Cyrus R. Safinya - US grants

The structure, phase behavior, and protein stability of membrane- associated proteins complexed with associating polymers which replace the lipid matrix will be investigated by x-ray diffraction and other techniques. The polymer-membrane protein associations represent a fundamentally new approach aimed at producing a new class of biomolecular materials. The first membrane-associated proteins to be studied are based on (i) integral memebrane proteins (e.g., bacteriorhodopsin) and (ii) self-assembled two-dimensional surface protein layers of bacteria. The two classes of associating polymers which we propose to consider consist of (i) hydrophobically associating copolymers, and (ii) ionomers.

This X-Ray facility will provide a rotating anode x-ray generator with accessories, a four-circle diffractometer and a two-circle diffractometer to scientists at the University of California, Santa Barbara. Research projects include studies of self-assembled biomaterials, polymer liquid crystals and copolymers, small angle x-ray reflectivity of thin complex fluid films, wide bandgap semiconductors, thin film and bulk ferroelectric oxides. This facility will provide a much needed high intensity source for material characterization and will complement facilities to be provided through the new Materials Research Laboratory being established at the University. This facility is being made available to all qualified users, and will provide first-hand experience to students and faculty.

w:\awards\awards96\*.doc 9624091 Safinya The structure of artificially developed self assembled membrane-associating-proteins and peptides in multilayers will be characterized by synchrotron x-ray diffraction techniques. The objective is to elucidate protein-protein interactions in these artificial self assemblies and to develop a new class of advanced materials consisting of functionalized interfaces manipulated at the molecular level. This should lead to advanced materials useful in optical, separations, chemical sensors, and high temperature catalysis applications. We will explore the structure and hydrogel behavior in a newly invented class of lamellar hydrogels based on fluid membranes and end-anchored polymer-lipids. "bioactive lamellar gels" useful in tissue healing or drug delivery applications will be developed with activity derived from biomolecules and mechanical stability from the polymer-lipid component. %%% This project seeks to develop a new class of materials consisting of multilayers of functionalized interfaces which can be manipulated at the molecular level. The components of these materials will consist of surfactants (surface active molecules), proteins, and peptides. The materials should be useful in molecular separations and purification technologies, biological and chemical sensors technologies, and high temperature catalysis applications. A new class of recently invented hydrogels invented in this laboratory will be explored further. The lamellar gels are made from liquid phases by the addition of water, a highly unusual behavior. Because the gels contains no solid component they have the potential of incorporating combinations of biologically active molecules. We will explore the development of "bioactive lamellar gels" useful in artificial tissue development, in tissue healing, and in drug delivery applications. ***

9512503 Stucky A charge coupled device (CCD), high intensity X-ray diffractometer will be acquired and utilized for materials synthesis and biotechnology research. The CCD detector and associated software allow for nearly single photon detection efficiency and rapid readout time of 512x512 pixels. The ease of use and rapid screening time of this instrument will permit the quick characterization of crystals as small as a few micrometers and of molecular crystals that are unstable and tend to deteriorate in the X-ray beam. Biomolecular phases and liquid crystal/membrane based composites with large unit cell structures that produce a large range of scattered intensities will be structurally accessible with this instrument. Zeolites, porous mesostructured materials, and fullerine-type structures that cannot be otherwise characterized because of their low scattering cross section, will also be studied. The large improvement in sensitivity provided by this instrument, in combination with available nuclear magnetic resonance (NMR) resources, represents a unique capability for studying complicated partially ordered polymeric materials. %%% The high sensitivity, fast data collection, x-ray diffractometer will enable a new materials characterization capability that will impact an existing interdisciplinary program of over one hundred students and faculty. It will facilitate research programs concerned with the design, synthesis, and processing of advanced materials, studies of non- equilibrium transformations in complex fluids and biological systems, and protein structure-property relationships. ***

An important goal of our proposal is developing a basic understanding of the essential protein-protein interactions, either direct or mediated through the membrane lipid, which are ultimately responsible for self-assembly. Thus we plan to characterize the structure and interactions in the bR reconstituted in model lipid membranes. Aside from the studies on bR, we also plan to develop novel temperature-stabilized protein-based biomaterials.

