is relatively limited by a low signal-to-noise ratio, such as with low allele frequency (AF) mutations in cancer. While enriching for rare alleles to increase their AF before sample analysis is one strategy that can greatly improve detection capability, current methods are limited in their generalizability, ease of use, and applicability to point mutations. Leveraging the robust single-base-pair specificity and generalizability of the CRISPR associated protein 9 (Cas9) system, we developed a deactivated Cas9 (dCas9)-based method of minor-allele enrichment capable of efficient single-target and multiplexed enrichment. The dCas9 protein was complexed with single guide RNAs targeted to mutations of interest and incubated with cfDNA samples containing mutant strands at low abundance. Mutation-bound dCas9 complexes were isolated, dissoci...
Nanoparticles promise to advance the field of cardiovascular theranostics. However, their sustain... more Nanoparticles promise to advance the field of cardiovascular theranostics. However, their sustained and targeted delivery remains an important obstacle. The body synthesizes some "natural" nanoparticles, including high-density lipoprotein (HDL), which may home to the atherosclerotic plaque and promote cholesterol efflux. In a recent article published in , investigators generated modified, radiolabeled HDL nanoparticles and confirmed they accumulated in atherosclerotic lesions from several different species. These approaches hold promise for the noninvasive diagnosis of vulnerable plaque and in the stratification of patients in whom HDL-mimetic therapy may have a clinical benefit.
Numerous techniques for isolating circulating tumor cells (CTCs) have been developed. Concurrentl... more Numerous techniques for isolating circulating tumor cells (CTCs) have been developed. Concurrently, single-cell techniques that can reveal molecular components of CTCs have become widely available. We discuss how the combination of isolation and multigene profiling of single CTCs in our platform can facilitate eventual translation to the clinic.
This presentation will focus on two aspects of the motor design. Firstly the use of self-assembli... more This presentation will focus on two aspects of the motor design. Firstly the use of self-assembling components whose function is to co-localise the necessary motor functions. We demonstrate that a coiled coil template can be adapted in order to program the self-assembly of three different coiled coils from a solution of six peptides. Secondly the role of linkers between components in controlling dynamics and hence both processivity and power strokes within our motor designs will be discussed. The use of cis-trans isomerization of azobenzene as a mechanism for driving conformational change within the motor will be demonstrated. 1. The Tumbleweed: towards a synthetic protein motor, EHC Bromley et al.
Pref-1 is an EGF-repeat-containing protein that inhibits adipocyte differentiation. To better und... more Pref-1 is an EGF-repeat-containing protein that inhibits adipocyte differentiation. To better understand the origin and development of white adipose tissue (WAT), we generated transgenic mouse models for transient or permanent fluorescent labeling of cells using the Pref-1 promoter, facilitating inducible ablation. We show that Pref-1-marked cells retain proliferative capacity and are very early adipose precursors, prior to expression of Zfp423 or PPARg. In addition, the Pref-1-marked cells establish that adipose precursors are mesenchymal, but not endothelial or pericytal, in origin. During embryogenesis, Pref-1-marked cells first appear in the dorsal mesenteric region as early as embryonic day 10.5 (E10.5). These cells become lipid-laden adipocytes at E17.5 in the subcutaneous region, whereas visceral WAT develops after birth. Finally, ablation of Pref-1marked cells prevents not only embryonic WAT development but also later adult adipose expansion upon high-fat feeding, demonstrating the requirement of Pref-1 cells for adipogenesis.
Page 1. Microfluidic Encapsulated NEMS Resonators for Sensor Applications Keith L. Aubin*, Seung-... more Page 1. Microfluidic Encapsulated NEMS Resonators for Sensor Applications Keith L. Aubin*, Seung-min Park, Jingqing Huang, Harold G. Craighead School of Applied and Engineering Physcis Cornell University Ithaca, NY USA *[email protected] ...
Biomolecular transport in nanofluidic confinement offers various means to investigate the behavio... more Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.
