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Kou B, Wang Z, Mousavi S, Wang P, Ke Y. Dynamic Gold Nanostructures Based on DNA Self Assembly. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2308862. [PMID: 38143287 DOI: 10.1002/smll.202308862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/10/2023] [Indexed: 12/26/2023]
Abstract
The combination of DNA nanotechnology and Nano Gold (NG) plasmon has opened exciting possibilities for a new generation of functional plasmonic systems that exhibit tailored optical properties and find utility in various applications. In this review, the booming development of dynamic gold nanostructures are summarized, which are formed by DNA self-assembly using DNA-modified NG, DNA frameworks, and various driving forces. The utilization of bottom-up strategies enables precise control over the assembly of reversible and dynamic aggregations, nano-switcher structures, and robotic nanomachines capable of undergoing on-demand, reversible structural changes that profoundly impact their properties. Benefiting from the vast design possibilities, complete addressability, and sub-10 nm resolution, DNA duplexes, tiles, single-stranded tiles and origami structures serve as excellent platforms for constructing diverse 3D reconfigurable plasmonic nanostructures with tailored optical properties. Leveraging the responsive nature of DNA interactions, the fabrication of dynamic assemblies of NG becomes readily achievable, and environmental stimulation can be harnessed as a driving force for the nanomotors. It is envisioned that intelligent DNA-assembled NG nanodevices will assume increasingly important roles in the realms of biological, biomedical, and nanomechanical studies, opening a new avenue toward exploration and innovation.
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Affiliation(s)
- Bo Kou
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Zhichao Wang
- Jiangsu Key Laboratory of Advanced Structural Materials and Application Technology, School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing, 211167, China
| | - Shikufa Mousavi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, 30322, USA
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2
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Yang J, Liang Y, Li X, Zhang Y, Qian L, Ke Y, Zhang C. A Spatially Programmable DNA Nanorobot Arm to Modulate Anisotropic Gold Nanoparticle Assembly by Enzymatic Excision. Angew Chem Int Ed Engl 2023; 62:e202308797. [PMID: 37691009 DOI: 10.1002/anie.202308797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Programmable assembly of gold nanoparticle superstructures with precise spatial arrangement has drawn much attention for their unique characteristics in plasmonics and biomedicine. Bio-inspired methods have already provided programmable, molecular approaches to direct AuNP assemblies using biopolymers. The existing methods, however, predominantly use DNA as scaffolds to directly guide the AuNP interactions to produce intended superstructures. New paradigms for regulating AuNP assembly will greatly enrich the toolbox for DNA-directed AuNP manipulation and fabrication. Here, we developed a strategy of using a spatially programmable enzymatic nanorobot arm to modulate anisotropic DNA surface modifications and assembly of AuNPs. Through spatial controls of the proximity of the reactants, the locations of the modifications were precisely regulated. We demonstrated the control of the modifications on a single 15 nm AuNP, as well as on a rectangular DNA origami platform, to direct unique anisotropic AuNP assemblies. This method adds an alternative enzymatic manipulation to DNA-directed AuNP superstructure assembly.
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Affiliation(s)
- Jing Yang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yuan Liang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Xiang Li
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yongpeng Zhang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Long Qian
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
| | - Yonggang Ke
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Cheng Zhang
- School of Computer Science, Key Lab of High Confidence Software Technologies, Peking University, Beijing, 100871, China
- Center for Quantitative Biology, Peking University, Beijing, 100871, China
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3
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Yang S, Wang Y, Wang Q, Li F, Ling D. DNA-Driven Dynamic Assembly/Disassembly of Inorganic Nanocrystals for Biomedical Imaging. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:340-355. [PMID: 37501793 PMCID: PMC10369495 DOI: 10.1021/cbmi.3c00028] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/20/2023] [Accepted: 04/07/2023] [Indexed: 07/29/2023]
Abstract
DNA-mediated programming is emerging as an effective technology that enables controlled dynamic assembly/disassembly of inorganic nanocrystals (NC) with precise numbers and spatial locations for biomedical imaging applications. In this review, we will begin with a brief overview of the rules of NC dynamic assembly driven by DNA ligands, and the research progress on the relationship between NC assembly modes and their biomedical imaging performance. Then, we will give examples on how the driven program is designed by different interactions through the configuration switching of DNA-NC conjugates for biomedical applications. Finally, we will conclude with the current challenges and future perspectives of this emerging field. Hopefully, this review will deepen our knowledge on the DNA-guided precise assembly of NCs, which may further inspire the future development of smart chemical imaging devices and high-performance biomedical imaging probes.
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Affiliation(s)
- Shengfei Yang
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - Yuqi Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Qiyue Wang
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
| | - Fangyuan Li
- Institute
of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
| | - Daishun Ling
- Frontiers
Science Center for Transformative Molecules, School of Chemistry and
Chemical Engineering, National Center for Translational Medicine,
State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- World
Laureates Association (WLA) Laboratories, Shanghai 201203, P. R. China
- Hangzhou
Institute of Innovative Medicine, Zhejiang
University, Hangzhou 310058, P. R. China
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4
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Jiang K, Wu J, Kim JE, An S, Nam JM, Peng YK, Lee JH. Plasmonic Cross-Linking Colorimetric PCR for Simple and Sensitive Nucleic Acid Detection. NANO LETTERS 2023; 23:3897-3903. [PMID: 37083438 DOI: 10.1021/acs.nanolett.3c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Simple, low-cost, and accurate nucleic acid assay platforms hold great promise for point-of-care (POC) pathogen detection, disease surveillance, and control. Plasmonic photothermal polymerase chain reaction (PPT-PCR) is a powerful and efficient nucleic acid amplification technique, but it lacks a simple and convenient analysis method for POC applications. Herein, we propose a novel plasmonic cross-linking colorimetric PCR (PPT-ccPCR) assay by integrating plasmonic magnetic nanoparticle (PMN)-based PPT-PCR with gold nanoparticle (AuNP)-based cross-linking colorimetry. AuNPs form assembled structures with the PMNs in the presence of amplicons and collect in a magnetic field, resulting in color changes to the supernatant. Target DNA with concentrations as low as 5 copies/μL can be visually detected within 40 min. The achieved limit of detection was 1.8 copies/μL based on the absorption signals. This simple and sensitive strategy needs no expensive instrumentation and demonstrates high potential for POC detection while enabling further applications in clinical diagnostics.
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Affiliation(s)
- Kunlun Jiang
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jingrui Wu
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Ji-Eun Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Sujin An
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
| | - Jwa-Min Nam
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Yung-Kang Peng
- Department of Chemistry, City University of Hong Kong, Kowloon 999077, Hong Kong, China
| | - Jung-Hoon Lee
- Department of Chemistry, Soonchunhyang University, Asan 31538, Korea
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5
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Ding Y, Zhang Y, Shi X, Liao L, Li Q, Duan T, Jiang H, Ding Z, Wang H, Liu H. Iodide etching for one-step quantitative assay of the number of DNA molecules capped on gold nanoparticles. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1232-1238. [PMID: 35254355 DOI: 10.1039/d1ay02212a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Developing a direct method to easily quantify the number of DNA capped on gold nanoparticles (GNPs) is of great significance. Herein, we found that the high concentration of iodine ion (I-) can not only replace the ligands on the surface of GNPs but can also completely etch the particles by virtue of its strong reducibility. According to this finding, a mild, cost-effective, environment-friendly, and non-toxic strategy was constructed to directly and accurately estimate the amount of DNA coupled on GNPs. Due to nanometal surface energy transfer (NSET) that happened between the DNA-FAM donor and the GNPs receptor, the fluorescence was quenched; after incubating with the etching reagent 6 M I-, the recuperative fluorescence was detected directly. This method can easily estimate the number of DNA attached on the GNPs surface by one step. In a nutshell, it is a smart strategy to apply iodide etching for DNA quantification on the surface of GNPs, which breaks through the drawbacks of traditional DNA quantification strategies such as pollution, being expensive and even dangerous. This strategy takes a solid step forward for the refinement and optimization of DNA quantification and can also be more effective in detecting the number of other molecules capped on the GNPs surface, indicating that the iodide etching method is greatly helpful in bio-detection assays and nanoparticle-based therapeutics.