We propose to apply synchrotron-based small- and wide-angle x-ray scattering to characterize the structure, phase behavior, and interlayer interactions of (1) reconstituted and native self-assembled membrane-associated-proteins (maps) and (2) a fundamentally new class of biomolecular materials comprised of surfactant and associating polymers complexed with (maps). An important goal of the research is to establish a scientific basis for the intermacromolecular interactions leading to (map) self-assembly.

Not available

9802591
Zasadzinski
Characterization of complex fluids and biomaterials from the micron to nanometer scale is extremely important for the design and optimization of novel drug delivery systems, new mesoporous materials, polymer-surfactant phases and other self-assembling and soft material systems. While more commonly used techniques such as x-ray, neutron, and light scattering reveal much about the averaged structural features over these length scales, it is difficult to examine the range from nanometers to hundreds of microns with a single experiment or even a single scattering technique. Imaging complex fluids and biomaterials with electron microscopy is a necessary complement to scattering studies, especially as microscopy directly addresses the main limitations of scattering. However, high resolution imaging has its own experimental limitations: the fluid sample must be replaced by a solid, conductive, low vapor pressure version of the original material to be compatible with the requirements of electron or scanning tunneling microscopy. Experience has shown that the best method of making samples for TEM of STM is by rapid freezing, followed by freeze-fracture replication. In freeze-fracture replication, the rapidly frozen specimen is fractured at low temperature and high vacuum to expose the interior structure of the fluid. The fracture surface is then replicated by evaporation of a metal shadowing film to provide contrast in the TEM image or conductivity for STM, followed by a carbon backing film to provide sufficient strength for subsequent processing and imaging. The resolution in the technique is about 2 nm lateral and 0.5 nm vertical. The technique has proven to be ideal for a range of complex fluids and biomaterials including polymer and surfactant gels, surfactant micelles and microemulsions, biomembranes, lamellar, hexagonal and cubic surfactant liquid crystals, vesicles, liposomes, themotropic liquid crystals, etc. and can simultaneously resolve nanometer sized particles and their order, orientation and defects to 100 micron length scales.

This award provides support for a new Freeze-fracture System which will significantly improve the throughput of samples, decreasing the turnaround times from about 8 hours to about 1 hour per sample run. In the new equipment, the samples are loaded through a vacuum airlock, and the electron beam evaporation sources can also be externally adjusted via airlocks. Hence, the main vacuum chamber is never vented. On our current instrument, vacuum must be broken to introduce the specimen, replace the evaporation sources, and to remove the specimen after processing. Each sample run requires that the main chamber be vented at least 3 times, with the necessary pump down time in between. The faster turnaround will allow us to examine more samples more efficiently and the better vacuum will give higher resolution and less artifacts due to contamination. The evaporators on the new equipment are externally controlled to provide higher resolution replicating films with less down time.

The freeze-fracture equipment will be available to other researchers in the department and the University. The instrumentation at the University of California at Santa Barbara is heavily used by a collaborative group of scientists studying complex fluids and biomaterials, and by industrial and academic collaborators in California (Depotech, Alliance Pharmaceuticals) and elsewhere (U. Delaware. Dow Chemical).
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9972246
Safinya

This project investigates the properties of biomolecular materials consisting of biological polymers (e.g. DNA; components of the cell cytoskeleton which consists of the filamental proteins: microtubules, intermediate filaments, and filamental-actin) condensed with oppositely charged chemical species such as multivalent counter-ions. These materials are useful models for statistical theories of polyelectrolytes. For example, the studies should shed light on the nature of the molecular forces in the condensation of DNA in vivo (i.e. the DNA packing problem). The project provides excellent training for graduate students within a diverse, interdisciplinary program enabling them to acquire skills that are currently in great demand in Industry, National Laboratories, and Universities. Advanced miniaturized materials will be produced from biological molecules self-assembled on patterned surfaces. The biological-semiconductor hybrid materials should be utilized in the next century in pharmaceutical, biomedical, and semiconductor industries emphasizing miniaturized materials (e.g. nano-conduits and nano-wires).
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This project offers excellent research and education opportunities for graduate students within a diverse, interdisciplinary program, focused on biomolecular materials, in particulal biological materials that self-assembled on patterned surfaces. Potential uses of these processed materials include chemical and biological sensors, micro-machine elements, and molecular sieves. The graduate students will acquire skills that are currently in great demand in a broad range of industries including those which combine nanometer scale fabrication systems with biomolecular materials in chemicals, pharmaceutical and biotechnology, and semiconductors. They will be trained in state-of the-art techniques which include, methods for preparing biomolecular self-assemblies, fabrication of micron and nanometer scale patterns on semiconducting surfaces, direct imaging with Atomic Force Microscopes and optical light microscopes, and structural measurements using quantitative x-ray diffraction methods at the National Synchrotron Facilities at Stanford and Argonne National Laboratories.
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Funds are requested for the purchase of an environmental scanning electron microscope to be used in a new Micro-Environmental Imaging and Analysis Facility. Among the projects that would benefit from the new equipment are studies of biofilm mobility in the soil, non-viral gene delivery methods, protein-inorganic biomineralization, and nanobiofabrication techniques. The major benefit of the new equipment would be its ability to image delicate materials such as biologicals without introducing artifacts in the sample preparation process. Faculty from numerous departments including Materials, Chemistry, Chemical Engineering, and Molecular, Cellular, and Developmental Biology would utilize the equipment.

