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Li Y, Chang Y, Ma J, Wu Z, Yuan R, Chai Y. Programming a Target-Initiated Bifunctional DNAzyme Nanodevice for Sensitive Ratiometric Electrochemical Biosensing. Anal Chem 2019; 91:6127-6133. [DOI: 10.1021/acs.analchem.9b00690] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Yunrui Li
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yuanyuan Chang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Jing Ma
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Zhongyu Wu
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Ruo Yuan
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
| | - Yaqin Chai
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, People’s Republic of China
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Hwang MT, Wang Z, Ping J, Ban DK, Shiah ZC, Antonschmidt L, Lee J, Liu Y, Karkisaval AG, Johnson ATC, Fan C, Glinsky G, Lal R. DNA Nanotweezers and Graphene Transistor Enable Label-Free Genotyping. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1802440. [PMID: 29984525 PMCID: PMC6326894 DOI: 10.1002/adma.201802440] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/16/2018] [Indexed: 05/04/2023]
Abstract
Electronic DNA-biosensor with a single nucleotide resolution capability is highly desirable for personalized medicine. However, existing DNA-biosensors, especially single nucleotide polymorphism (SNP) detection systems, have poor sensitivity and specificity and lack real-time wireless data transmission. DNA-tweezers with graphene field effect transistor (FET) are used for SNP detection and data are transmitted wirelessly for analysis. Picomolar sensitivity of quantitative SNP detection is achieved by observing changes in Dirac point shift and resistance change. The use of DNA-tweezers probe with high-quality graphene FET significantly improves analytical characteristics of SNP detection by enhancing the sensitivity more than 1000-fold in comparison to previous work. The electrical signal resulting from resistance changes triggered by DNA strand-displacement and related changes in the DNA geometry is recorded and transmitted remotely to personal electronics. Practical implementation of this enabling technology will provide cheaper, faster, and portable point-of-care molecular health status monitoring and diagnostic devices.
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Affiliation(s)
- Michael T Hwang
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Zejun Wang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Jinglei Ping
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Deependra Kumar Ban
- Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Zi Chao Shiah
- Department of Electrical and Computer Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Leif Antonschmidt
- NMR Based Structural Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Joon Lee
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Yushuang Liu
- School of Life Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot, 010018, China
| | - Abhijith G Karkisaval
- Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Alan T Charlie Johnson
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Chunhai Fan
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201800, China
| | - Gennadi Glinsky
- Institute of Engineering in Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Ratnesh Lal
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Mechanical and Aerospace Engineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Bioengineering, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
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Janetanakit W, Wang L, Santacruz-Gomez K, Landon PB, Sud PL, Patel N, Jang G, Jain M, Yepremyan A, Kazmi SA, Ban DK, Zhang F, Lal R. Gold-Embedded Hollow Silica Nanogolf Balls for Imaging and Photothermal Therapy. ACS APPLIED MATERIALS & INTERFACES 2017; 9:27533-27543. [PMID: 28752765 DOI: 10.1021/acsami.7b08398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Hybrid nanocarriers with multifunctional properties have wide therapeutic and diagnostic applications. We have constructed hollow silica nanogolf balls (HGBs) and gold-embedded hollow silica nanogolf balls (Au@SiO2 HGBs) using the layer-by-layer approach on a symmetric polystyrene (PS) Janus template; the template consists of smaller PS spheres attached to an oppositely charged large PS core. ζ Potential measurement supports the electric force-based template-assisted synthesis mechanism. Electron microscopy, UV-vis, and near-infrared (NIR) spectroscopy show that HGBs or Au@SiO2 HGBs are composed of a porous silica shell with an optional dense layer of gold nanoparticles embedded in the silica shell. To visualize their cellular uptake and imaging potential, Au@SiO2 HGBs were loaded with quantum dots (QDs). Confocal fluorescent microscopy and atomic force microscopy imaging show reliable endocytosis of QD-loaded Au@SiO2 HGBs in adherent HeLa cells and circulating red blood cells (RBCs). Surface-enhanced Raman spectroscopy of Au@SiO2 HGBs in RBC cells show enhanced intensity of the Raman signal specific to the RBCs' membrane specific spectral markers. Au@SiO2 HGBs show localized surface plasmon resonance and heat-induced HeLa cell death in the NIR range. These hybrid golf ball nanocarriers would have broad applications in personalized nanomedicine ranging from in vivo imaging to photothermal therapy.