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Affiliation(s)
- Yan Ding
- First Affiliated Hospital of Anhui Medical University, Hefei 230000, China.
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Yu Zhang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Xiaoqi Shi
- First Affiliated Hospital of Anhui Medical University, Hefei 230000, China.
| | - Lingling Liao
- First Affiliated Hospital of Anhui Medical University, Hefei 230000, China.
| | - Qinghe Li
- First Affiliated Hospital of Anhui Medical University, Hefei 230000, China.
| | - Tingmei Duan
- First Affiliated Hospital of Anhui Medical University, Hefei 230000, China.
| | - Hao Jiang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| | - ZhongXiang Ding
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
| | - Hongyan Wang
- First Affiliated Hospital of Anhui Medical University, Hefei 230000, China.
| | - Honglin Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China.
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6
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Djebbi K, Shi B, Weng T, Bahri M, Elaguech MA, Liu J, Tlili C, Wang D. Highly Sensitive Fluorescence Assay for miRNA Detection: Investigation of the DNA Spacer Effect on the DSN Enzyme Activity toward Magnetic-Bead-Tethered Probes. ACS OMEGA 2022; 7:2224-2233. [PMID: 35071911 PMCID: PMC8771974 DOI: 10.1021/acsomega.1c05775] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/29/2021] [Indexed: 05/28/2023]
Abstract
Researchers have recently designed various biosensors combining magnetic beads (MBs) and duplex-specific nuclease (DSN) enzyme to detect miRNAs. Yet, the interfacial mechanisms for surface-based hybridization and DSN-assisted target recycling are relatively not well understood. Thus, herein, we developed a highly sensitive and selective fluorescent biosensor to study the phenomenon that occurs on the local microenvironment surrounding the MB-tethered DNA probe via detecting microRNA-21 as a model. Using the above strategy, we investigated the influence of different DNA spacers, base-pair orientations, and surface densities on DSN-assisted target recycling. As a result, we were able to detect as low as 170 aM of miR-21 under the optimized conditions. Moreover, this approach exhibits a high selectivity in a fully matched target compared to a single-base mismatch, allowing the detection of miRNAs in serum with improved recovery. These results are attributed to the synergetic effect between the DSN enzyme activity and the neutral DNA spacer (triethylene glycol: TEG) to improve the miRNA detection's sensitivity. Finally, our strategy could create new paths for detecting microRNAs since it obliterates the enzyme-mediated cascade reaction used in previous studies, which is more expensive, more time-consuming, less sensitive, and requires double catalytic reactions.
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Affiliation(s)
- Khouloud Djebbi
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
- University
of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Biao Shi
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
| | - Ting Weng
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
| | - Mohamed Bahri
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
- University
of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Mohamed Amin Elaguech
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
- University
of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
| | - Jin Liu
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
- Department
of Pathology, Chongqing General Hospital, University of Chinese Academy of Sciences (UCAS), Chongqing 400013, P. R. China
| | - Chaker Tlili
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
| | - Deqiang Wang
- Chongqing
Institute of Green and Intelligent Technology, Chinese Academy of
Sciences, Chongqing 400714, P. R. China
- Chongqing
School, University of Chinese Academy of
Sciences (UCAS), Chongqing 400714, P. R. China
- University
of Chinese Academy of Sciences (UCAS), Beijing 100049, P. R. China
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7
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Wang W, Li X, Tang K, Song Z, Luo X. A AuNP-capped cage fluorescent biosensor based on controlled-release and cyclic enzymatic amplification for ultrasensitive detection of ATP. J Mater Chem B 2021; 8:5945-5951. [PMID: 32667018 DOI: 10.1039/d0tb00666a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gold nanodevices have attracted extensive interest in the detection of specific targets within cells. However, constructing gold sensing devices that can be activated by the simulation of remote applications remains a huge challenge. Here, we report a Au nanoparticle (AuNP)-capped cage fluorescent biosensor based on controlled-release and Exonuclease III (Exo III) assisted cyclic enzymatic amplification that can be activated by adenosine triphosphate (ATP). In the system, AuNPs were used as the building blocks to cap the pores of Au nanocages (AuNCs) loaded with Rhodamine B (RhB) molecules through the hybridization of DNA. The RhB fluorescent molecules were finally released with the help of Exo III in the presence of ATP for detection purposes. Ultimately, the biosensor leads to a wide linear ATP detection range from 1.0 × 10-9 to 1.0 × 10-7 M with a limit of detection (LOD) down to 0.88 nM. In addition, it also has good selectivity for ATP to distinguish between ATP and ATP analogues such as cytidine triphosphate (CTP), guanosine triphosphate (GTP), and uridine triphosphate (UTP). Therefore, as a convenient and sensitive biosensor, it is expected to be widely used in the biomedical field.
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Affiliation(s)
- Wei Wang
- Key Laboratory of Optic-eletric Sensing and Analytical Chemistry for Life Science, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China.
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8
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Srivastava I, Misra SK, Bangru S, Boateng KA, Soares JANT, Schwartz-Duval AS, Kalsotra A, Pan D. Complementary Oligonucleotide Conjugated Multicolor Carbon Dots for Intracellular Recognition of Biological Events. ACS APPLIED MATERIALS & INTERFACES 2020; 12:16137-16149. [PMID: 32182420 PMCID: PMC7982005 DOI: 10.1021/acsami.0c02463] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
By using complementary DNA sequences as surface ligands, we selectively allow two individual diffusing "dual-color" carbon dots to interact in situ and in vitro. Spontaneous nanoscale oxidation of surface-abundant nitroso-/nitro-functionalities leads to two distinctly colored carbon dots (CD) which are isolated by polarity driven chromatographic separation. Green- and red-emitting carbon dots (gCD and rCD) were decorated by complementary single-stranded DNAs which produce a marked increase in the fluorescence emission of the respective carbon dots. Mutual colloidal interactions are achieved through hybridization of complementary DNA base pairs attached to the respective particles, resulting in quenching of their photoluminescence. The observed post-hybridization quenching is presumably due to a combined effect from an aggregation of CDs post duplex DNA formation and close proximity of multicolored CDs, having overlapped spectral regions leading to a nonradiative energy transfer process possibly released as heat. This strategy may contribute to the rational design of mutually interacting carbon dots for a better control over the resulting assembly structure for studying different biological phenomenon including molecular cytogenetics. One of the newly synthesized CDs was successfully used to image intracellular location of GAPDH mRNA using an event of change in fluorescence intensity (FI) of CDs. This selectivity was introduced by conjugating an oligonucleotide harboring complementary sequence to GAPDH mRNA. FI of this conjugated carbon dot, rCD-GAPDH, was also found to decrease in the presence of Ca2+, varied in relation to H+ concentrations, and could serve as a tool to quantify the intracellular concentrations of Ca2+ and pH value (H+) which can give important information about cell survival. Therefore, CD-oligonucleotide conjugates could serve as efficient probes for cellular events and interventions.
