Progress 06/01/07 to 05/30/11
Outputs
OUTPUTS: Our proposed research objectives are: 1) to develop a SPM-based single molecule recognition technology and use it to study ligand-receptor interactions at the single-cell and single molecule level for applications in agricultural, food safety, environmental assessment, bio-processing, and health care concerns; 2) to use the technology to detect pathogens and toxins in food with single molecule sensitivity and provide methodologies for key scientific advances in understanding, identifying, and developing therapies that promote animal and human health. In the whole project period, we used a parallel approach and carried out multiple activities in order to simultaneously make progress under each of the above objectives. 1. Developed several protocols for AFM tip modification and sample immobilization. These include our invention of a simple, two step click chemistry AFM tip modification with anti-ricin antibody, and DNA aptamers for single ricin detection; 4-dibenzocyclooctynol functionalized AFM tip to map spatial arrangements of surface functional groups on the multifunctional organic nanoparticles; Peptide functionalized AFM tip for single-molecule receptor-ligand interactions on cancer cell membrane, and the protocols for immobilizing receptor molecules on gold, mica, silicon, and lipid bilayer surfaces. 2. Studied the biophysical principles of ligand--ricin single molecule interactions and used the single molecular recognition and sensing technology to detect the toxin ricin at the single molecule level. 3. Developed single molecule interaction techniques that can be used to study the single molecule interactions on the real biomembranes. 4. Computational modeling using AMBER 11 for single molecule interaction dynamics and kinetics. 5. Expended this technology to monitor the fibrinogen self-assembly on gold surface and gold nanoparticles in real-time. 6. Extended this technology in plant cell wall strcutural and CBM-cellulose intercations study. PARTICIPANTS: The participients include: Prof. Bingqian Xu; Dr. Bosson Park; Prof. Geet-Jan Boons; Dr. Guojun Chen (then PhD student in Xu's group); Dr. Cunlan Guo; Mr. Bin Wang (PhD student in XCu's group); Dr. Jianfeng Zhou (then PhD student in Xu's group). TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The research will significantly advance new radical methodology to realize robust, repeatable, and highly reliable characterization and detection of single molecule interactions and recognitions. The novelty of this project lies in the following areas: 1). The highly integrated and effective methods combine Scanning Probe Microscope (SPM) nanolithography, microscopes (SPM and inverted optical microscope), SPM spectroscopy and SPM-based break junction (SPMBJ) methods to study single molecular interaction properties, such as cellulose binding module binding to cellulose for legitimate design of better enzymes for cellulose hydrolysis. 2). Integrating nanolithography, imaging and chemical and physical property detections capabilities into a single technique that make it possible to study multiple molecules under identical conditions. 3). By precisely control the movement of the SPM tip, it is highly possible to resolve the lateral distribution of cell surface components in real-time with nanometer resolution without labeling with fluorescence, radioactive, or enzyme probes; in addition, the new methodology will make it possible to determine the type and location of a single molecular binding event occurring in the cell surface membrane, reorganize the different proteins involved in the biological binding events, and measure the biomechanical interactions between the membrane-bound proteins and the underlying membrane. This study will develop a multifunctional technique that potentially provide capabilities in studying protein structures, cellular expression, and may have relevance to drug discovery and functionality, cell biology etc.