There is currently a surge of activity in developing synthetic nonviral gene delivery systems for gene therapeutic applications because of their low toxicity, nonimmunogenicity, and ease of production. Cationic liposome-DNA (CL-DNA) complexes have shown gene expression in vivo in targeted organs, and human clinical protocols are ongoing. Moreover, the single largest advantage of nonviral over viral methods for gene delivery is the potential of transferring extremely large pieces of DNA into cells. This was clearly demonstrated when partial fractions of order Mega base pairs of human artificial chromosome (HAC) was transferred into cells using cationic liposomes (CLs) as a vector although extremely inefficiently. However, because the mechanism of action of CL-DNA complexes remains largely unknown, transfection efficiencies are at present very low and vary by up to a factor of 100 in different cell lines. The low transfection efficiencies with nonviral delivery methods are the result of poorly understood transfection-related mechanisms at the molecular and self-assembled levels, in particular, a general lack of knowledge of structures of CL-DNA complexes and their interactions with cellular components inside animal cells which lead to gene release and expression. The aims of this research application are (1) to explore the various self-assembled structures in CL-DNA complexes and to identify the critical parameters which control the intermolecular interactions and give rise to the structures, and (2) to determine the relation between the CL-DNA complex structures and transfection efficiency in animal cell culture. To achieve the goals of this application we will use state-of the-art techniques involving synchrotron x-ray scattering and diffraction (at the Stanford Synchrotron Radiation Laboratory) and video-enhanced optical microscopy to probe the structures of CL-DNA complexes and their interactions with animal cells. The structures will be correlated to transfection efficiencies by modern molecular biology methods of quantitatively measuring expression of the luciferase reporter gene in animal cells. The broad long-range goal of the research is to develop optimal synthetic nonviral carriers of DNA for gene therapy and disease control.

0076357
Cyrus

This is an instrument development award from the Instrumentation for Materials Research program to the University of California Santa Barbara (UCSB). Investigators at UCSB will develop a scanning microprobe short wavelength (3.1 A - 0.31 A, photon energy 4 keV - 40 keV ) x-ray microscope capable of multiple imaging modes with 50 nm - 500 nm spatial resolution at the Advanced Photon Source (APS). The microscope will allow co-localized determination of elemental distribution and chemical states by x-ray fluorescence and absorption spectroscopy. Using a combination of K and L shell fluorescence, it will be possible to map the spatial distribution of all elements in the periodic table with detection sensitivity approaching parts-per-billion (ppb), surpassing by orders of magnitude the current level set by charged-particle microprobes. Spectroscopic micro-imaging will be accomplished by spatially resolved X-ray Absorption Near Edge Structure (XANES) measurements, which provide definitive information on the local oxidation states of heavy metallo-ions vitally important in many biological (e.g. cellular development) and environmental (e.g. contaminated soil remediation) studies. The microscope will be constructed at UCSB and installed at the APS accessible by the broader user community through the 25% of total beam time allocated to general users. At a later stage, a second generation microscope will be installed at the Stanford Synchrotron Radiation Laboratory. This instrument development provides excellent opportunities for the training of graduate and undergraduate students. The project will also contribute to enriching of science education for local K-12, and community college.
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An important goal of our proposal is developing a basic understanding of the essential protein-protein interactions, either direct or mediated through the membrane lipid, which are ultimately responsible for self-assembly. Thus we plan to characterize the structure and interactions in the bR reconstituted in model lipid membranes. Aside from the studies on bR, we also plan to develop novel temperature-stabilized protein-based biomaterials.