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Affiliation(s)
- Indrajit Srivastava
- Departments of Bioengineering, Materials Science and Engineering and Beckman Institute, University of Illinois at Urbana-Champaign, Mills Breast Cancer Institute, and Carle Foundation Hospital, Urbana, IL, 61801, USA
| | - Santosh K. Misra
- Departments of Bioengineering, Materials Science and Engineering and Beckman Institute, University of Illinois at Urbana-Champaign, Mills Breast Cancer Institute, and Carle Foundation Hospital, Urbana, IL, 61801, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center @ Illinois, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Kingsley A. Boateng
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Julio A. N. T. Soares
- Frederick Seitz Materials Research Laboratories Central Facilities, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Aaron S. Schwartz-Duval
- Departments of Bioengineering, Materials Science and Engineering and Beckman Institute, University of Illinois at Urbana-Champaign, Mills Breast Cancer Institute, and Carle Foundation Hospital, Urbana, IL, 61801, USA
| | - Auinash Kalsotra
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
- Cancer Center @ Illinois, University of Illinois, Urbana-Champaign, Urbana, IL, 61801, USA
| | - Dipanjan Pan
- Departments of Bioengineering, Materials Science and Engineering and Beckman Institute, University of Illinois at Urbana-Champaign, Mills Breast Cancer Institute, and Carle Foundation Hospital, Urbana, IL, 61801, USA
- Departments of Diagnostic Radiology and Nuclear Medicine and Pediatrics, University of Maryland Baltimore, Health Sciences Facility III, 670 W Baltimore St., Baltimore, Maryland, 21201, United States
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Interdisciplinary Health Sciences Facility, 1000 Hilltop Circle Baltimore, Maryland, 21250, United States
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9
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Haladjova E, Ugrinova I, Rangelov S. One-pot synthesis of oligonucleotide-grafted polymeric nanoparticles. SOFT MATTER 2020; 16:191-199. [PMID: 31774098 DOI: 10.1039/c9sm01796h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A feasible one-pot approach for constructing oligonucleotide-grafted polymeric nanoparticles is reported. The approach involves formation of mesoglobules from a thermoresponsive polymer, coating of the mesoglobules with a cross-linked polymeric shell, and grafting the latter with oligonucleotide strands. Dynamic and static light scattering are used to parameterize the novel constructs. They are relatively large structures with hydrodynamic radii and molar masses reaching 200 nm and 150.0 × 106 g mol-1, respectively. The oligonucleotide-grafted polymeric nanoparticles are of spherical morphology and moderately negative (-12.4 to -19.1 mV) ζ potential as revealed by AFM, TEM, and electrophoretic light scattering. In accordance with their large size, they are found to carry thousands of oligonucleotide strands per particle. The novel constructs are thermoresponsive. They undergo reversible collapse upon heating and swelling upon cooling, which is associated with changes in the grafting density and, hence, the conformation of the oligonucleotide strands from unextended at room temperature to a more extended one at elevated temperatures. The versatility of the approach is demonstrated by varying the type of the cross-linked shell and content of the oligonucleotide strands and, hence, the grafting density. Appropriate diversification and modifications are suggested as well.
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Affiliation(s)
- Emi Haladjova
- Institute of Polymers, Bulgarian Academy of Sciences, "Akad. G. Bonchev" St., Bl. 103-A, 1113 Sofia, Bulgaria.
| | - Iva Ugrinova
- Institute of Molecular Biology, Bulgarian Academy of Sciences, "Akad. G. Bonchev" St., Bl. 21, 1113 Sofia, Bulgaria
| | - Stanislav Rangelov
- Institute of Polymers, Bulgarian Academy of Sciences, "Akad. G. Bonchev" St., Bl. 103-A, 1113 Sofia, Bulgaria.
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10
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Yu H, Canoura J, Guntupalli B, Alkhamis O, Xiao Y. Sensitive Detection of Small-Molecule Targets Using Cooperative Binding Split Aptamers and Enzyme-Assisted Target Recycling. Anal Chem 2018; 90:1748-1758. [PMID: 29294287 PMCID: PMC5803384 DOI: 10.1021/acs.analchem.7b03625] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Signal amplification via enzyme-assisted target recycling (EATR) offers a powerful means for improving the sensitivity of DNA detection assays, but it has proven challenging to employ EATR with aptamer-based assays for small-molecule detection due to insensitive target response of aptamers. Here, we describe a general approach for the development of rapid and sensitive EATR-amplified small-molecule sensors based on cooperative binding split aptamers (CBSAs). CBSAs contain two target-binding domains and exhibit enhanced target response compared with single-domain split aptamers. We introduced a duplexed C3 spacer abasic site between the two binding domains, enabling EATR signal amplification through exonuclease III's apurinic endonuclease activity. As a demonstration, we engineered a CBSA-based EATR-amplified fluorescence assay to detect dehydroisoandrosterone-3-sulfate. This assay achieved 100-fold enhanced target sensitivity relative to a non-EATR-based assay, with a detection limit of 1 μM in 50% urine. We further developed an instrument-free colorimetric assay employing EATR-mediated aggregation of CBSA-modified gold nanoparticles for the visual detection of low-micromolar concentrations of cocaine. On the basis of the generalizability of CBSA engineering and the robust performance of EATR in complex samples, we believe that such assays should prove valuable for detecting small-molecule targets in diverse fields.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Juan Canoura
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Bhargav Guntupalli
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Obtin Alkhamis
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW Eighth Street, Miami, Florida 33199, United States
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11
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Liang P, Canoura J, Yu H, Alkhamis O, Xiao Y. Dithiothreitol-Regulated Coverage of Oligonucleotide-Modified Gold Nanoparticles To Achieve Optimized Biosensor Performance. ACS APPLIED MATERIALS & INTERFACES 2018; 10:4233-4242. [PMID: 29313333 PMCID: PMC5794567 DOI: 10.1021/acsami.7b16914] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
DNA-modified gold nanoparticles (AuNPs) are useful signal-reporters for detecting diverse molecules through various hybridization- and enzyme-based assays. However, their performance is heavily dependent on the probe DNA surface coverage, which can influence both target binding and enzymatic processing of the bound probes. Current methods used to adjust the surface coverage of DNA-modified AuNPs require the production of multiple batches of AuNPs under different conditions, which is costly and laborious. We here develop a single-step assay utilizing dithiothreitol (DTT) to fine-tune the surface coverage of DNA-modified AuNPs. DTT is superior to the commonly used surface diluent, mercaptohexanol, as it is less volatile, allowing for the rapid and reproducible controlling of surface coverage on AuNPs with only micromolar concentrations of DTT. Upon adsorption, DTT forms a dense monolayer on gold surfaces, which provides antifouling capabilities. Furthermore, surface-bound DTT adopts a cyclic conformation, which reorients DNA probes into an upright position and provides ample space to promote DNA hybridization, aptamer assembly, and nuclease digestion. We demonstrate the effects of surface coverage on AuNP-based sensors using DTT-regulated DNA-modified AuNPs. We then use these AuNPs to visually detect DNA and cocaine in colorimetric assays based on enzyme-mediated AuNP aggregation. We determine that DTT-regulated AuNPs with lower surface coverage achieve shorter reaction times and lower detection limits relative to those for assays using untreated AuNPs or DTT-regulated AuNPs with high surface coverage. Additionally, we demonstrate that our DTT-regulated AuNPs can perform cocaine detection in 50% urine without any significant matrix effects. We believe that DTT regulation of surface coverage can be broadly employed for optimizing DNA-modified AuNP performance for use in biosensors as well as drug delivery and therapeutic applications.