Publications
- 1.Xu BQ. 2007. Modulating the conductance of a Au-octanedithiol-Au molecular junction. Small 3:2061-5 2.Sun HQ, Bai Y, Liu HJ, Jin WQ, Xu NP, et al. 2008. Mechanism of nitrogen-concentration dependence on pH value: Experimental and theoretical studies on nitrogen-doped TiO2. J. Phys. Chem. C,112:13304-9 3.Chen GJ, Ning XG, Park B, Boons GJ, Xu BQ. 2009. Simple, Clickable Protocol for Atomic Force Microscopy Tip Modification and Its Application for Trace Ricin Detection by Recognition Imaging. Langmuir 25:2860-4 4.Chen GJ, Zhou JF, Park B, Xu BQ. 2009. Single ricin detection by atomic force microscopy chemomechanical mapping. Appl. Phys. Lett. 95(4): 043103/1-043103/3 5.Liu B, Li XY, Li BL, Xu BQ, Zhao YL. 2009. Carbon Nanotube Based Artificial Water Channel Protein: Membrane Perturbation and Water Transportation. Nano Lett. 9:1386-94 6.Wang L, Wu ZZ, Xu BQ, Zhao YP, Kisaalita WS. 2009. SU-8 microstructure for quasi-three-dimensional cell-based biosensing. Sensor. .Actuat. B-Chem. 140:349-55 7.Zhou JF, Chen F, Xu BQ. 2009. Fabrication and Electronic Characterization of Single Molecular Junction Devices: A Comprehensive Approach. J..Am. Chem. Soc. 131:10439-46 8.Chen F, Zhou JF, Chen GJ, Xu BQ. 2010. A Novel Highly Integrated SPM System for Single Molecule Studies. IEEE Sens. J. 10:485-91 9.Chen GJ, Ni NT, Wang BH, Xu BQ. 2010. Fibrinogen Nanofibril Growth and Self-Assembly on Au (1,1,1) Surface in the Absence of Thrombin. Chemphyschem 11:565-8 10.Guo J, Chen GJ, Ning XH, Wolfert MA, Li XR, et al. 2010. Surface Modification of Polymeric Micelles by Strain-Promoted Alkyne-Azide Cycloadditions. Chem. Eur. J.16:13360-6 11.Zhou JF, Xu BQ, 2010. Recent Patents of nanopore DNA Sequencing Technology: Progress and Challenges, Recent Pat. Gene Seq. 4 (3), 192-201 12.Zhou JF, Chen GJ, Xu BQ. 2010. Probing the Molecule-Electrode Interface of Single-Molecule Junctions by Controllable Mechanical Modulations. Journal of Physical Chemistry C 114:8587-92 13.Chen GJ, Ni NT, Zhou JF, Chuang YJ, Wang BH, et al. 2011. Fibrinogen Clot Induced by Gold-Nanoparticle In Vitro. J. .Nanosci. .Nanotechno. 11:74-81 14.Sheng J, Hassan AEA, Zhang W, Zhou JF, Xu BQ, et al. 2011. Synthesis, structure and imaging of oligodeoxyribonucleotides with tellurium-nucleobase derivatization. Nucleic Acid Res. 39:3962-71 15.Zhou JF, Xu BQ. 2011. Determining contact potential barrier effects on electronic transport in single molecular junctions. Appl. Phys. Lett. 99(4): 042104/1-042104/3 16.Nie,JX, Guo L, Li KM, Wang YH, Chen GJ, et.al. 2012 Axonal Fiber Terminations Concentrate on Gyri Cerebral Cortex, Epub (doi: 10.1093/cercor/bhr361) 17.Guo J, Chen GJ, Ning XH, Li XR, Zhou JF, et al. 2012. A Chemo-Mechanical Tweezer for Single-Molecular Characterization of Soft Materials. Chem. Eur. J. 18:4568-74 18.Negri P, Chen GJ, Kage A, Nitsche A, Naumann D, et al. 2012. Direct Optical Detection of Viral Nucleoprotein Binding to an Anti-Influenza Aptamer. Anal. Chem. 84:5501-8 19.Wang B, Guo CL, Chen GJ, Park B, Xu BQ. 2012. Following aptamer-ricin specific binding by single molecule recognition and force spectroscopy measurements. Chem. Commun., 48:1644-6 20.Wang B, Guo CL, Zhang MM, Park B, Xu BQ. 2012. High-Resolution Single-Molecule Recognition Imaging of the Molecular Details of Ricin-Aptamer Interaction. J. Phys. Chem. B., 116:5316-22 21.Yan L, Zheng YB, Zhao F, Li SJ, Gao XF, et al. 2012. Chemistry and physics of a single atomic layer: strategies and challenges for functionalization of graphene and graphene-based materials. Chem. Soc. Rev. 41:97-114 22.Zhang MM, Wu SC, Zhou W, Xu BQ. 2012. Imaging and Measuring Single-Molecule Interaction between a Carbohydrate-Binding Module and Natural Plant Cell Wall Cellulose. J. Phys. Chem. B., 116:9949-56 23.Zhou JF, Guo CL, Xu BQ. 2012. Electron transport properties of single molecular junctions under mechanical modulations. J. Phys. Condens. Matt. 24, 164029/1-164029/9
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Progress 01/01/10 to 12/31/10
Outputs
