Jose M. Moran-Mirabal

Supported lipid bilayer/carbon nanotube hybrids

Carbon nanotube transistors combine molecular-scale dimensions with excellent electronic properties, offering unique opportunities for chemical and biological sensing. Here, we form supported lipid bilayers over single-walled carbon nanotube transistors. We first study the physical properties of the nanotube/supported lipid bilayer structure using fluorescence techniques. Whereas lipid molecules can diffuse freely across the nanotube, a membrane-bound protein (tetanus toxin) sees the nanotube as a barrier. Moreover, the size of the barrier depends on the diameter of the nanotube--with larger nanotubes presenting bigger obstacles to diffusion. We then demonstrate detection of protein binding (streptavidin) to the supported lipid bilayer using the nanotube transistor as a charge sensor. This system can be used as a platform to examine the interactions of single molecules with carbon nanotubes and has many potential applications for the study of molecular recognition and other biological processes occurring at cell membranes.

Fluorescent Labeling and Characterization of Cellulose Nanocrystals with Varying Charge Contents

Cotton-source cellulose nanocrystals (CNCs) with a range of surface charge densities were fluorescently labeled with 5-(4, 6-dichlorotriazinyl) aminofluorescein (DTAF) in a facile, one-pot reaction under alkaline conditions. Three CNC samples were labeled: (I) anionic CNCs prepared by sulfuric acid hydrolysis with a sulfur content of 0.47 wt %, (II) a partially desulfated, sulfuric acid-hydrolyzed CNC sample, which was less anionic with an intermediate sulfur content of 0.21 wt %, and (III) uncharged CNCs prepared by HCl hydrolysis. The DTAF-labeled CNCs were characterized by dynamic light scattering, atomic force microscopy, fluorescence spectroscopy and microscopy, and polarized light microscopy. Fluorescent CNCs exhibited similar colloidal stability to the starting CNCs, with the exception of the HCl-hydrolyzed sample, which became less agglomerated after the labeling reaction. The degree of labeling depended on the sulfur content of the CNCs, indicating that the presence of sulfate half-ester groups on the CNC surfaces hindered labeling. The labeling reaction produced CNCs that had detectable fluorescence, without compromising the overall surface chemistry or behavior of the materials, an aspect relevant to studies that require a fluorescent cellulose substrate with intact native properties. The DTAF-labeled CNCs were proposed as optical markers for the dispersion quality of CNC-loaded polymer composites. Electrospun polyvinyl alcohol fibers loaded with DTAF-labeled CNCs appeared uniformly fluorescent by fluorescence microscopy, suggesting that the nanoparticles were well dispersed within the polymer matrix.

Zero-mode waveguides: Sub-wavelength nanostructures for single molecule studies at high concentrations

The study of single fluorescent molecules allows individual measurements which can reveal characteristics typically obscured by ensemble averages. Yet, single molecule spectroscopy through traditional optical techniques is hindered by the diffraction limit of light. This restricts the accessible concentrations for single molecule experiments to the nano- to picomolar range. Zero-mode waveguides (ZMWs), optical nanostructures fabricated in a thin aluminum film, confine the observation volume to the range of atto- to zeptoliters. Thus, they extend the accessible concentrations for single molecule spectroscopy to the micro- to millimolar regime. Through the combination of ZMWs and fluorescence correlation spectroscopy, a number of biologically relevant systems have been studied at physiological concentrations. In this review, the concept and implementation of ZMWs is outlined, along with their application to the study of freely diffusing, and membrane-bound fluorescent biomolecules.

Suspended glass nanochannels coupled with microstructures for single molecule detection

We present a nonlithographic approach for forming free standing nanochannels, made of a variety of materials, that can be easily integrated with microfabricated structures. The approach uses a deposited polymeric fiber as a sacrificial template around which a deposited coating forms a tube. We formed suspended nanochannels of silica glass spanning a trench on a silicon wafer and used these structures for detection of single fluorescently labeled proteins. This geometry provides excellent isolation of the molecules of interest and also separates them from surrounding material that could create unwanted background fluorescence. The same geometry provides a platform for observing motion and mechanical response of the suspended nanochannel, and we measured the mechanical resonance of a glass channel of the type used for the fluorescent detection. This type of structure provides a general approach for integrating fluid carrying nanochannels with microstructures.