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Affiliation(s)
| | - Liping Wang
- School of Biomedical Engineering, Shanghai Jiaotong University , Shanghai 200241, P. R. China
| | | | | | | | | | | | | | | | | | | | - Feng Zhang
- Agricultural Nanocenter, School of Life Sciences, Inner Mongolia Agricultural University , Inner Mongolia, Hohhot 010018, P. R. China
- Department of Biomedical Engineering, School of Basic Medical Sciences, Guangzhou Medical University , Guangzhou 511436, P. R. China
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Cui L, Lu M, Yang XY, Tang B, Zhang CY. A sensitive ratiometric electrochemical biosensor based on DNA four-way junction formation and enzyme-assisted recycling amplification. Analyst 2017; 142:1562-1568. [DOI: 10.1039/c7an00342k] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We develop a ratiometric electrochemical biosensor for DNA assay based on DNA four-way junction formation and enzyme-assisted recycling amplification.
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Affiliation(s)
- Lin Cui
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Mengfei Lu
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Xiao-yun Yang
- Department of Pathology
- Affiliated Hospital of Guangdong Medical University
- Zhanjiang 524001
- China
| | - Bo Tang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
| | - Chun-yang Zhang
- College of Chemistry
- Chemical Engineering and Materials Science
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
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Dual-color encoded DNAzyme nanostructures for multiplexed detection of intracellular metal ions in living cells. Biosens Bioelectron 2016; 85:573-579. [DOI: 10.1016/j.bios.2016.05.058] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/15/2016] [Accepted: 05/19/2016] [Indexed: 11/19/2022]
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Highly specific SNP detection using 2D graphene electronics and DNA strand displacement. Proc Natl Acad Sci U S A 2016; 113:7088-93. [PMID: 27298347 DOI: 10.1073/pnas.1603753113] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Single-nucleotide polymorphisms (SNPs) in a gene sequence are markers for a variety of human diseases. Detection of SNPs with high specificity and sensitivity is essential for effective practical implementation of personalized medicine. Current DNA sequencing, including SNP detection, primarily uses enzyme-based methods or fluorophore-labeled assays that are time-consuming, need laboratory-scale settings, and are expensive. Previously reported electrical charge-based SNP detectors have insufficient specificity and accuracy, limiting their effectiveness. Here, we demonstrate the use of a DNA strand displacement-based probe on a graphene field effect transistor (FET) for high-specificity, single-nucleotide mismatch detection. The single mismatch was detected by measuring strand displacement-induced resistance (and hence current) change and Dirac point shift in a graphene FET. SNP detection in large double-helix DNA strands (e.g., 47 nt) minimize false-positive results. Our electrical sensor-based SNP detection technology, without labeling and without apparent cross-hybridization artifacts, would allow fast, sensitive, and portable SNP detection with single-nucleotide resolution. The technology will have a wide range of applications in digital and implantable biosensors and high-throughput DNA genotyping, with transformative implications for personalized medicine.
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Ma L, Wu G, Li Y, Qin P, Meng L, Liu H, Li Y, Diao A. A reversible metal ion fueled DNA three-way junction molecular device for "turn-on and -off" fluorescence detection of mercury ions (II) and biothiols respectively with high selectivity and sensitivity. NANOSCALE 2015; 7:18044-18048. [PMID: 26487480 DOI: 10.1039/c5nr04688b] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We constructed a reversible molecular device in the nanoscale based on a DNA three-way junction (3WJ) fueled by Hg(2+) binding and sequestration. It is highly responsive to external stimuli, which brings about optically detectable global structural changes. Such a DNA device can serve as a novel "turn-on and -off" fluorescent sensor for Hg(2+) and biothiol detection with high selectivity and sensitivity.
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Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China. and Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Guanrong Wu
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Yufeng Li
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Ping Qin
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Lingpei Meng
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Haiyan Liu
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Yuyin Li
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
| | - Aipo Diao
- Tianjin Key Laboratory of Industry Microbiology, School of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China and Biomolecular Sciences Research Complex, EaStCHEM School of Chemistry, University of St Andrews, Fife KY16 9ST, UK.
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Hwang MT, Landon PB, Lee J, Mo A, Meckes B, Glinsky G, Lal R. DNA nano-carrier for repeatable capture and release of biomolecules. NANOSCALE 2015; 7:17397-17403. [PMID: 26439640 DOI: 10.1039/c5nr05124j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
DNA can be manipulated to design nano-machines through specific sequence recognition. We report a switchable DNA carrier for repeatable capture and release of a single stranded DNA. The activity of the carrier was regulated by the interactions among a double-stranded actuator, single stranded target, fuel, and anti-fuel DNA strands. Inosine was used to maintain a stable triple-stranded complex when the actuator's conformation was switched between open (capture) and closed (release) configurations. Time lapse fluorescence measurements show repeatable capture and release of target strands. TEM images also show visible capture of target DNA strands when gold nanoparticles were attached to the DNA carrier and the target DNA strand. The carrier activity was controlled by length of toeholds, number of mismatches, and inosine substitutions. Significantly, unlike in previously published work that reported the devices functioned only when there is a perfect match between the interacting DNA strands, the present device works only when there are mismatches in the fuel strand and the best performance is achieved for 1-3 mismatches. The device was used to successfully capture and release gold nanoparticles when linked to the target single-stranded DNA. In general, this type of devices can be used for transport and delivery of theranostic molecules.