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Affiliation(s)
| | | | | | | | - Yi Xiao
- Corresponding Author: . Tel: 305-348-4536
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12
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Premaratne G, Al Mubarak ZH, Senavirathna L, Liu L, Krishnan S. Measuring Ultra-low Levels of Nucleotide Biomarkers Using Quartz Crystal Microbalance and SPR Microarray Imaging Methods: A Comparative Analysis. SENSORS AND ACTUATORS. B, CHEMICAL 2017; 253:368-375. [PMID: 29200660 PMCID: PMC5703433 DOI: 10.1016/j.snb.2017.06.138] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Circulating serum nucleotide biomarkers are useful indicators for early diagnosis of cancer, respiratory illnesses, and other deadly diseases. In this work, we compared detection performances of a quartz crystal microbalance (QCM), which is a mass sensor, with that of a surface plasmon resonance (SPR) microarray for an oligonucleotide mimic of a microRNA-21 biomarker. A surface immobilized capture oligonucleotide probe was used to hybridize with the target oligonucleotide (i.e., the microRNA-21 mimic) to facilitate selective detection. To obtain ultra-low femtomolar (fM) detection sensitivity, gold nanoparticles (50 nm) were conjugated with the target oligonucleotide. We achieved detection limits of 28and 47 fM for the target oligonucleotide by the QCM and SPRi microarray, respectively. We also conducted sample recovery studies and performed matrix effect analysis. Although the QCM had a lower detection limit, the microarray approach offered better throughput for analysis of up to 16 samples. We confirmed that the designed assay was selective for the target oligonucleotide and did not show signals for the control oligonucleotide with five mismatch sites relative to the target sequence. Combination of the QCM and microarray methods that utilize the same assay chemistry on gold are useful for overcoming clinical sample matrix effects and achieving ultra-low detection of small nucleotide biomarkers with quantitative insights.
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Affiliation(s)
- Gayan Premaratne
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
| | - Zainab H Al Mubarak
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
| | - Lakmini Senavirathna
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Lin Liu
- Department of Physiological Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Sadagopan Krishnan
- Department of Chemistry, Oklahoma State University, Stillwater, OK 74078, USA
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13
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Kim E, Baaske MD, Schuldes I, Wilsch PS, Vollmer F. Label-free optical detection of single enzyme-reactant reactions and associated conformational changes. SCIENCE ADVANCES 2017; 3:e1603044. [PMID: 28435868 PMCID: PMC5371424 DOI: 10.1126/sciadv.1603044] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/09/2017] [Indexed: 05/21/2023]
Abstract
Monitoring the kinetics and conformational dynamics of single enzymes is crucial to better understand their biological functions because these motions and structural dynamics are usually unsynchronized among the molecules. However, detecting the enzyme-reactant interactions and associated conformational changes of the enzyme on a single-molecule basis remains as a challenge to established optical techniques because of the commonly required labeling of the reactants or the enzyme itself. The labeling process is usually nontrivial, and the labels themselves might skew the physical properties of the enzyme. We demonstrate an optical, label-free method capable of observing enzymatic interactions and associated conformational changes on a single-molecule level. We monitor polymerase/DNA interactions via the strong near-field enhancement provided by plasmonic nanorods resonantly coupled to whispering gallery modes in microcavities. Specifically, we use two different recognition schemes: one in which the kinetics of polymerase/DNA interactions are probed in the vicinity of DNA-functionalized nanorods, and the other in which these interactions are probed via the magnitude of conformational changes in the polymerase molecules immobilized on nanorods. In both approaches, we find that low and high polymerase activities can be clearly discerned through their characteristic signal amplitude and signal length distributions. Furthermore, the thermodynamic study of the monitored interactions suggests the occurrence of DNA polymerization. This work constitutes a proof-of-concept study of enzymatic activities using plasmonically enhanced microcavities and establishes an alternative and label-free method capable of investigating structural changes in single molecules.
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Affiliation(s)
- Eugene Kim
- Corresponding author. (E.K.); (M.D.B.); (F.V.)
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14
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Yu H, Xu X, Liang P, Loh KY, Guntupalli B, Roncancio D, Xiao Y. A Broadly Applicable Assay for Rapidly and Accurately Quantifying DNA Surface Coverage on Diverse Particles. Bioconjug Chem 2017; 28:933-943. [PMID: 28156100 DOI: 10.1021/acs.bioconjchem.6b00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
DNA-modified particles are used extensively for applications in sensing, material science, and molecular biology. The performance of such DNA-modified particles is greatly dependent on the degree of surface coverage, but existing methods for quantitation can only be employed for certain particle compositions and/or conjugation chemistries. We have developed a simple and broadly applicable exonuclease III (Exo III) digestion assay based on the cleavage of phosphodiester bonds-a universal feature of DNA-modified particles-to accurately quantify DNA probe surface coverage on diverse, commonly used particles of different compositions, conjugation chemistries, and sizes. Our assay utilizes particle-conjugated, fluorophore-labeled probes that incorporate two abasic sites; these probes are hybridized to a complementary DNA (cDNA) strand, and quantitation is achieved via cleavage and digestion of surface-bound probe DNA via Exo III's apurinic endonucleolytic and exonucleolytic activities. The presence of the two abasic sites in the probe greatly speeds up the enzymatic reaction without altering the packing density of the probes on the particles. Probe digestion releases a signal-generating fluorophore and liberates the intact cDNA strand to start a new cycle of hybridization and digestion, until all fluorophore tags have been released. Since the molar ratio of fluorophore to immobilized DNA is 1:1, DNA surface coverage can be determined accurately based on the complete release of fluorophores. Our method delivers accurate, rapid, and reproducible quantitation of thiolated DNA on the surface of gold nanoparticles, and also performs equally well with other conjugation chemistries, substrates, and particle sizes, and thus offers a broadly useful assay for quantitation of DNA surface coverage.
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Affiliation(s)
- Haixiang Yu
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Xiaowen Xu
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Pingping Liang
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Kang Yong Loh
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Bhargav Guntupalli
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Daniel Roncancio
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Florida International University , 11200 SW Eighth Street, Miami, Florida 33199, United States
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15
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Xu X, Wang L, Huang Y, Gao W, Li K, Jiang W. Model-Guided Interface Probe Arrangement for Sensitive Protein Detection. Anal Chem 2016; 88:9885-9889. [DOI: 10.1021/acs.analchem.6b02972] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaowen Xu
- Key
Laboratory for Colloid and Interface Chemistry of Education Ministry,
School of Chemistry and Chemical Engineering and ‡School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Lei Wang
- Key
Laboratory for Colloid and Interface Chemistry of Education Ministry,
School of Chemistry and Chemical Engineering and ‡School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Yongqi Huang
- Key
Laboratory for Colloid and Interface Chemistry of Education Ministry,
School of Chemistry and Chemical Engineering and ‡School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Wushuang Gao
- Key
Laboratory for Colloid and Interface Chemistry of Education Ministry,
School of Chemistry and Chemical Engineering and ‡School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Kan Li
- Key
Laboratory for Colloid and Interface Chemistry of Education Ministry,
School of Chemistry and Chemical Engineering and ‡School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250100, China
| | - Wei Jiang
- Key
Laboratory for Colloid and Interface Chemistry of Education Ministry,
School of Chemistry and Chemical Engineering and ‡School of Pharmaceutical Sciences, Shandong University, Jinan, Shandong 250100, China
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16
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Nanoparticles based DNA conjugates for detection of pathogenic microorganisms. INTERNATIONAL NANO LETTERS 2016. [DOI: 10.1007/s40089-015-0177-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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McGinley JT, Wang Y, Jenkins IC, Sinno T, Crocker JC. Crystal-Templated Colloidal Clusters Exhibit Directional DNA Interactions. ACS NANO 2015; 9:10817-10825. [PMID: 26439813 DOI: 10.1021/acsnano.5b03272] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Spherical colloids covered with grafted DNA have been used in the directed self-assembly of a number of distinct crystal and gel structures. Simulation suggests that the use of anisotropic building blocks greatly augments the variety of potential colloidal assemblies that can be formed. Here, we form five distinct symmetries of colloidal clusters from DNA-functionalized spheres using a single type of colloidal crystal as a template. The crystals are formed by simple sedimentation of a binary mixture containing a majority "host" species that forms close-packed crystals with the minority "impurity" species occupying substitutional or interstitial defect sites. After the DNA strands between the two species are hybridized and enzymatically ligated, the results are colloidal clusters, one for each impurity particle, with a symmetry determined by the nearest neighbors in the original crystal template. By adjusting the size ratio of the two spheres and the timing of the ligation, we are able to generate clusters having the symmetry of tetrahedra, octahedra, cuboctahedra, triangular orthobicupola, and icosahedra, which can be readily separated from defective clusters and leftover spheres by centrifugation. We further demonstrate that these clusters, which are uniformly covered in DNA strands, display directional binding with spheres bearing complementary DNA strands, acting in a manner similar to patchy particles or proteins having multiple binding sites. The scalable nature of the fabrication process, along with the reprogrammability and directional nature of their resulting DNA interactions, makes these clusters suitable building blocks for use in further rounds of directed self-assembly.
