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Award Abstract #0304569
Nanoscale Arrays for Direct RNA Profiling in Single Cells and their Compartments
| NSF Org: |
EF
Emerging Frontiers
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| Initial Amendment Date: |
September 10, 2003 |
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| Latest Amendment Date: |
August 26, 2005 |
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| Award Number: |
0304569 |
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| Award Instrument: |
Continuing grant |
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| Program Manager: |
Wilson A. Francisco
EF Emerging Frontiers
BIO Directorate for Biological Sciences
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| Start Date: |
September 1, 2003 |
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| Expires: |
November 30, 2008 (Estimated) |
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| Awarded Amount to Date: |
$1973227 |
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| Investigator(s): |
Weihong Tan tan@chem.ufl.edu (Principal Investigator)
Harold Craighead (Co-Principal Investigator)
Steven Benner (Co-Principal Investigator)
Stephen Pearton (Co-Principal Investigator)
Leonid Moroz (Co-Principal Investigator)
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| Sponsor: |
University of Florida
1 UNIVERSITY OF FLORIDA
GAINESVILLE, FL 32611 352/392-3516
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| NSF Program(s): |
CGP FUND, PROGRAM EXPENSES,
EAST ASIA AND PACIFIC PROGRAM,
BIOMEDICAL ENGINEERING,
RESEARCH TO AID THE DISABLED,
NANOSCALE: INTRDISCPL RESRCH T,
PHYSICS-OTHER
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| Field Application(s): |
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| Program Reference Code(s): |
OTHR, 5936, 5921, 1767, 1674, 0000
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| Program Element Code(s): |
V724, T200, 8268, 5978, 5345, 5342, 1674, 1248
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ABSTRACT
This Nanoscale Interdisciplinary Research Team (NIRT) award supports a group of five faculty, including four at the University of Florida and one at Cornell University, to develop tools capable of measuring the distribution and concentration of specific messenger RNA molecules (mRNAs) in defined subcellular regions of single nerve cells. Initial effort will use neurons from the model organism, Aplysia. Use of the tools will then be extended to neurons from higher organisms with the goal of understanding how neurons establish new connections or synapses. Using electron beam technology, the team will fabricate one dimensional (1-D) DNA nanoarrays for the capture and direct assay of the mRNAs. Detection will employ molecular beacons to generate a fluorescent signal in the presence of specific target mRNAs; the beacons are fluorescent nanoparticles consisting of self-assembling branched DNA nanostructures designed using an artificially expanded genetic alphabet (AEGIS). Nanofluidics and dip-pen nanolithography will be tasked with delivery of the nanoparticles to specific sites in the DNA array. Fluorescence will be detected by optical imaging. Software specialized for analyzing biological molecules will archive and interpret recovered mRNA sequences using interpretive proteomics tools developed from evolutionary models. The project will benefit from a collaborative setting where students at all levels engage multiple disciplines. If successful, this will provide an educational paradigm for the training of the scientists of the future, as well as demonstrating the utility of nanoscience and engineering in the study of classical problems in biology.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
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(Showing: 1 - 10 of 65)
(Showing: 1 - 65 of 65)
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B. S. Kang, S. J. Pearton, J. J. Chen, F. Ren, J. W. Johnson, R. J. Therrien, P. Rajagopal, J. C. Roberts, E. L. Piner, and K. J. Linthicum. "Electrical detection of deoxyribonucleic acid hybridization with AlGaN/GaN high electron mobility transistors," Appl. Phys.Lett, v.89, 2006, p. 122102.
B.S. Kang, S.J.Pearton and F.Ren. "Low temperature (<100°C) patterned growth of ZnO nanorods arrays on Si," Appl.Phys.Lett, v.90, 2007, p. 083104.
B.S. Kang, F. Ren, B.S. Jeong, Y.W. Kwon, K.H. Baik, D.P. Norton and S.J. Pearton,. "Use of 370 nm UV light for selective-area fibroblast cell growth," J. Vac. Sci, v.B 23, 2005, p. 57.
B.S. Kang, F. Ren, L. Wang, C. Lofton, W.W. Tan, S.J. Pearton, A. Dabiran, A. Osinsky and P.P.Chow. "Electrical detection of immobilized proteins with ungated AlGaN/GaN HEMTs," Appl.Phys.Lett., v.87, 2005, p. 023508.