OUTPUTS: Our proposed research objectives are: 1) to develop a SPM-based single molecule recognition technology and use it to study ligand-receptor interactions at the single-cell and single molecule level for applications in agricultural, food safety, environmental assessment, bio-processing, and health care concerns; 2) to use the technology to detect pathogens and toxins in food with single molecule sensitivity and provide methodologies for key scientific advances in understanding, identifying, and developing therapies that promote animal and human health. In the year of 2010, we used a parallel approach and carried out multiple activities in order to simultaneously make progress under each of the above objectives. 1. Further Developed several protocols for AFM tip modification and sample immobilization. These include our invention of a simple, two step click chemistry AFM tip modification with anti-ricin antibody, and DNA aptamers for single ricin detection; 4-dibenzocyclooctynol functionalized AFM tip to map spatial arrangements of surface functional groups on the multifunctional organic nanoparticles; Peptide functionalized AFM tip for single-molecule receptor-ligand interactions on cancer cell membrane, and the protocols for immobilizing receptor molecules on gold, mica, silicon, and lipid bilayer surfaces. 2. Studied the biophysical principles of ligand--ricin single molecule interactions and used the single molecular recognition and sensing technology to detect the toxin ricin at the single molecule level. 3. Developed (and are still developing) single molecule interaction techniques that can be used to study the single molecule interactions on the real biomembranes. 4. Computational modeling using AMBER 11 for single molecule interaction dynamics and kinetics. 5. Expended this technology to monitor the fibrinogen self-assembly on gold surface and gold nanoparticles in real-time. PARTICIPANTS: Dr. Jiafeng Zhou; Mr. Guojun Chen; Mr. Bin Wang, Ms. Mengmeng Zhang TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.
Impacts
The research will significantly advance new radical methodology to realize robust, repeatable, and highly reliable characterization and detection of single molecule interactions and recognitions. The novelty of this project lies in the following areas: 1). The highly integrated and effective methods combine Scanning Probe Microscope (SPM) nanolithography, microscopes (SPM and inverted optical microscope), SPM spectroscopy and SPM-based break junction (SPMBJ) methods to study single molecular interaction properties, such as cellulose binding module binding to cellulose for legitimate design of better enzymes for cellulose hydrolysis. 2). Integrating nanolithography, imaging and chemical and physical property detections capabilities into a single technique that make it possible to study multiple molecules under identical conditions. 3). By precisely control the movement of the SPM tip, it is highly possible to resolve the lateral distribution of cell surface components in real-time with nanometer resolution without labeling with fluorescence, radioactive, or enzyme probes; in addition, the new methodology will make it possible to determine the type and location of a single molecular binding event occurring in the cell surface membrane, reorganize the different proteins involved in the biological binding events, and measure the biomechanical interactions between the membrane-bound proteins and the underlying membrane. This study will develop a multifunctional technique that potentially provide capabilities in studying protein structures, cellular expression, and may have relevance to drug discovery and functionality, cell biology etc.
Publications
- Sheng J, Abdalla H, Zhang W, Zhou JF, Xu BQ, Soares AS, Huang Z, 2011. Sythesis, Structure and Imaging of Oligodeoxyribonucleotide with Tellurium-derivatized Nucleobase Derivatization, Nucleic Acid Res. 39, ASAP
- Chen GJ, Ni NT, Zhou JF, Chuang YJ, Wang BH, Pan ZW, Xu BQ. 2011. Fibrinogen Clot Induced by Gold-nanoparticle in Vitro, J. Nanosci. Nanotechno., 11, 74-81.