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Affiliation(s)
- James T McGinley
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Yifan Wang
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Ian C Jenkins
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - Talid Sinno
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
| | - John C Crocker
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania , 220 South 33rd Street, Philadelphia, Pennsylvania 19104, United States
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18
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Banerjee A, Grazon C, Nadal B, Pons T, Krishnan Y, Dubertret B. Fast, Efficient, and Stable Conjugation of Multiple DNA Strands on Colloidal Quantum Dots. Bioconjug Chem 2015; 26:1582-9. [PMID: 25992903 DOI: 10.1021/acs.bioconjchem.5b00221] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A novel method for covalent conjugation of DNA to polymer coated quantum dots (QDs) is investigated in detail. This method is fast and efficient: up to 12 DNA strands can be covalently conjugated per QD in optimized reaction conditions. The QD-DNA conjugates can be purified using size exclusion chromatography and the QDs retain high quantum yield and excellent stability after DNA coupling. We explored single-stranded and double-stranded DNA coupling, as well as various lengths. We show that the DNA coupling is most efficient for short (15 mer) single-stranded DNA. The DNA coupling has been performed on QDs emitting at four different wavelengths, as well as on gold nanoparticles, suggesting that this technique can be generalized to a wide range of nanoparticles.
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Affiliation(s)
- Anusuya Banerjee
- †Laboratoire de Physique et d'Etude des Matériaux, ESPCI ParisTech, CNRS UMR 8213, Université Pierre et Marie Curie, 10 Rue Vauquelin, 75005 Paris, France
| | | | - Brice Nadal
- ‡Nexdot, 10 rue Vauquelin, 75005 Paris, France
| | - Thomas Pons
- †Laboratoire de Physique et d'Etude des Matériaux, ESPCI ParisTech, CNRS UMR 8213, Université Pierre et Marie Curie, 10 Rue Vauquelin, 75005 Paris, France
| | - Yamuna Krishnan
- §E305A, Physical Sciences Division, Gordon Centre for Integrative Science, 929 57th Street, Chicago, Illinois 60637 United States
| | - Benoit Dubertret
- †Laboratoire de Physique et d'Etude des Matériaux, ESPCI ParisTech, CNRS UMR 8213, Université Pierre et Marie Curie, 10 Rue Vauquelin, 75005 Paris, France
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19
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Wong PT, Choi SK. Mechanisms of Drug Release in Nanotherapeutic Delivery Systems. Chem Rev 2015; 115:3388-432. [DOI: 10.1021/cr5004634] [Citation(s) in RCA: 349] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Pamela T. Wong
- Michigan
Nanotechnology Institute
for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Seok Ki Choi
- Michigan
Nanotechnology Institute
for Medicine and Biological Sciences, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
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20
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Takada T, Takemura M, Kawano Y, Nakamura M, Yamana K. Photoresponsive DNA monolayer prepared by primer extension reaction on the electrode. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:3993-3998. [PMID: 25807074 DOI: 10.1021/la505013u] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We describe a simple and convenient method for the preparation of photoresponsive DNA-modified electrodes using primer extension (PEX) reactions. A naphthalimide derivative was used as the photosensitizer that was attached to the C5-position of 2'-deoxyuridine-5'-triphosphate (dUTP(NI)). It has been found that dUTP(NI) is a good substrate for the PEX reactions using KOD Dash and Vent (exo-) enzymes in solutions to incorporate naphthalimide (NI) moieties into the DNA sequences. On the electrode surface immobilized with the primer/template DNA, the PEX reactions to incorporate dUTP(NI) molecules into the DNA sequence were found to efficiently proceed. With this solid-phase method, the DNA monolayers capable of generating photocurrent due to the photoresponsive NI molecule can be constructed. It was shown that the photocurrent generation was significantly suppressed by a single-nucleotide mismatch included in the primer/template DNA, which is applicable for the design of photoelectrochemical sensors to discriminate single-nucleotide sequences.
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Affiliation(s)
- Tadao Takada
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Mai Takemura
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Yuta Kawano
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Mitsunobu Nakamura
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
| | - Kazushige Yamana
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan
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21
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Armstrong RE, Riskowski RA, Strouse GF. Nanometal Surface Energy Transfer Optical Ruler for Measuring a Human Telomere Structure. Photochem Photobiol 2015; 91:732-8. [DOI: 10.1111/php.12423] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/01/2015] [Indexed: 12/23/2022]
Affiliation(s)
- Rachel E. Armstrong
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL
| | - Ryan A. Riskowski
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL
| | - Geoffrey F. Strouse
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL
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22
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Armstrong RE, Strouse GF. Rationally manipulating aptamer binding affinities in a stem-loop molecular beacon. Bioconjug Chem 2014; 25:1769-76. [PMID: 25170558 PMCID: PMC4198099 DOI: 10.1021/bc500286r] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Single-stranded
DNA sequences that are highly specific for a target
ligand are called aptamers. While the incorporation of aptamer sequences
into stem-loop molecular beacons has become an essential tool in optical
biosensors, the design principles that determine the magnitude of
binding affinity and its relationship to placement of the aptamer
sequence in the stem-loop architecture are not well defined. By controlled
placement of the aptamer along the loop region of the molecular beacon,
it is observed that the binding affinity can be tuned over 4 orders
of magnitude (1.3 nM – 203 μM) for the Huizenga and Szostak
ATP DNA aptamer sequence. It is observed that the Kd is enhanced for the fully exposed sequence, with reduced
binding affinity when the aptamer is part of the stem region of the
beacon. Analysis of the ΔG values indicate
a clear correlation between the aptamer hybridized length in the stem
and its observed Kd. The use of a nanometal
surface energy transfer probe method for monitoring ATP binding to
the aptamer sequence allows the observation of negative cooperativity
between the two ATP binding events. Maintenance of the high binding
affinity of this ATP aptamer and the observation of two separate Kd’s for ATP binding indicate NSET as
an effective, nonmanipulative, optical method for tracking biomolecular
changes.