Proceedings of the National Academy of Sciences, 2009
Nanofluidics represents a promising solution to problems in fields ranging from biomolecular anal... more Nanofluidics represents a promising solution to problems in fields ranging from biomolecular analysis to optical property tuning. Recently a number of simple nanofluidic fabrication techniques have been introduced that exploit the deformability of elastomeric materials like polydimethylsiloxane (PDMS). These techniques are limited by the complexity of the devices that can be fabricated, which can only create straight or irregular channels normal to the direction of an applied strain. Here, we report a technique for nanofluidic fabrication based on the controlled collapse of microchannel structures. As is demonstrated, this method converts the easy to control vertical dimension of a PDMS mold to the lateral dimension of a nanochannel. We demonstrate here the creation of complex nanochannel structures as small as 60 nm and provide simple design rules for determining the conditions under which nanochannel formation will occur. The applicability of the technique to biomolecular analysis...
Discriminating cellular heterogeneity is important for understanding cellular physiology. However... more Discriminating cellular heterogeneity is important for understanding cellular physiology. However, it is limited by the technical difficulties of single-cell measurements. Here, we develop a two-stage system to determine cellular heterogeneity. In the first stage, we perform multiplex single-cell RNA-cytometry in a microwell array containing over 60,000 reaction chambers. In the second stage, we use the RNA-cytometry data to determine cellular heterogeneity by providing a heterogeneity likelihood score. Moreover, we use Monte-Carlo simulation and RNA-cytometry data to calculate the minimum number of cells required for detecting heterogeneity. We applied this system to characterize the RNA distributions of aging related genes in a highly purified mouse hematopoietic stem cell population. We identified genes that reveal novel heterogeneity of these cells. We also show that changes in expression of genes such as Birc6 during aging can be attributed to the shift of relative portions of cells in the high-expressing subgroup versus lowexpressing subgroup.
Hemolysis, involving the rupture of red blood cells (RBCs) and release of their contents into blo... more Hemolysis, involving the rupture of red blood cells (RBCs) and release of their contents into blood plasma, is a major issue of concern in clinical fields. Hemolysis in vitro can occur as a result of errors in clinical trials; in vivo, hemolysis can be caused by a variety of medical conditions. Blood plasma separation is often the first step in blood-based clinical diagnostic procedures. However, inhibitors released from RBCs due to hemolysis during plasma separation can lead to problems in diagnostic tests such as low sensitivity, selectivity and inaccurate results. In particular, a general lack of simple and reliable blood plasma separation methods has been a major obstacle for microfluidic-based point-of-care (POC) diagnostic devices. Here we present a hemolysis-free microfluidic blood plasma separation platform. A membrane filter was positioned on top of a vertical up-flow channel (filter-in-top configuration) to reduce clogging of RBCs by gravity-assisted cells sedimentation. With this device, separated plasma volume was increased approximately 4-fold (2.4 μL plasma after 20 min with 38% hematocrit human whole blood), and hemoglobin concentration in separated plasma was decreased approximately 90% due to the prevention of RBCs hemolysis, when compared to conventional filter-in-bottom configuration blood plasma separation platforms. On-chip plasma contained ~90% of protein and ~100% of nucleic acids found in off-chip centrifuged plasma, confirming comparable target molecule recovery efficiency. This simple and robust on-chip blood plasma separation device integrates with downstream detection modules to ultimately create sample-to-answer microfluidic POC diagnostics devices.
RNA and DNA aptamers that bind to target molecules with high specificity and affinity have been a... more RNA and DNA aptamers that bind to target molecules with high specificity and affinity have been a focus of diagnostics and therapeutic research. These aptamers are obtained by SELEX (Systematic Evolution of Ligands by EXponential enrichment) often requiring more than 10 successive cycles of selection and amplification, where each cycle normally takes 2 days per cycle of SELEX. Here, we have demonstrated the use of sol-gel arrays of proteins in a microfluidic system for efficient selection of RNA aptamers against multiple target molecules. The microfluidic chip incorporates five sol-gel binding droplets, within which specific target proteins are imbedded. The droplets are patterned on top of individually addressable electrical microheaters used for selective elution of aptamers bound to target proteins in the sol-gel droplets. We demonstrate that specific aptamers bind their respective protein targets and can be selectively eluted by micro-heating. Finally, our microfluidic SELEX system greatly improved selection efficiency, reducing the number of selection cycles needed to produce high affinity aptamers. The process is readily scalable to larger arrays of sol-gel-embedded proteins. To our knowledge, this is the first demonstration of a chip-based selection of aptamers using microfluidics, thereby allowing development of a high throughput and efficient SELEX procedures.