B.S. Kang, F. Ren, M.C. Kang, C. Lofton, Weihong Tan, S.J. Pearton, A. Dabiran, A. Osinsky, and P.P. Chow. "Detection of halide ions with AlGaN/GaN high electron mobility transistors," Appl. Phys. Lett, v.86, 2005, p. 173502.
B.S. Kang, F. Ren, Y.W. Heo, L.C. Tien, D.P. Norton and S.J. Pearton. "pH measurements with single ZnO nanorods integrated with a microchannel," Appl. Phys. Lett, v.86, 2005, p. 112105.
B.S. Kang, S. Kim, F. Ren, B.P. Gila, C.R. Abernathy and S.J. Pearton. "AlGaN/GaN ?Based Diodes and Gateless HEMTs for Gas and Chemical Sensing," IEEE Sensors Journal, v.5, 2005, p. 677.
Bagwe, Rahul P.; Hilliard, Lisa R.; Tan, Weihong.. "Surface Modification of Silica Nanoparticles to Reduce Aggregation and Nonspecific Binding.," Langmuir, v.22(9),, 2006, p. 4357.
Benner, S. A.. "Understanding nucleic acids using synthetic chemistry," Accounts Chem. Res., v.37, 2004, p. 784.
C. W. Lee, H. Choi, M. K. Oh, D. J. Ahn, J. Kim, J.-M. Kim, F. Ren and S. J. Pearton. "ZnO-Based Cyclodextrin Sensor Using Immobilized Polydiacetylene Vesicles," Electrochem. Solid-State Lett, v.10, 2007, p. J1.
Cao, Zehui; Huang, Chih-Ching; Tan, Weihong. "Nuclease Resistance of Telomere-like Oligonucleotides Monitored in Live Cells by Fluorescence Anisotropy Imaging," Analytical Chemistry, v.78(5), 2006, p. 1478.
Cao, Zehui; Tan, Weihong.. "Molecular aptamers for real-time protein-protein interaction study.," Chemistry--A European Journal, v.11(15), 2005, p. 4502.
Carrigan, M., Ricardo, A., Ang, D. N., Benner, S. A.. "Quantitative analysis of a deoxyribonucleotide catalyst obtained via in vitro selection. A DNA ribonuclease.," Biochemistry, v.43, 2004, p. 11446.
Chang, Jia-Yaw; Wu, Huimeng; Chen, Hui; Ling, Yong-Chien; Tan, Weihong.. "Oriented assembly of Au nanorods using biorecognition system," Chemical Communications (Cambridge, United Kingdom), v.(8), 2005, p. 1092.
Drake, Timothy J.; Jezzini, Sami; Lovell, Peter; Moroz, Leonid L.; Tan, Weihong. "Single cell glutamate analysis in Aplysia sensory neurons.," Journal of Neuroscience Methods, v.144(1), 2005, p. 73.
Drake, Timothy J.; Medley, Colin D.; Sen, Arup; Rogers, Richard J.; Tan, Weihong.. "Stochasticity of manganese superoxide dismutase mRNA expression in breast carcinoma cells by molecular beacon imaging," ChemBioChem, v.6(11), 2005, p. 2041.
Ha TJ, Kohn AB, Bobkova YV, Moroz LL. "Molecular characterization of NMDA-like receptors in Aplysia and Lymnaea: relevance to memory mechanisms.," Biol Bull, v.210, 2006, p. 255.
Herr, Joshua K.; Smith, Joshua E.; Medley, Colin D.; Shangguan, Dihua; Tan, Weihong.. "Aptamer-Conjugated Nanoparticles for Selective Collection and Detection of Cancer Cells.," Analytical Chemistry, v.78(9), 2006, p. 2918.
Heyland A, Price DA, Bodnarova-Buganova M, Moroz LL. "Thyroid hormone metabolism and peroxidase function in two non-chordate animals.," J Exp Zoolog B Mol Dev Evol, v.306, 2006, p. 551.
Huang, Chih-Ching; Huang, Yu-Fen; Cao, Zehui; Tan, Weihong; Chang, Huan-Tsung.. "Aptamer-modified gold nanoparticles for colorimetric determination of platelet-derived growth factors and their receptors.," Analytical Chemistry, v.77(17), 2005, p. 5735.