Abstract
CTS-0103516
M.Tirrell, University of California-Santa Barbara


The work proposed here aims to develop the science of spontaneously dividing three-dimensional space into compartments, that is, into controlled environments, at the nanometer size scale, in order to accomplish several engineering objectives. The objectives include: controlled release of therapeutic agents (e.g., drugs, genetic materials); controlled access to biofunctional components (switching or masking activities when desirable); embedding biological signaling within 3D matrices (nano-phase-separated block co-polypeptides decorated with targeting or "homing" ligands) and using surface patterning and templating to produce novel or tailored structures and environments. Four project areas encompass and organize our overall plan: 1. Creating nano-environments via lipid encapsulation; 2. Nano-environments from peptide amphiphiles; 3. Amphiphilic block copolypeptides with hierarchical structures; 4. Patterned surfaces for self-assembly. The work we will do is conceptually similar to creating artificial cells in the sense of separating regions for different functions (without any attempt to build in self-replication). We are aiming toward bio-mimetic structures for functions that may not be naturally occurring, and that mimic or supply interesting functionality. The kinds of functions we wish to incorporate vary from biological (e.g., cell adhesion) to non-biological (e.g., fluid connectivity).

The science we will pursue is the principle of spontaneously creating compartments or confined regions with a definite inside and outside. As a practical matter, this means delving deeper into controlled formation of micelles, vesicles, domains, tubules and other controlled regions, as part of larger assemblies of nanoscale components. We will synthesize new lipid-like and macromolecular architectures to drive self-assembly in ways that can encapsulate some species and exclude or display others, controllably, on the interiors and exteriors, respectively, of defined regions. Our research will produce new materials for biomedical applications, new therapeutic approaches based on controllable binding and transport processes and new ways of integrating biological structures with semiconductor fabricated devices. Our core expertise includes extensive experience with lipid and macromolecular structure and phase behavior, based on substantial ability to synthesize new molecules. We have experience with assessing and influencing biological activities and functions, ranging from cell adhesion, to drug delivery and gene transfection, to the roles of metal ions in growth processes and pathological conditions. Characterization expertise and facilities for all of this work are readily available among the members of this collaboration: electron microscopy (adapted in several ways for soft, wet, biological samples), scanning probe nicroscopies, optical microscopy (with fluorescence, confocal, interference and video capabilities), surface force measurements, x-ray and neutron scattering, neutron reflectometry and organic synthesis.

The interdisciplinary talents of this team are essential to educate students broadly in the new fields of nanotechnology and biotechnology. The five graduate students and one postdoctoral fellow supported by this proposed grant will work in broad areas of the overall project where interests of several groups overlap strongly. In this way, the students will have continued exposure to the full interdisciplinary group of biochemists, chemists, physicists, chemical engineers and materials scientists that make up our team. An active effort is planned to attract a diverse population of students to this project. We believe that the students and fellow trained in the course of this research will be extraordinarily flexible in their talents, and therefore exceptionally, well-prepared for careers in industry or universities, because of the multiple advisor, multiple technique environment we will provide. The PI and co-PI's will manage this project to continuously promote this interdisciplinary approach in the selection of specific projects to be pursued. The efforts from this project will feed new ideas, examples and practical experience into a new laboratory-based course under development entitled, "Biomaterials Preparation and Characterization".