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Affiliation(s)
- Michael T Hwang
- Materials Science and Engineering Program, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
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Glinsky GV. Transposable Elements and DNA Methylation Create in Embryonic Stem Cells Human-Specific Regulatory Sequences Associated with Distal Enhancers and Noncoding RNAs. Genome Biol Evol 2015; 7:1432-54. [PMID: 25956794 PMCID: PMC4494056 DOI: 10.1093/gbe/evv081] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Despite significant progress in the structural and functional characterization of the human genome, understanding of the mechanisms underlying the genetic basis of human phenotypic uniqueness remains limited. Here, I report that transposable element-derived sequences, most notably LTR7/HERV-H, LTR5_Hs, and L1HS, harbor 99.8% of the candidate human-specific regulatory loci (HSRL) with putative transcription factor-binding sites in the genome of human embryonic stem cells (hESC). A total of 4,094 candidate HSRL display selective and site-specific binding of critical regulators (NANOG [Nanog homeobox], POU5F1 [POU class 5 homeobox 1], CCCTC-binding factor [CTCF], Lamin B1), and are preferentially located within the matrix of transcriptionally active DNA segments that are hypermethylated in hESC. hESC-specific NANOG-binding sites are enriched near the protein-coding genes regulating brain size, pluripotency long noncoding RNAs, hESC enhancers, and 5-hydroxymethylcytosine-harboring regions immediately adjacent to binding sites. Sequences of only 4.3% of hESC-specific NANOG-binding sites are present in Neanderthals’ genome, suggesting that a majority of these regulatory elements emerged in Modern Humans. Comparisons of estimated creation rates of novel TF-binding sites revealed that there was 49.7-fold acceleration of creation rates of NANOG-binding sites in genomes of Chimpanzees compared with the mouse genomes and further 5.7-fold acceleration in genomes of Modern Humans compared with the Chimpanzees genomes. Preliminary estimates suggest that emergence of one novel NANOG-binding site detectable in hESC required 466 years of evolution. Pathway analysis of coding genes that have hESC-specific NANOG-binding sites within gene bodies or near gene boundaries revealed their association with physiological development and functions of nervous and cardiovascular systems, embryonic development, behavior, as well as development of a diverse spectrum of pathological conditions such as cancer, diseases of cardiovascular and reproductive systems, metabolic diseases, multiple neurological and psychological disorders. A proximity placement model is proposed explaining how a 33–47% excess of NANOG, CTCF, and POU5F1 proteins immobilized on a DNA scaffold may play a functional role at distal regulatory elements.
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Affiliation(s)
- Gennadi V Glinsky
- Institute of Engineering in Medicine, University of California, San Diego The Stanford University School of Medicine, Department of Surgery, Stanford, California
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Mo AH, Landon PB, Emerson CD, Zhang C, Anzenberg P, Akkiraju S, Lal R. Synthesis of nano-bowls with a Janus template. NANOSCALE 2015; 7:771-775. [PMID: 25431230 PMCID: PMC4353600 DOI: 10.1039/c4nr05153j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Colloidal particles with two or more different surface properties (Janus particles) are of interest in catalysis, biological imaging, and drug delivery. Eccentric nanoparticles are a type of Janus particle consisting of a shell that envelops the majority of a core particle, leaving a portion of the core surface exposed. Previous work to synthesize eccentric nanoparticles from silica and polystyrene have only used microemulsion techniques. In contrast we report the sol-gel synthesis of eccentric Janus nanoparticles composed of a silica shell around a carboxylate-modified polystyrene core (Janus templates). In addition, we have synthesized nano-bowl-like structures after the removal of the polystyrene core by organic solvent. These Janus templates and nanobowls can be used as a versatile platform for site-specific functionalization or controlled theranostic delivery.
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Affiliation(s)
- Alexander H. Mo
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Preston B. Landon
- Dept. of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
- Dept. of Mechanical and Aerospace Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Chris D. Emerson
- Dept of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Chen Zhang
- Dept of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Paula Anzenberg
- Dept. of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Siddhartha Akkiraju
- Dept of Nanoengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
| | - Ratnesh Lal
- Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
- Dept. of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
- Dept. of Mechanical and Aerospace Engineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
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