J.Kim, S.J.Pearton and F.Ren. "Immobilization of Heterogeneous Polydiacetylene Supramolecules on SiC Substrate for Cyclodextrin sensors," Physica Stat. Solidi, v.A 203, 2006, p. R79.
Jezzini SH, Bodnarova M, Moroz LL. "Two-color in situ hybridization in the CNS of Aplysia californica," J Neurosci Methods, v.149, 2005, p. 15.
Jezzini SH, Reagin S, Kohn AB, Moroz LL. "Molecular characterization and expression of a two-pore domain potassium channel in the CNS of Aplysia californica," Brain Res, v.1094, 2006, p. 47.
Jun Kameoka, Reid Orth, Yanou Yang, David Czaplewski, Robert Mathers, Geoffrey Coates and Harold Craighead. "A Scanning Tip Electrospinning Source for Deposition of Oriented Nanofibres," Nanotechnology, v.14, 2003, p. 1124.
Jun Kameoka, Reid Orth, Yanou Yang, David Czaplewski, Robert Mathers, Geoffrey Coates and Harold Craighead. "A Scanning Tip Electrospinning Source for Deposition of Oriented Nanofibres," Nanotechnology, v.14, 2003, p. 1124.
Kang, B. S.; Ren, F.; Kang, M. C.; Lofton, C.; Tan, Weihong; Pearton, S. J.; Dabiran, A.; Osinsky, A.; Chow, P. P.. "Detection of halide ions with AlGaN/GaN high electron mobility transistors.," Applied Physics Letters, v.86(17), 2005, p. 173502/1.
Kang, B. S.; Ren, F.; Wang, L.; Lofton, C.; Tan, Weihong W.; Pearton, S. J.; Dabiran, A.; Osinsky, A.; Chow, P. P.. "Electrical detection of immobilized proteins with ungated AlGaN/GaN high-electron-mobility transistors.," Applied Physics Letters, v.87(2), 2005, p. 023508/1.
Kohn AB, Lea JM, Moroz LL, Greenberg RM. "Schistosoma mansoni: use of a fluorescent indicator to detect nitric oxide and related species in living parasites.," Exp Parasitol, v.113, 2006, p. 130.
Liu, Heping; Wang, Hong; Shi, Zhiyang; Wang, Hua; Yang, Chaoyong; Silke, Spering; Tan, Weihong; Lu, Zuhong.. "TaqMan probe array for quantitative detection of DNA targets," Nucleic Acids Research, v.34(1), 2006, p. e4/1.
Lovell P, Jezzini SH, Moroz LL. "Electroporation of neurons and growth cones in Aplysia californica," J Neurosci Methods, v.151, 2006, p. 114.
Lovell P, Moroz LL. "The largest growth cones in the animal kingdom and dynamics of neuronal growth in cell culture of Aplysia," Integr Comp Biol, v.46, 2006, p. 847.
Mallikaratchy, Prabodhika; Stahelin, Robert V.; Cao, Zehui; Cho, Wonhwa; Tan, Weihong. "Selection of DNA ligands for protein kinase C-?Ô," Chemical Communications (Cambridge, United Kingdom), v.(30), 2006, p. 3229.
Mechery, Shelly John; Zhao, Xiaojun Julia; Wang, Lin; Hilliard, Lisa R.; Munteanu, Alina; Tan, Weihong.. "Using bioconjugated nanoparticles to monitor E. coli in a flow channel," Chemistry--An Asian Journal, v.1(3), 2006, p. 384.
Medley, Colin D.; Drake, Timothy J.; Tomasini, Jeffrey M.; Rogers, Richard J.; Tan, Weihong.. "Simultaneous Monitoring of the Expression of Multiple Genes Inside of Single Breast Carcinoma Cells," Analytical Chemistry, v.77(15), 2005, p. 4713.
Medley, Colin D.; Tan, Weihong.. "Molecular beacons for intracellular analysis," Cellscience Reviews, v.2, 2005, p. 2.