This combined experiment and theory project is in the area of soft condensed matter physics. The research will explore phases, structures, and interactions, in supramolecular assemblies of filamentous cytoskeletal proteins and their associated biomolecules. The importance of the experiments lies in their potential to uncover the origin of fundamentally new attractive forces between charged biological polymers, which can lead to new states or arrangements of matter. The project should shed light on the physics of charged polymers, which constitute a group of technologically important industrial materials. The program trains graduate students in state-of-the-art techniques required to address complex multidisciplinary problems at the interface between physics, engineering, chemistry, and biology. The research includes structure characterization at National Synchrotron X-ray Laboratories and in-house imaging with laser-scanning confocal microscopy. This will provide student training in research settings where traditional discipline boundaries between physics, engineering, chemistry, and biology, have been removed, and teamwork and problem solving are emphasized. This will prepare the students to tackle and solve complex technological problems in their careers in academe, industry, or government.
This combined experiment and theory project is in the area of soft condensed matter physics. The research focuses on producing and characterizing novel materials that are obtained when biological polymers (e.g. proteins) are brought together to form new structures with dimensions between one-billionth of a meter and one-thousandths of a meter. New "composite" materials in this size range can have technological applications in areas such as molecular-based chemical sensors, molecular sieves for separations and purification technologies, and chemical and drug delivery vehicles. The project is highly interdisciplinary and exposes graduate students to a broad spectrum of techniques. These include state-of-the-art structure characterization with synchrotron x-ray diffraction at National Synchrotron X-ray Laboratories, and in-house imaging with cutting edge optical and electron microscopes. The educational significance and impact of this interdisciplinary project, at the interface between physics, engineering, chemistry, and biology, is in the training of students with a broad outlook toward problem solving. They will be valuable not only in academic settings, but also in the industrial and government job force where interdisciplinary research is required and rewarded.

DESCRIPTION (provided by applicant): There is currently a surge of activity in developing virus-free lipid-based gene delivery systems for therapeutic applications because of their low toxicity, nonimmunogenicity, and ease of production. Cationic liposome-DNA (CL-DNA) complexes have shown gene expression in vivo in targeted organs, and human clinical protocols are ongoing. These lipid-gene complexes have the potential of transferring large pieces of DNA into cells. Indeed, partial fractions of order 1 million base-pairs of human artificial chromosome have been transferred into cells using cationic lipids as a vector although extremely inefficiently. Because our understanding of the mechanisms of action of CL-DNA complexes remains poor, transfection efficiencies are very low compared to gene delivery with viral vectors. The low transfection efficiencies with virus-free delivery methods are the result of poorly understood transfection-related mechanisms at the molecular and supramolecular levels, and a general lack of knowledge of interactions of lipid-gene complexes with components inside cells which lead to gene release and expression. The aims of this research application are (1) to clarify the relation between the physical and chemical parameters of CL-DNA complexes with a distinct nanostructure, and transfection efficiency in mammalian cells, and (2) to determine the nanostructures and transfection efficiency properties of a new class of surface-functionalized CL-DNA complexes, which are designed for specific interactions with cellular components. The structure of the lipid-gene complexes will be solved by using state-of the-art synchrotron x-ray diffraction techniques at the Stanford Synchrotron Radiation Laboratory. Laser scanning confocal microscopy will enable us to track the CL-DNA particles and observe their interactions with cells. The structures will be correlated to transfection efficiencies by modern molecular biology methods of quantitatively measuring expression of the luciferase reporter gene in mammalian cells. The broad long-range goal of the research is to develop optimal synthetic virus-free carriers of DNA for gene therapy and disease control.

PROPOSAL NO.: CTS-0404444
PRINCIPAL INVESTIGATOR: CARL MEINHART
INSTITUTION: UNIVERSITY OF CALIFORNIA- SANTA BARBARA


NIRT: TITANIUM-BASED BIOMOLECULAR MANIPULATION TOOLS

This proposal was received in response to Nanoscale Science and Engineering initiative, NSF 03-043, category NIRT. Novel micro/nanofluidic chips will be develop and optimized for separating, mixing, concentrating and positioning biomolecules and cells. Pioneering work in titanium micro/nanofabrication technology with alternating current electrokinetics & microfluidics will be developed to provide unique tools for the biotechnology industry. Titanium is a relatively new platform for fabrication of nanostructures. It allows complicated 3-D electrode structures to be fabricated, and is biologically compatible. Theoretical and experimental analysis of electrokinetic phenomena will be conducted to investigate details of the underlying physics. The titanium fabrication technology has the potential to revolutionize micro/nanoscale devices, especially in the areas of biotechnology, drug delivery, and in vivo sensing & probing, where durability and bio-compatibility are critical. The advanced electrokinetics and nanoscale electrode structures can be used to concentrate small (~50 nm) proteins and viral particles, which has not been achievable previously using dielectrophoresis. This research project will provide an opportunity to educate graduate students in the areas of micro/nano fabrication, nanofluidics, electrokinetics, and cell culturing in micro/nanodevices. The PIs teach a newly-developed three course sequence at the senior/graduate level on MEMS/NEMS design & fabrication, micro/nanofluidics & electrokinetics. These courses give students broad exposure to fundamental issues and the current state of the art in MEMS/NEMS and train students for careers and research opportunities in nanotechnology. The research program will also be used to advance underrepresented groups in science and engineering. In addition, the PIs will continue their outreach activities at local high schools, educating students and teachers about how science and technology impacts society, and encouraging students to pursue careers in nanotechnology & science.