- Guo J, Chen GJ, Ning XH, Wolfert MA, Li XR, Xu BQ, Boons GJ, 2010. Surface Modification of Polymeric Micelles by Strain-Promoted Alkyne-Azide Cycloadditions, Chem. Eur. J. 16 , 13360-13366
- Zhou JF, Xu BQ, 2010. Recent Patents of nanopore DNA Sequencing Technology: Progress and Challenges, Recent Pat. Gene Seq. 4 (3), 192-201
- Zhou JF, Chen GJ, Xu BQ. 2010. Probing the Molecule-Electrode Interface of Single-Molecule Junctions by Controllable Mechanical Modulations, J. Phys. Chem. C., 114(18), 8587-8592
- Chen GJ, Ni NT, Wang BH, Xu BQ. 2010. Fibrinogen Nanofibril Growth and Self-Assembly on Au (1,1,1) Surface in the Absence of Thrombin, ChemPhysChem, 11 (3), 565-568
- Chen F, Zhou JF, Chen GJ, Xu BQ. 2010. A Novel Highly-integrated SPM System for Single Molecule Studies, IEEE Sensors Journal, 10(3), 485-491
- Chen GJ, Zhou JF, Park B, Xu BQ. 2009. Single Ricin Detection by Atomic Force Microscopy Chemomechanical Mapping, Appl. Phys. Lett. 95(4): 043103/1-043103/3
- Wang LN, Wu ZZ, Xu BQ, Zhao YP, Kisaalita WS. 2009. SU-8 microstructure for quasi-three-dimensional cell-based biosensing, Sensors and Actuators B: Chemical, 140(2), 349-355
- Zhou JF, Chen F, Xu BQ. 2009. Fabrication and electronic characterization of single molecular junction devices: A comprehensive approach, J AM CHEM SOC 131 (30): 10439-10446
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Progress 01/01/08 to 12/31/08
Outputs
OUTPUTS: Our proposed research objectives are: 1) to develop a SPM-based single molecule recognition technology and use it to study ligand-receptor interactions at the single-cell and single molecule level for applications in agricultural, food safety, environmental assessment, bio-processing, and health care concerns; 2) to use the technology to detect pathogens and toxins in food with single molecule sensitivity and provide methodologies for key scientific advances in understanding, identifying, and developing therapies that promote animal and human health In the past few months, we used a parallel approach and carried out multiple activities in order to simultaneously make progress under each of the above objectives in 2008. 1. Developed several protocols for AFM tip modification and sample immobilization. These include our invention of a simple, two step click chemistry AFM tip modification for single ricin detection; Alkyne functionalized AFM tip to characterize the ligands on the multifunctional organic nanoparticles;Peptide functionalized AFM tip for single-molecule receptor-ligand interactions on cancer cell membrane, and the protocols for immobilizing receptor molecules on gold, mica, silicon, and lipid bilayer surfaces. 2. Studied the biophysical principles of anti-ricin--ricin single molecule interactions and used the single molecular mecognition and sensing technology to detect the toxin ricin at the single molecule level. 3. Developed (and are still developing) single molecule interaction techniques that can be used to study the single molecule interactions on the real biomembranes. 4.Establishing theoretical modeling for single peptide-receptor interaction for designing peptide-based anticaner drugs. 5. Generated a 3 year NSF research grant of $240,000. PARTICIPANTS: Not relevant to this project. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The research will significantly advance new methodology to realize robust, repeatable, and highly reliable characterization and detection of single molecule interactions and recognitions. The novelty of this project lies in the following areas: 1). The highly integrated and effective methods combine Scanning Probe Microscope (SPM) nanolithography, microscopes (SPM and inverted optical microscope), SPM spectroscopy and SPM-based break juction (SPMBJ) methods to study single molecular interaction properties. 2). Integrating nanolithography, imaging and chemical and physical property detections capabilities into a single technique that make it possible to study multiple molecules under identical conditions. 3). By precisely control the movement of the SPM tip, it is highly possible to resolve the lateral distribution of cell surface components in real-time with nanometer resolution without labeling with fluorescence, radioactive, or enzyme probes; in addition, the new methodology will make it possible to determine the type and location of a single molecular binding event occurring in the cell surface membrane, reorganize the different proteins involved in the biological binding events, and measure the biomechanical interactions between the membrane-bound proteins and the underlying membrane. This study will develop a multifunctional technique that potentially provide capabilities in studying protein structures, cellular expression, and may have relevance to drug discovery and functionality, cell biology etc.