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Affiliation(s)
- Rachel E Armstrong
- Department of Chemistry and Biochemistry, Florida State University , 95 Chieftan Way, Room 118 DLC, Tallahassee, Florida 32306, United States
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23
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Preparation of ferrocene-functionalized gold nanoparticles by primer extension reaction on the particle surface. Bioorg Med Chem Lett 2014; 24:2661-3. [DOI: 10.1016/j.bmcl.2014.04.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Revised: 04/09/2014] [Accepted: 04/16/2014] [Indexed: 11/20/2022]
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24
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Pastré D, Joshi V, Curmi PA, Hamon L. Detection of single DNA molecule hybridization on a surface by atomic force microscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:3630-3638. [PMID: 23674511 DOI: 10.1002/smll.201300546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Indexed: 06/02/2023]
Abstract
Improving the detection of DNA hybridization is a critical issue for several challenging applications encountered in microarray and biosensor domains. Herein, it is demonstrated that hybridization between complementary single-stranded DNA (ssDNA) molecules loosely adsorbed on a mica surface can be achieved thanks to fine-tuning of the composition of the hybridization buffer. Single-molecule DNA hybridization occurs in only a few minutes upon encounters of freely diffusing complementary strands on the mica surface. Interestingly, the specific hybridization between complementary ssDNA is not altered in the presence of large amounts of nonrelated DNA. The detection of single-molecule DNA hybridization events is performed by measuring the contour length of DNA in atomic force microscopy images. Besides the advantage provided by facilitated diffusion, which promotes hybridization between probes and targets on mica, the present approach also allows the detection of single isolated DNA duplexes and thus requires a very low amount of both probe and target molecules.
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Affiliation(s)
- David Pastré
- Inserm U829, Laboratoire Structure-Activité des, Biomolécules Normales et Pathologiques, Université d'Evry-Val d'Essonne, Evry 91025, France
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25
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Dean SL, Morrow TJ, Patrick S, Li M, Clawson G, Mayer TS, Keating CD. Biorecognition by DNA oligonucleotides after exposure to photoresists and resist removers. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:11535-11545. [PMID: 23952639 PMCID: PMC3832179 DOI: 10.1021/la402362u] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Combining biological molecules with integrated circuit technology is of considerable interest for next generation sensors and biomedical devices. Current lithographic microfabrication methods, however, were developed for compatibility with silicon technology rather than bioorganic molecules, and consequently it cannot be assumed that biomolecules will remain attached and intact during on-chip processing. Here, we evaluate the effects of three common photoresists (Microposit S1800 series, PMGI SF6, and Megaposit SPR 3012) and two photoresist removers (acetone and 1165 remover) on the ability of surface-immobilized DNA oligonucleotides to selectively recognize their reverse-complementary sequence. Two common DNA immobilization methods were compared: adsorption of 5'-thiolated sequences directly to gold nanowires and covalent attachment of 5'-thiolated sequences to surface amines on silica coated nanowires. We found that acetone had deleterious effects on selective hybridization as compared to 1165 remover, presumably due to incomplete resist removal. Use of the PMGI photoresist, which involves a high temperature bake step, was detrimental to the later performance of nanowire-bound DNA in hybridization assays, especially for DNA attached via thiol adsorption. The other three photoresists did not substantially degrade DNA binding capacity or selectivity for complementary DNA sequences. To determine whether the lithographic steps caused more subtle damage, we also tested oligonucleotides containing a single base mismatch. Finally, a two-step photolithographic process was developed and used in combination with dielectrophoretic nanowire assembly to produce an array of doubly contacted, electrically isolated individual nanowire components on a chip. Postfabrication fluorescence imaging indicated that nanowire-bound DNA was present and able to selectively bind complementary strands.
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Affiliation(s)
- Stacey L. Dean
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Thomas J. Morrow
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
| | - Sue Patrick
- Department of Pathology, Biochemistry and Molecular Biology, and Gittlen Cancer Research Foundation, Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Mingwei Li
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, USA
| | - Gary Clawson
- Department of Pathology, Biochemistry and Molecular Biology, and Gittlen Cancer Research Foundation, Hershey Medical Center, Hershey, Pennsylvania, USA
| | - Theresa S. Mayer
- Department of Electrical Engineering, Pennsylvania State University, University Park, PA, USA
- Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Christine D. Keating
- Department of Chemistry, Pennsylvania State University, University Park, PA, USA
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27
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Lee JK, Kim MR, Choi IS, Kim YG, Jung YH. Surface-initiated, reversible polymerization from surface-tethered oligonucleotides by enzymatic processes. Chem Asian J 2013; 8:908-11. [PMID: 23281246 DOI: 10.1002/asia.201201092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Indexed: 11/07/2022]
Abstract
Back and forth: Enzymatic, reversible polymerization on gold surfaces was efficiently carried out from surface-tethered self-priming oligodeoxynucleotides in a sequence-specific fashion by using two kinds of enzymes. Taq DNA polymerase, acting as a catalyst, facilitated DNA polymerization, and DNA restriction enzymes cut DNA polymers from the surface.
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Affiliation(s)
- Jungkyu K Lee
- Department of Chemistry, Kyungpook National University, Daegu, Korea
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28
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Xiang Y, Wu P, Tan LH, Lu Y. DNAzyme-functionalized gold nanoparticles for biosensing. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 140:93-120. [PMID: 24026635 DOI: 10.1007/10_2013_242] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent progress in using DNAzyme-functionalized gold nanoparticles (AuNPs) for biosensing is summarized in this chapter. A variety of methods, including those for attaching DNA on AuNPs, detecting metal ions and small molecules by DNAzyme-functionalized AuNPs, and intracellular applications of DNAzyme-functionalized AuNPs are discussed. DNAzyme-functionalized AuNPs will increasingly play more important roles in biosensing and many other multidisciplinary applications. This chapter covers the recent advancement in biosensing applications of DNAzyme-functionalized gold nanoparticles, including the detection of metal ions, small molecules, and intracellular imaging.
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Affiliation(s)
- Yu Xiang
- Department of Chemistry and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Pei H, Li F, Wan Y, Wei M, Liu H, Su Y, Chen N, Huang Q, Fan C. Designed diblock oligonucleotide for the synthesis of spatially isolated and highly hybridizable functionalization of DNA-gold nanoparticle nanoconjugates. J Am Chem Soc 2012; 134:11876-9. [PMID: 22799460 DOI: 10.1021/ja304118z] [Citation(s) in RCA: 358] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Conjugates of DNA and gold nanoparticles (AuNPs) typically exploit the strong Au-S chemistry to self-assemble thiolated oligonucleotides at AuNPs. However, it remains challenging to precisely control the orientation and conformation of surface-tethered oligonucleotides and finely tune the hybridization ability. We herein report a novel strategy for spatially controlled functionalization of AuNPs with designed diblock oligonucleotides that are free of modifications. We have demonstrated that poly adenine (polyA) can serve as an effective anchoring block for preferential binding with the AuNP surface, and the appended recognition block adopts an upright conformation that favors DNA hybridization. The lateral spacing and surface density of DNA on AuNPs can also be systematically modulated by adjusting the length of the polyA block. Significantly, this diblock oligonucleotide strategy results in DNA-AuNPs nanoconjugates with high and tunable hybridization ability, which form the basis of a rapid plasmonic DNA sensor.