The project is expected to elucidate the key parameters that control the interactions between proteins derived from the cell cytoskeleton, which lead to hierarchical supramolecular structures on the nanometer to micron scale. Experiments with custom synthesized macromolecular counter-ions with defined chemical structure, will distinguish between the differing roles of charge and size of the counter-ion in controlling intermolecular interactions. Peptide-based counter-ions will be used to clarify the role of the shape of the counter-ion on the symmetry of the self-assembly. From a broader perspective, the research will lead to the rather exciting and formidable task of unraveling the biophysics of the cell cytoskeleton. The elucidation of the basic rules of assembly of filamentous proteins has potential for developing novel miniaturized materials for the 21st century. The multidisciplinary project integrates research and education in order to train students and postdoctoral researchers in modern methods required to address important problems at the interface between physics, biology, chemistry, and engineering with potential applications in biotechnology and nanotechnology.
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The project centers on discovering the key parameters that control the interactions and forces between proteins, which are used as the building blocks of the skeleton of cells. To a large extent Nature uses electrostatic forces to assemble its building blocks in distinct shapes and sizes for specific functions. The learned concepts should lead to the exciting possibility of developing advanced nanometer scale materials for nanoscience applications in the electronic, chemical, and pharmaceutical industries. The multidisciplinary project integrates research and education in order to train students and postdoctoral researchers in modern methods required to address important problems at the interface between physics, biology, chemistry, and engineering with potential applications in biotechnology and nanotechnology. The acquired interdisciplinary skills, which include synchrotron x-ray diffraction at National Facilities and state-of-the-art optical and electron microscopy methods, prepare the trainees for careers in academe, national laboratories, and industry.

Technical Abstract

The development project is aimed at advancing the design technology for ultra-high-resolution small angle x-ray scattering (SAXS) instrumentation and x-ray optics with broad applications in nanoscale structure characterization. A new optical design concept that can significantly enhance (up to 10-fold) the resolution and signal-to-noise ratio in SAXS measurements will be developed. The superior performance results from a compound optical configuration incorporating both a primary monochromator mirror and a pre-sample secondary focusing mirror to increase resolution and peak intensity. This unique design is expected to supplant the prevalent three-pinhole configuration in current SAXS instruments. The scientific and engineering problems of interest cover a range of multidisciplinary fields including soft condensed matter, biological physics and bioengineering, neuroscience, and bioinorganic chemistry. The instrument will operate out of the x-ray facility of the Materials Research Laboratory, with an established user base of more than 250 researchers from campus, other institutions and local industry. The development should broadly impact the national academic research infrastructure by advancing the optical design and performance of SAXS instrumentation used in diverse research areas in nanoscience and nanotechnology. The investigators of this project will continue their involvement in their numerous outreach programs available at UCSB to improve access to science for diverse groups, including undergraduate and graduate student training, outreach to K-12 students and teachers, and community outreach.

Lay Abstract

Enhancing structure characterization of nanomaterials is critical to the emerging areas of nanoscience, nanotechnology, and biotechnology. We will develop a laboratory-based microbeam x-ray scattering instrument for discovering the structures of novel new materials on the 1 nanometer to 1000 nanometer scale. The performance of this new instrument will exceed the best commercially available x-ray instrument and will provide a significant enhancement to the campus infrastructure in nanoscience and technology. The development of this cutting edge x-ray characterization tool will establish UCSB as one of strongest institutions in the x-ray characterization area, which will attract users not only from multiple campus groups but also from other research institutions as well. The project provides an excellent training opportunity to graduate students and postdoctoral researchers who will not only participate in building the cutting-edge x-ray tool but also be able to utilize it in a series of research projects which will take advantage of the new capability afforded by the instrument. The x-ray development program will be integrated with the ongoing outreach activities of the principle investigators in mentoring undergraduate students and local high school teachers participating in the large number of ongoing summer internship programs at UCSB.