Biological systems continuously acquire and use energy sources to perform various functions. This... more Biological systems continuously acquire and use energy sources to perform various functions. This energy is, in part, transduced to generate the forces that control the mechanical behavior of the cell (e.g. cell shape and motion). In this case, the system is in the non-equilibrium state and the material may be called ''Active Soft Matter''. To investigate the mechanical properties of soft, active systems, we have synthesized an active gel with a well-known semi-flexible biopolymer, DNA, and DNA-associated motor proteins. We study the mechanics of this system using two kinds of microrheological techniques. First, we use a passive measurement in which the intrinsic fluctuation of embedded particles gives information on gel mechanics. Second, we use an active measurement utilizing the forced oscillating motion of embedded particles by an external magnetic field. We discuss these results in comparison to cytoskeletal systems, and seek to establish universal principles of motor-driven active gels.
We present the integration of a cyclo olefin copolymer microfluidic chip with electrochemical pum... more We present the integration of a cyclo olefin copolymer microfluidic chip with electrochemical pumps and an SU-8 tip for electrospray ionization mass spectrometry. The electrochemical pump, using electrolysis as an internal pressure source, was fabricated directly on the surface of the polymer chip. The triangular SU-8 emitter tip was fabricated on a glass wafer using standard photolithography. After release from the glass wafer, this tip was aligned to the microchannel and bonded between two polymer plates. The electrochemical pump and the electrospray tip were tested with electrospray ionization mass spectrometry. Mass spectrometry confirmed the stability of the electrochemical pump and the electrospray tip.
Aptamers are well-known protein capture reagents that bind to specific proteins and can be effect... more Aptamers are well-known protein capture reagents that bind to specific proteins and can be effective in inhibiting the protein's normal interactions. Here, we have described a process for selective binding and elution of aptimers from the nanoporous silicate sol-gel droplets within which target proteins are immobilized. These silicate sol-gel droplets are incorporated with polydimethylsiloxane (PDMS) microfluidic systems and individually addressable
ABSTRACT The Al nanoapertures surrounded by periodic patterns on the pyramid were fabricated. The... more ABSTRACT The Al nanoapertures surrounded by periodic patterns on the pyramid were fabricated. The nanosize aperture surrounded by equidistant elliptic groove patterns presented greater transmission than the aperture with circular groove patterns. The translocation of λ-DNA through these fabricated nanostructures was examined.
Biomolecular transport in nanofluidic confinement offers various means to investigate the behavio... more Biomolecular transport in nanofluidic confinement offers various means to investigate the behavior of biomolecules in their native aqueous environments, and to develop tools for diverse single-molecule manipulations. Recently, a number of simple nanofluidic fabrication techniques has been demonstrated that utilize electrospun nanofibers as a backbone structure. These techniques are limited by the arbitrary dimension of the resulting nanochannels due to the random nature of electrospinning. Here, a new method for fabricating nanofluidic systems from size-reduced electrospun nanofibers is reported and demonstrated. As it is demonstrated, this method uses the scanned electrospinning technique for generation of oriented sacrificial nanofibers and exposes these nanofibers to harsh, but isotropic etching/heating environments to reduce their cross-sectional dimension. The creation of various nanofluidic systems as small as 20 nm is demonstrated, and practical examples of single biomolecular handling, such as DNA elongation in nanochannels and fluorescence correlation spectroscopic analysis of biomolecules passing through nanochannels, are provided.
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Papers by Seung-min Park