Cell investigation of nanostructures: zero-mode waveguides for plasma membrane studies with single molecule resolution

Plasma membranes are highly dynamic structures, with key molecular interactions underlying their functionality occurring at nanometre scales. A?fundamental challenge in biology is to observe these interactions in living cells. Although fluorescence microscopy has enabled advances in characterizing molecular distributions in cells, optical techniques are restricted by the diffraction limit. We address this limitation with an approach based on zero-mode waveguides (ZMWs), which are optical nanostructures that confine fluorescence excitation to sub-diffraction volumes. Successful use of ZMWs with cell membranes is reported in this paper. We demonstrate that plasma membranes from live cells penetrate these nanostructures. Cellular exploration of the nanoapertures depends heavily on actin filaments but not on microtubules. Thus, membranes enter the confined excitation volume, and diffusion of individual fluorescent lipids can be monitored. Through fluorescence correlation spectroscopy, we compared DiIC12 and DiIC16 fluorescent labels incorporated into plasma membranes and found distinctive diffusion behaviours. These results show that the use of optical nanostructures enables the measurement of membrane events with single molecule resolution in sub-diffraction volumes.

Observing and modeling BMCC degradation by commercial cellulase cocktails with fluorescently labeled Trichoderma reseii Cel7A through confocal microscopy.

Understanding the depolymerization mechanisms of cellulosic substrates by cellulase cocktails is a critical step towards optimizing the production of monosaccharides from biomass. The Spezyme CP cellulase cocktail combined with the Novo 188 β‐glucosidase blend was used to depolymerize bacterial microcrystalline cellulose (BMCC), which was immobilized on a glass surface. The enzyme mixture was supplemented with a small fraction of fluorescently labeled Trichoderma reseii Cel7A, which served as a reporter to track cellulase binding onto the physical structure of the cellulosic substrate. Both micro‐scale imaging and bulk experiments were conducted. All reported experiments were conducted at 50°C, the optimal temperature for maximum hydrolytic activity of the enzyme cocktail. BMCC structure was observed throughout degradation by labeling it with a fluorescent dye. This method allowed us to measure the binding of cellulases in situ and follow the temporal morphological changes of cellulose during its depolymerization by a commercial cellulase mixture. Three kinetic models were developed and fitted to fluorescence intensity data obtained through confocal microscopy: irreversible and reversible binding models, and an instantaneous binding model. The models were successfully used to predict the soluble sugar concentrations that were liberated from BMCC in bulk experiments. Comparing binding and kinetic parameters from models with different assumptions to previously reported constants in the literature led us to conclude that exposing new binding sites is an important rate‐limiting step in the hydrolysis of crystalline cellulose. Biotechnol. Bioeng. 2013; 110: 108–117.

Reversibility and binding kinetics of Thermobifida fusca cellulases studied through fluorescence recovery after photobleaching microscopy

Cellulases are enzymes capable of depolymerizing cellulose. Understanding their interactions with cellulose can improve biomass saccharification and enzyme recycling in biofuel production. This paper presents a study on binding and binding reversibility of Thermobifida fusca cellulases Cel5A, Cel6B, and Cel9A bound onto Bacterial Microcrystalline Cellulose. Cellulase binding was assessed through fluorescence recovery after photobleaching (FRAP) at 23, 34, and 45 °C. It was found that cellulase binding is only partially reversible. For processive cellulases Cel6B and Cel9A, an increase in temperature resulted in a decrease of the fraction of cellulases reversibly bound, while for endocellulase Cel5A this fraction remained constant. Kinetic parameters were obtained by fitting the FRAP curves to a binding-dominated model. The unbinding rate constants obtained for all temperatures were highest for Cel5A and lowest for Cel9A. The results presented demonstrate the usefulness of FRAP to access the fast binding kinetics characteristic of cellulases operating at their optimal temperature.