DESCRIPTION (provided by applicant): There is currently a very large research activity in developing lipid- based vectors for therapeutic applications because of their nonimmunogenicity, low toxicity, ease of production, and the potential of transferring large pieces of DNA into cells. Indeed cationic liposome (CL) based vectors are among the prevalent synthetic carriers of nucleic acids currently used in human clinical gene therapy trials worldwide. The vectors are studied both for gene delivery with CL-DNA complexes and gene silencing with CL-siRNA (short-interfering RNA) complexes. However, their transfection efficiencies and silencing efficiencies remain low compared to those of engineered viral vectors. The low efficiencies are the result of poorly understood transfection-related mechanisms at the molecular and self-assembled levels, and a general lack of knowledge about interactions between membranes and double stranded nucleic acids resulting in stable complex formation, and between membrane-nucleic acid complexes and cellular components. The aims of this research application are (1) to use custom synthesized degradable and PEGylated lipids, and biophysical characterization, in order to clarify the interactions between lipid-nucleic acid complexes and cellular components for improved understanding of structure-function properties, and (2) to clarify structures and interactions between cationic membranes and siRNA in CL-siRNA complexes used in gene silencing. Modern methods of organic and solid phase chemistry will be employed to synthesize multivalent degradable lipids, peptide-PEG-lipids, and acid labile PEG-lipids. The structure of the lipid-nucleic acid complexes will be solved by using synchrotron x-ray diffraction techniques at the Stanford Synchrotron Radiation Laboratory and cryo-electron microscopy at UCSB and the Scripps Research Institute. Confocal microscopy will enable us to track the lipid-nucleic acid complexes and observe their interactions with cells. The structures will be correlated to the biological activity of complexes interacting with cells by quantitative measurements of transfection efficiency and silencing efficiency both in DMEM and in high-serum for in vivo applications. The broad long-range goal of the research is to develop a mechanistic understanding of the biophysical interactions between cationic membranes and biologically active double stranded nucleic acids and between CL-nucleic acid complexes and cells, which will generate custom lipid-carriers of nucleic acids ultimately for use in gene therapeutics and disease control. PUBLIC HEALTH RELEVANCE: The project proposes to use a mechanistic approach to further the understanding of lipid carriers of therapeutic DNA and RNA. This, in turn, will lead to new materials and methods and the development of efficient lipidic DNA and RNA carriers for disease control. The goals will be accomplished by applying biophysical scientific methods to custom designed lipids and therapeutic molecules, made available by advanced synthetic methods.

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Complexes comprising siRNA and lipidic aminoglycoside derivatives have been recently imaged by Cryo-EM, displaying a typical layered microstructure. In our lab we prepared lipid-siRNA constructs using a variety of lipid systems which have been successfully employed in gene silencing activities. The lipid-siRNA phase behavior appears to be very rich and so far we have identified by X-ray scattering three categories of supramolecular structures. Specifically: i) a lamellar phase obtained with commercially available cationic/non-ionic lipids, ii) a 2D hexagonal structure obtained with multivalent cationic lipids synthesized in our lab, and finally iii) a bicontinuous cubic phase obtained by a combination of a "cubic forming" neutral lipid and "home synthesized" multivalent cationic lipids (as well as commercially available). In addition, we have observed that the nature of the phase has a great impact on SE. We propose Cryo-EM experiments to obtain 2D images of the lipid nanoparticles alone and upon aggregation with siRNA. Our long-term goals are to locate the siRNA domains in the lipid-siRNA aggregate.