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Affiliation(s)
- Hao Pei
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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30
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Borovok N, Gillon E, Kotlyar A. Synthesis and assembly of conjugates bearing specific numbers of DNA strands per gold nanoparticle. Bioconjug Chem 2012; 23:916-22. [PMID: 22515478 DOI: 10.1021/bc200485r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Here, we present a relatively simple, efficient, and high-yielding polymerase-based method for the synthesis of 15 nm gold nanoparticle conjugates bearing a specific number of 25 base oligonucleotide strands. We have shown that the conjugates bearing one or two oligonucleotide strands per particle, with the conjugates comprising a single complementary strand, self-assemble into nanoparticle dimers and trimers, respectively. Incubation of fully coated AuNPs, containing tens of oligonucleotide strands, with a conjugate bearing a single complementary strand leads to the formation of flower-shaped structures. The assembly of particles into nanoparticle structures shown here is a prerequisite for more complex controlled assembly of particles into three-dimensional macrostructures.
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Affiliation(s)
- Natalia Borovok
- Department of Biochemistry, George S. Wise Faculty of Life Sciences and ‡The Center of Nanoscience and Nanotechnology, Tel-Aviv University , Ramat Aviv 69978, Israel
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31
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Zanoli LM, D’Agata R, Spoto G. Functionalized gold nanoparticles for ultrasensitive DNA detection. Anal Bioanal Chem 2011; 402:1759-71. [DOI: 10.1007/s00216-011-5318-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Revised: 07/13/2011] [Accepted: 08/04/2011] [Indexed: 12/18/2022]
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Kobayashi K, Tateishi-Karimata H, Tsutsui K, Wada Y, Sugimoto N. DNA Morphologic Changes Induced by Spermine on a Gold Surface under DNA Crowding Conditions. CHEM LETT 2011. [DOI: 10.1246/cl.2011.855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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33
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Liu C, Zeng GM, Tang L, Zhang Y, Li YP, Liu YY, Li Z, Wu MS, Luo J. Electrochemical detection of Pseudomonas aeruginosa 16S rRNA using a biosensor based on immobilized stem–loop structured probe. Enzyme Microb Technol 2011; 49:266-71. [DOI: 10.1016/j.enzmictec.2011.06.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Revised: 06/02/2011] [Accepted: 06/06/2011] [Indexed: 10/18/2022]
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34
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Keller S, Marx A. The use of enzymes for construction of DNA-based objects and assemblies. Chem Soc Rev 2011; 40:5690-7. [PMID: 21637873 DOI: 10.1039/c1cs15040e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA has found wide applications in DNA-based nanotechnology due to its simplicity and predictability of its secondary structure. Selecting DNA for the nanoconstruction of objects and assemblies bears the inherent potential for manipulations and control by DNA modifying enzymes. In this tutorial review, we present an overview of the enzyme-catalysed construction of DNA-based objects and assemblies. It is illustrated how a diversity of enzyme-based biochemical reactions are transferred in nanotechnological applications.
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Affiliation(s)
- Sascha Keller
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
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He S, Huang BH, Tan J, Luo QY, Lin Y, Li J, Hu Y, Zhang L, Yan S, Zhang Q, Pang DW, Li L. One-to-one quantum dot-labeled single long DNA probes. Biomaterials 2011; 32:5471-7. [PMID: 21546079 DOI: 10.1016/j.biomaterials.2011.04.013] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 04/05/2011] [Indexed: 10/18/2022]
Abstract
Quantum dots (QDs) have been received most attention due to their unique properties. Constructing QDs conjugated with certain number of biomolecules is considered as one of the most important research goals in nanobiotechnology. In this study, we report polymerase chain reaction (PCR) amplification of primer oligonucleotides bound to QDs, termed as QD-based PCR. Characterization of QD-based PCR products by gel electrophoresis and atomic force microscopy showed that QD-labeled long DNA strands were synthesized and only a single long DNA strand was conjugated with a QD. The QD-based PCR products still kept fluorescence properties. Moreover, the one-to-one QD-labeled long DNA conjugates as probes could detect a single-copy gene on maize chromosomes by fluorescence in situ hybridization. Labeling a single QD to a single long DNA will make detection of small single-copy DNA fragments, quantitative detection and single molecule imaging come true by nanotechnology, and it will promote medical diagnosis and basic biological research as well as nano-material fabrication.
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Affiliation(s)
- Shibin He
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, PR China
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Loaiza OA, Lamas-Ardisana PJ, Jubete E, Ochoteco E, Loinaz I, Cabañero G, García I, Penadés S. Nanostructured Disposable Impedimetric Sensors as Tools for Specific Biomolecular Interactions: Sensitive Recognition of Concanavalin A. Anal Chem 2011; 83:2987-95. [DOI: 10.1021/ac103108m] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Oscar A. Loaiza
- Sensors and Photonics Unit, New Materials Department, CIDETEC-IK4, Parque Tecnológico de San Sebastián, 20009 Donostia-San Sebastián, Spain
| | - Pedro J. Lamas-Ardisana
- Sensors and Photonics Unit, New Materials Department, CIDETEC-IK4, Parque Tecnológico de San Sebastián, 20009 Donostia-San Sebastián, Spain
| | - Elena Jubete
- Sensors and Photonics Unit, New Materials Department, CIDETEC-IK4, Parque Tecnológico de San Sebastián, 20009 Donostia-San Sebastián, Spain
| | - Estibalitz Ochoteco
- Sensors and Photonics Unit, New Materials Department, CIDETEC-IK4, Parque Tecnológico de San Sebastián, 20009 Donostia-San Sebastián, Spain
| | - Iraida Loinaz
- Sensors and Photonics Unit, New Materials Department, CIDETEC-IK4, Parque Tecnológico de San Sebastián, 20009 Donostia-San Sebastián, Spain
| | - Germán Cabañero
- Sensors and Photonics Unit, New Materials Department, CIDETEC-IK4, Parque Tecnológico de San Sebastián, 20009 Donostia-San Sebastián, Spain
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37
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Fan H, Xu Y, Chang Z, Xing R, Wang Q, He P, Fang Y. A non-immobilizing electrochemical DNA sensing strategy with homogenous hybridization based on the host–guest recognition technique. Biosens Bioelectron 2011; 26:2655-9. [DOI: 10.1016/j.bios.2010.02.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 02/17/2010] [Accepted: 02/19/2010] [Indexed: 12/28/2022]
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38
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Cederquist KB, Keating CD. Hybridization efficiency of molecular beacons bound to gold nanowires: effect of surface coverage and target length. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:18273-80. [PMID: 21038880 PMCID: PMC2994276 DOI: 10.1021/la1031703] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/13/2010] [Indexed: 05/22/2023]
Abstract
Surface-bound nucleic acid probes designed to adopt specific secondary structures are becoming increasingly important in a range of biosensing applications but remain less well characterized than traditional single-stranded probes, which are typically designed to avoid secondary structure. We report the hybridization efficiency for surface-immobilized hairpin DNA probes. Our probes are molecular beacons, carrying a 3' dye moiety and a 5' thiol for attachment to gold nanowires, which serve as both scaffolds for probe attachment and quenchers. Hybridization efficiency was dependent on probe surface coverage, reaching a maximum of ∼90% at intermediate coverages of (1-2) × 10(12) probes/cm(2) and dropping to ≤20% at higher or lower coverages. Fluorescence intensity did not track with the number of target molecules bound, and was highest for high probe coverage despite the lower bound targets per square centimeter. Backfilling with short thiolated oligoethylene glycol spacers increased hybridization efficiency at low hairpin probe coverages (∼(3-4) × 10(11) probes/cm(2)), but not at higher probe coverages (1 × 10(12)/cm(2)). We also evaluated the effect of target length by adding up to 50 nonhybridizing nucleotides to the 3' or 5' end of the complementary target sequence. Additional nucleotides on the 3' end of the complementary target sequence (i.e., the end near the nanowire surface) had a much greater impact on hybridization efficiency as compared to nucleotides added to the 5' end. This work provides guidance in designing sensors in which surface-bound probes designed to adopt secondary structures are used to detect target sequences from solution.