Nonspecific binding removal from protein microarrays using thickness shear mode resonators

Nonspecific binding is a universal problem that reduces bioassay sensitivity and specificity. We demonstrate that ultrasonic waves, generated by 5-MHz quartz crystal resonators, accelerate nonspecifically bound protein desorption from sensing and nonsensing areas of micropatterned protein arrays, controllably and nondestructively cleaning the micropatterns. Nonsensing area fluorescent intensity values dropped by more than 85% and sensing area fluorescent intensity dropped 77% due to nonspecific binding removal at an input power of 14 W. After patterning, antibody films were many layers thick with nonspecifically bound protein, and aggregates obscured patterns. Quartz crystal resonators removed excess antibody layers and aggregates leaving highly uniform films, as evidenced by smaller spatial variations in fluorescent intensity and atomic force microscope surface roughness values. Fluorescent intensity values obtained after 14-W QCR operation were more repeatable and uniform.

Immobilization of cellulose fibrils on solid substrates for cellulase‐binding studies through quantitative fluorescence microscopy

Cellulases, enzymes capable of depolymerizing cellulose polymers into fermentable sugars, are essential components in the production of bioethanol from lignocellulosic materials. Given the importance of these enzymes to the evolving biofuel industry considerable research effort is focused on understanding the interaction between cellulases and cellulose fibrils. This manuscript presents a method that addresses challenges that must be overcome in order to study such interactions through high‐resolution fluorescence microscopy. First, it is shown that cellulose can be immobilized on solid substrates through a polymer lift‐off technique. The immobilized cellulose aggregates present characteristic morphologies influenced by the patterned feature size used to immobilize it. Thus, through a variety of pattern sizes, cellulose can be immobilized in the form of cellulose particles, cellulose mats or individual cellulose fibrils. Second, it is shown that both cellulose and Thermobifida fusca cellulases Cel5A, Cel6B, and Cel9A can be fluorescently tagged and that the labeling does not inhibit the capability of these cellulases to depolymerize cellulose. The combination of the immobilization technique together with fluorescence labeling yields a system that can be used to study cellulose–cellulase interactions with spatial and temporal resolution not available through more conventional techniques which measure ensemble averages. It is shown that with such a system, the kinetics of cellulase binding onto cellulose fibrils and mats can be followed through sequences of fluorescence images. The intensity from the images can then be used to reconstruct binding curves for the cellulases studied. It was found that the complexity of cellulose morphology has a large impact on the binding curve characteristics, with binding curves for individual cellulose fibrils closely following a binding saturation model and binding curves for cellulose mats and particles deviating from it. The behavior observed is interpreted as the effect pore and interstice penetration play in cellulase binding to the accessible surface of cellulose aggregates. These results validate our method for immobilizing nanoscale cellulose fibrils and fibril aggregates on solid supports and lay the foundation for future studies on cellulase–cellulose interactions. Biotechnol. Bioeng.

Determination of the molecular states of the processive endocellulase Thermobifida fusca Cel9A during crystalline cellulose depolymerization

Detailed understanding of cell wall degrading enzymes is important for their modeling and industrial applications, including in the production of biofuels. Here we used Cel9A, a processive endocellulase from Thermobifida fusca, to demonstrate that cellulases that contain a catalytic domain (CD) attached to a cellulose binding module (CBM) by a flexible linker exist in three distinct molecular states. By measuring the ability of a soluble competitor to reduce Cel9A activity on an insoluble substrate, we show that the most common state of Cel9A is bound via its CBM, but with its CD unoccupied by the insoluble substrate. These findings are relevant for kinetic modeling and microscopy studies of modular glycoside hydrolases.