Moroz LL, Edwards JR, Puthanveettil SV, Kohn AB, Ha T, Heyland A, Knudsen B, Sahni A, Yu F, Liu L, Jezzini S, Lovell P, Iannucculli W, Chen M, Nguyen T, Sheng H, Shaw R, Kalachikov S, Panchin YV, Farmerie W, Russo JJ, Ju J, Kandel ER. "Neuronal transcriptome of aplysia: neuronal compartments and circuitry," Cell, v.127, 2006, p. 1453.
P. W. Sadik, S. J. Pearton, D. P. Norton, E. Lambers and F. Ren. "Functionalizing Zn- and O-terminated ZnO with thiols," J. Appl. Phys, v.101, 2007, p. 104514.
Santra, Swadeshmukul; Bagwe, Rahul P.; Dutta, Debamitra; Stanley, Jessie T.; Walter, Glenn A.; Tan, Weihong; Moudgil, Brij M.; Mericle, Robert A. "Synthesis and characterization of fluorescent, radio-opaque, and paramagnetic silica nanoparticles for multimodal bioimaging applications," Advanced Materials (Weinheim, Germany), v.17(18), 2005, p. 2165.
Santra, Swadeshmukul; Liesenfeld, Bernd; Bertolino, Chiara; Dutta, Debamitra; Cao, Zehui; Tan, Weihong; Moudgil, Brij M.; Mericle, Robert A. "Fluorescence lifetime measurements to determine the core-shell nanostructure of FITC-doped silica nanoparticles: an optical approach to evaluate nanoparticle photostability," Journal of Luminescence, v.117(1), 2006, p. 75.
Santra, Swadeshmukul; Liesenfeld, Bernd; Dutta, Debamitra; Chatel, David; Batich, Christopher D.; Tan, Weihong; Moudgil, Brij M.; Mericle, Robert A.. "Folate conjugated fluorescent silica nanoparticles for labeling neoplastic cells.," Journal of Nanoscience and Nanotechnology, v.5(6), 2005, p. 899.
Schiavone, Douglas L.; Tan, Weihong.. "Biomedical nanotechnology Edited by Neelina H. Malsch," Small, v.2(2),, 2006, p. 288.
Shangguan, Dihua; Cao, Zehui Charles; Li, Ying; Tan, Weihong.. "Aptamers evolved from cultured cancer cells reveal molecular differences of cancer cells in patient samples," Clinical Chemistry (Washington, DC, United States), v.53(6), 2007, p. 1153.
Shangguan, Dihua; Li, Ying; Tang, Zhiwen; Cao, Zehui Charles; Chen, Hui William; Mallikaratchy, Prabodhika; Sefah, Kwame; Yang, Chaoyong James; Tan, Weihong.. "Aptamers evolved from live cells as effective molecular probes for cancer study.," Proceedings of the National Academy of Sciences of the United States of America, v.103(32), 2006, p. 11838.
Shangguan, Dihua; Tang, Zhiwen; Mallikaratchy, Prabodika; Xiao, Zeyu; Tan, Weihong.. "Optimization and modifications of aptamers selected from live cancer cell lines.," ChemBioChem, v.8(6), 2007, p. 603.
Sismour, A. M., Benner, S. A.. "The use of thymidine analogs to improve the replication of an extra DNA base pair: A synthetic biological system," Nucl. Acids Res, v.33, 2005, p. 5640.
Smith, Joshua E.; Medley, Colin D.; Tang, Zhiwen; Shangguan, Dihua; Lofton, Charles; Tan, Weihong.. "Aptamer-Conjugated Nanoparticles for the Collection and Detection of Multiple Cancer Cells.," Analytical Chemistry, v.79(8), 2007, p. 3075.
Tan, Li; Li, Ying; Drake, Timothy J.; Moroz, Leonid; Wang, Kemin; Li, Jun; Munteanu, Alina; Yang, Chaoyong James; Martinez, Karen; Tan, Weihong. "Molecular beacons for bioanalytical applications.," Analyst (Cambridge, United Kingdom), v.130(7), 2005, p. 1002.
Tang, Zhiwen; Shangguan, Dihua; Wang, Kemin; Shi, Hui; Sefah, Kwame; Mallikratchy, Prabodhika; Chen, Hui William; Li, Ying; Tan, Weihong.. "Selection of Aptamers for Molecular Recognition and Characterization of Cancer Cells.," Analytical Chemistry, v.79(13), 2007, p. 4900.