Publications
- Chen F, JF Zhou, GJ Chen, BQ Xu. 2009. A Novel Highly-integrated SPM System for Single Molecule Studies, IEEE Sensors Journal, in press
- Chen GJ, XH Ning, B Park, GJ Boons, BQ Xu. 2009. simple, clickable protocol for AFM tip modification and its application for trace ricin detection by recognition imaging, Langmuir, 25, 2860-2864
- Liu B, XY Li, BL Li, BQ Xu, YL Zhao. 2009. Carbon Nanotube Based Artificial Water Channel Protein: Membrane Perturbation and Water Transportation, Nano Lett. ASAP
- Sun HQ, Y Bai, HJ Liu, WQ Jin, NP Xu, GJ Chen, BQ Xu. 2008. Mechanism of Nitrogen-Concentration Dependence on pH Value: Experimental and Theoretical Studies on Nitrogen-Doped TiO2, J. Phys. Chem. C, 112(34) 13304 - 13309
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Progress 01/01/07 to 12/31/07
Outputs
Our proposed research objectives are: 1) to develop a SPM-based single molecule recognition technology and use it to study ligand-receptor interactions at the single-cell and single molecule level for applications in agricultural, food safety, environmental assessment, bio-processing, and health care concerns; 2) to use the technology to detect pathogens and toxins in food with single molecule sensitivity and provide methodologies for key scientific advances in understanding, identifying, and developing therapies that promote animal and human health In the past few months, we used a parallel approach and carried out multiple activities in order to simultaneously make progress under each of the above objectives. These activities included the SPM-based single molecule recognition technology development, calibrations and tests using simple molecules and systems, and application of the technology on real biological samples. Activities in each of these areas are summarized
below. In the area of SPM-based single molecule recognition technology development, we successfully combined several major technologies, namely inverted optical microscope, AFM spectroscopy and picoTRECTM (pico Topography and RECognition from Agilent) to achieve a highly-integrated AFM-based lable-less, fast single-molecule interaction recognition system (HASMIRS). It starts with functionalizing the SPM tip by using a strand of polymer to connect the probe molecules (e.g. antibody) that bond to the target molecules (e.g. antigen) to the tip. A magnetically excited cantilever causes the tip to oscillate up and down to make the antibodies disconnect and reconnect and keep the probe moving. We transform the binding events to the recognition image and together with the topographic image, we can actually count the number of target molecules in the scanned area. The resolution can be as good as a single molecule (e.g. 2nm). Our preliminary results show that individual sites on 20nm tiles
are easily addressed and 2,500 individual sites can be mapped in one minute. Increased digital resolution and somewhat slower scanning (ten minutes) would easily allow the readout to be increased to ten microns by ten microns, probing 250,000 sites with each scan. We also developed and calibrated protocols for AFM tip and substrate modification and immobilization. As a real application research, we applied the technology as a radical new approach to detect pathogens and toxins in food (ricin molecules were used in this study) at the nano and subnano scale (single molecule level), quickly (within 10 minutes) and specifically (using single molecule interaction and recognition). With these promising results, we predict that this research will also provide the capacity to simultaneously map the structure and chemomechanical interactions of whole cells, membranes, and individual molecular receptors at or below the nanoscale. This enables systematic, in situ characterization of the
mechanisms governing drug-cell interactions at the in vitro level.
Impacts
Our newly developed highly-integrated AFM-based lable-less, fast single-molecule interaction recognition system (HASMIRS) enables us to directly and quickly "read out" species that are engaged in molecular binding events as well as dynamic properties, such as the conductance and binding force. The ability to identify the specific proteins on a membrane surface will provide the fundamental knowledge needed to develop new drugs. The ability for single molecular biosensors for pathogen and toxin detection in food, such as salmonella pathogens detection and ricin toxin detection, will be key for food safety and biosecurity.
Publications
- Zhou JF, Chen F, Chen GJ, and Xu BQ. 2007. Multiple groups of conductance in molecular junction measurements, Applied Physics Letters (in review)
- Chen F, Zhou JF, Chen GJ, and Xu BQ. 2007. Dual-mode conductive-AFM break junction system for single molecular studies in molecular junctions, Review of the Scientific Instruments (in review)
- Chen GJ, Zhou JF, Chen F, and Xu BQ. 2007. Single Molecular Recognition of Ricin Immobilized on Modified Mica Surface, Langmuir (in review)
- Xu, BQ. 2007. Modulating the Conductance of Au-octanedithiol-Au Molecule Junction, Small, 3, (12), 2061-2065.
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