DESCRIPTION (provided by applicant): The current level of research activity involving gene therapy with either synthetic vectors (carriers) or engineered viruses is unprecedented. Cationic liposomes (CLs) have emerged worldwide as among the most prevalent synthetic vectors employed in human clinical trials, due to their near lack of immune response and low toxicity. CL-vectors are also able to carry large pieces of DNA (consisting of entire genes and regulatory regions) into cells, which is not feasible with engineered viral vectors due to the limited size of virus capsids. CL_nucleic acid (CL_NA) complexes are employed both as DNA carriers and as siRNA (short interfering RNA; for gene silencing) carriers. However, the transfection efficiency and silencing efficiency of CL-vectors compared to viral vectors remains low for in vivo applications. Improvement of the efficiencies of synthetic vectors intended for in vivo applications requires a knowledge of the structures of CL-DNA and CL-siRNA complexes (in particular, the electrostatic interactions stabilizing assemblies of membranes and double-stranded NAs) as well as a mechanistic understanding of their interactions with cell membranes and the events leading to release of DNA and siRNA inside the cell. The aims of this research application are (1) to develop a new class of multi-component surface-functionalized CL-NA complexes, which will enable a mechanistic understanding of the initial pathway of complex uptake by the cell and the subsequent release of the NA-containing complex into the cell interior (cytosol), and (2) to understand the influence of lipid shape and membrane elastic properties on the formation of a new class of CL-DNA complexes possessing the membrane shape desired for interactions with endosome membranes inside the cell that optimally facilitate endosomal escape. Modern methods of organic and peptide chemistry will be employed to synthesize distinct PEG-lipids for cell targeting and endosome escape properties. These will be strategically combined in order to prepare high efficiency PEGylated CL-DNA complexes. The structures of CL-NA complexes will be solved using modern synchrotron x-ray diffraction techniques at the Stanford Synchrotron Radiation Lightsource and cryo-electron microscopy at the National Resource for Automated Molecular Microscopy at the Scripps Research Institute. Live-cell imaging with state-of-the-art optical fluorescence microscopes will allow us to visualize the interactions between CL-NA complexes and cellular components. Their structures will be correlated to their biological activity by quantitative measurements of transfection efficiency and silencing efficiency. The broad, long-term objective of our research is to develop a fundamental science base (via mechanistic studies of interactions of CL-NA complexes and cells) that will lead to the design and synthesis of synthetic carriers of DNA and siRNA optimized for gene therapeutics and disease control.

Project Summary/Abstract The current level of research activity involving gene therapy with either synthetic vectors (carriers) or engineered viruses is unprecedented. Liposomes are the most widely studied nonviral carriers worldwide for nucleic acid (NA) and drug delivery applications. Cationic liposomes (CLs) are relatively safe nonviral vectors used in ongoing clinical trials. CLs may either be complexed via electrostatic interactions with therapeutic NAs (anionic DNA or short interfering RNA) for gene delivery and silencing, or used as vectors of potent cytotoxic hydrophobic drugs, encapsulated within their lipid bilayer, in cancer therapeutics. Among the biggest advantages of nonviral vectors (over viral vectors which are currently more efficient in in vivo settings) are their safety, their low immunogenicity and their ability to transfer entire genes (containing coding and noncoding sequences) and regulatory sequences into cells (currently not feasible with engineered viruses because of capsid size limitations). The development of nonviral lipid-based vectors with efficacy competitive with viral vectors in vivo will require a mechanistic understanding of how synthetic vectors may be functionalized to overcome the major intracellular hurdle of endosomal escape. Successful endosomal escape is required for release of therapeutic nucleic acid within the cell cytosol and therefore maximum efficacy. The first aim of this research application is to employ modern biophysical and synthetic approaches to the rational design of functionalized CL?NA nanoparticles (NPs) with synergistic, complementary dual-function PEG-lipid and fusogenic components for optimized endosomal escape. Modern methods of organic and solid phase chemistry will be employed to synthesize dual-function PEG-lipids with cell targeting and endosome escaping properties. The second aim of this research application is to optimize efficacy of a new class of CL-based carriers of the hydrophobic drug paclitaxel (PTXL) for cancer therapeutics. This will be achieved by developing a mechanistic understanding of the relation between physical and chemical properties of the carrier (i.e. size of the functionalized CL carrier, membrane spontaneous curvature, and lipid tail structure) and functional efficacy (i.e. PTXL membrane solubility, cell uptake of vector and PTXL delivery leading to cytotoxicity against human cancer cells). The structures of CL-based vectors of NAs and hydrophobic drugs will be characterized using cryogenic electron microscopy and synchrotron x-ray diffraction techniques. The interactions between CL vectors and cell organelles will be directly visualized with spinning disk confocal fluorescence microscopy. Their structures will be correlated to their biological activity in human cancer cells. The broad, long-term objective of our research is to develop a fundamental science base through mechanistic studies that will lead to the design and synthesis of nonviral vectors of nucleic acids and hydrophobic drugs for gene and cancer therapeutics.