Wang, Lin, Wang, Kemin, Swadeshmukul Santra, Julia Zhao, Lisa R. Hilliard, Josh Smith, Yanrong Wu and Weihong Tan,. "Watching Nanoparticles Glow in the Biotechnology World," Anal. Chem., v.78, 2006, p. 648.
Wang, Lin; Lofton, Charles; Popp, Michael; Tan, Weihong.. "Using Luminescent Nanoparticles as Staining Probes for Affymetrix GeneChips," Bioconjugate Chemistry, v.18(3), 2007, p. 610.
Wang, Lin; Lofton, Charles; Tan, Weihong. "Bioconjugated nanoparticles for biotechnology and bioanalysis," Nanotechnology in Biology and Medicine, 2007, p. 19/1.
Wang, Lin; O'Donoghue, Meghan B.; Tan, Weihong.. "Nanoparticles for multiplex diagnostics and imaging," Nanomedicine (London, United Kingdom), v.1(4), 2006, p. 413.
Wang, Lin; Tan, Weihong. "Multicolor FRET Silica Nanoparticles by Single Wavelength Excitation," Nano Letters, v.6(1), 2006, p. 84.
Wang, Lin; Yang, Chaoyong James; Medley, Colin D.; Benner, Steven A.; Tan, Weihong. "Locked Nucleic Acid Molecular Beacons," Journal of the American Chemical Society, v.127(45), 2005, p. 15664.
Wang, Lin; Yang, Chaoyong; Tan, Weihong.. "Dual-luminophore-doped silica nanoparticles for multiplexed signaling.," Nano Letters, v.5(1), 2005, p. 37.
Wang, Lin; Zhao, Wenjun; O'Donoghue, Meghan B.; Tan, Weihong. "Fluorescent Nanoparticles for Multiplexed Bacteria Monitoring," Bioconjugate Chemistry, v.18(2), 2007, p. 297.
Wenjun Zhao, Lin Wang and Weihong Tan,. "Fluorescent Nanoparticle for Bacteria and DNA Detection," Bio-Applications of Nanoparticles, Ed. Warren C.W. Chan, 2007.
Xu, Changjiang, Xu, Luzhou, F. Yu, Weihong Tan, Leonid Moroz and Jian Li. "Nonparametric Estimation of the number of unique sequences in biological samples," IEEE Transaction on Signal Processing, v.54 (10), 2006, p. 3759.
Yang, Chaoyong James; Jockusch, Steffen; Vicens, Marie; Turro, Nicholas J.; Tan, Weihong. "Light-switching excimer probes for rapid protein monitoring in complex biological fluids," Proceedings of the National Academy of Sciences of the United States of America, v.102(48), 2005, p. 17278.
Yang, Chaoyong James; Li, Jeff Jianwei; Tan, Weihong. "Using molecular beacons for sensitive fluorescence assays of the enzymatic cleavage of nucleic acids.," Methods in Molecular Biology (Totowa, NJ, United States), v.335(Flu, 2006, p. 71.
Yang, Chaoyong James; Lin, Hui; Tan, Weihong.. "Molecular Assembly of Superquenchers in Signaling Molecular Interactions.," Journal of the American Chemical Society, v.127(37), 2005, p. 2165.
Yang, Chaoyong James; Martinez, Karen; Lin, Hui; Tan, Weihong.. "Hybrid Molecular Probe for Nucleic Acid Analysis in Biological Samples.," Journal of the American Chemical Society, v.128(31), 2006, p. 9986.
Yang, Chaoyong James; Pinto, Mauricio; Schanze, Kirk; Tan, Weihong.. "Direct synthesis of an oligonucleotide-poly(phenylene ethynylene) conjugate with a precise one-to-one molecular ratio.," Angewandte Chemie, International Edition, v.44(17), 2005, p. 2572.
Yao, Gang; Mechery, John Shelly; Tan, Weihong.. "Molecular beacon DNA probes based on fluorescence biosensing.," Fluorescence Sensors and Biosensors, 2006, p. 67.
Yao, Gang; Wang, Lin; Wu, Yanrong; Smith, Josh; Xu, Jinsheng; Zhao, Wenjun; Lee, Eunjung; Tan, Weihong.. "FloDots: luminescent nanoparticles.," Analytical and Bioanalytical Chemistry, v.385(3), 2006, p. 518.
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