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Affiliation(s)
- Kristin B. Cederquist
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Christine D. Keating
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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39
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Fan H, Xing R, Wang X, Xu Y, Wang Q, He P, Fang Y. A Host-Guest-Recognition-Based Electrochemical Sensor for Sequence-Specific DNA Detection. ELECTROANAL 2010. [DOI: 10.1002/elan.200900623] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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40
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Sperling RA, Parak WJ. Surface modification, functionalization and bioconjugation of colloidal inorganic nanoparticles. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2010; 368:1333-83. [PMID: 20156828 DOI: 10.1098/rsta.2009.0273] [Citation(s) in RCA: 875] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Inorganic colloidal nanoparticles are very small, nanoscale objects with inorganic cores that are dispersed in a solvent. Depending on the material they consist of, nanoparticles can possess a number of different properties such as high electron density and strong optical absorption (e.g. metal particles, in particular Au), photoluminescence in the form of fluorescence (semiconductor quantum dots, e.g. CdSe or CdTe) or phosphorescence (doped oxide materials, e.g. Y(2)O(3)), or magnetic moment (e.g. iron oxide or cobalt nanoparticles). Prerequisite for every possible application is the proper surface functionalization of such nanoparticles, which determines their interaction with the environment. These interactions ultimately affect the colloidal stability of the particles, and may yield to a controlled assembly or to the delivery of nanoparticles to a target, e.g. by appropriate functional molecules on the particle surface. This work aims to review different strategies of surface modification and functionalization of inorganic colloidal nanoparticles with a special focus on the material systems gold and semiconductor nanoparticles, such as CdSe/ZnS. However, the discussed strategies are often of general nature and apply in the same way to nanoparticles of other materials.
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Affiliation(s)
- R A Sperling
- Institut Català de Nanotecnologia, Campus Universitat Autònoma de Barcelona, Bellaterra, Spain.
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41
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Zikich D, Borovok N, Molotsky T, Kotlyar A. Synthesis and AFM characterization of poly(dG)-poly(dC)-gold nanoparticle conjugates. Bioconjug Chem 2010; 21:544-7. [PMID: 20166677 DOI: 10.1021/bc900527a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present work, we have synthesized conjugates between the 5 nm gold nanoparticles (Au-NP) and 5' thiol-functionalized, 700 bp poly(dG)-poly(dC). We have completely separated and purified to homogeneity conjugates bearing different number of poly(dG)-poly(dC) molecules per Au-NP by electrophoresis and HPLC. The conjugates were directly visualized by atomic force microscopy. We have demonstrated that Au NP-bound poly(dG)-poly(dC) can be considerably extended by Klenow exo(-) polymerase in the presence of dCTP and dGTP.
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Affiliation(s)
- Dragoslav Zikich
- Department of Biochemistry, George S. Wise Faculty of Life Sciences, Tel Aviv University, The Center for Nanoscience and Nanotechnology, Tel Aviv University, Ramat Aviv, 69978
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42
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Liu T, Zhao J, Zhang D, Li G. Novel Method to Detect DNA Methylation Using Gold Nanoparticles Coupled with Enzyme-Linkage Reactions. Anal Chem 2009; 82:229-33. [DOI: 10.1021/ac902198v] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tao Liu
- Department of Biochemistry and National Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, P. R. China, and Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Jing Zhao
- Department of Biochemistry and National Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, P. R. China, and Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Dongmei Zhang
- Department of Biochemistry and National Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, P. R. China, and Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Genxi Li
- Department of Biochemistry and National Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210093, P. R. China, and Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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43
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Baram-Pinto D, Shukla S, Perkas N, Gedanken A, Sarid R. Inhibition of herpes simplex virus type 1 infection by silver nanoparticles capped with mercaptoethane sulfonate. Bioconjug Chem 2009; 20:1497-502. [PMID: 21141805 DOI: 10.1021/bc900215b] [Citation(s) in RCA: 210] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interactions between biomolecules and nanoparticles suggest the use of nanoparticles for various medical interventions. The attachment and entry of herpes simplex virus type 1 (HSV-1) into cells involve interaction between viral envelope glycoproteins and cell surface heparan sulfate (HS). Based on this mechanism, we designed silver nanoparticles that are capped with mercaptoethane sulfonate (Ag-MES). These nanoparticles are predicted to target the virus and to compete for its binding to cellular HS through their sulfonate end groups, leading to the blockage of viral entry into the cell and to the prevention of subsequent infection. Structurally defined Ag-MES nanoparticles that are readily redispersible in water were sonochemically synthesized. No toxic effects of these nanoparticles on host cells were observed. Effective inhibition of HSV-1 infection in cell culture by the capped nanoparticles was demonstrated. However, application of the soluble surfactant MES failed to inhibit viral infection, implying that the antiviral effect of Ag-MES nanoparticles is imparted by their multivalent nature and spatially directed MES on the surface. Our results suggest that capped nanoparticles may serve as useful topical agents for the prevention of infections with pathogens dependent on HS for entry.
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44
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Cederquist KB, Keating CD. Curvature effects in DNA:Au nanoparticle conjugates. ACS NANO 2009; 3:256-260. [PMID: 19236058 DOI: 10.1021/nn9000726] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
DNA-coated Au nanoparticles have myriad applications as versatile building blocks in nanomaterials assembly, powerful amplification tags for bioanalysis, and promising new approaches to medical therapeutics. Characterization, control, and a thorough understanding of the DNA surface interface are essential in the development of these conjugates. A new paper in this issue explores the impact of nanosphere diameter on DNA adsorption and demonstrates that particle curvature plays an important role in controlling the DNA surface density. The study proposes a model that can be used to predict DNA packing on nonspherical particles and validates it using Au nanorods. This work paves the way for improved understanding of the DNA:Au interface in these versatile bioconjugates.
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Affiliation(s)
- Kristin B Cederquist
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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45
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Duchesne L, Wells G, Fernig DG, Harris SA, Lévy R. Supramolecular domains in mixed peptide self-assembled monolayers on gold nanoparticles. Chembiochem 2009; 9:2127-34. [PMID: 18698565 DOI: 10.1002/cbic.200800326] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Self-organization in mixed self-assembled monolayers of small molecules provides a route towards nanoparticles with complex molecular structures. Inspired by structural biology, a strategy based on chemical cross-linking is introduced to probe proximity between functional peptides embedded in a mixed self-assembled monolayer at the surface of a nanoparticle. The physical basis of the proximity measurement is a transition from intramolecular to intermolecular cross-linking as the functional peptides get closer. Experimental investigations of a binary peptide self-assembled monolayer show that this transition happens at an extremely low molar ratio of the functional versus matrix peptide. Molecular dynamics simulations of the peptide self-assembled monolayer are used to calculate the volume explored by the reactive groups. Comparison of the experimental results with a probabilistic model demonstrates that the peptides are not randomly distributed at the surface of the nanoparticle, but rather self-organize into supramolecular domains.
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Affiliation(s)
- Laurence Duchesne
- School of Biological Sciences and Liverpool Institute of Nanoscale Science, Engineering and Technology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L697ZB, UK
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46
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Castronovo M, Radovic S, Grunwald C, Casalis L, Morgante M, Scoles G. Control of steric hindrance on restriction enzyme reactions with surface-bound DNA nanostructures. NANO LETTERS 2008; 8:4140-4145. [PMID: 19367999 DOI: 10.1021/nl802370g] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
To understand better enzyme/DNA interactions and to design innovative detectors based on DNA nanoarrays, we need to study the effect of nanometric confinement on the biochemical activity of the DNA molecules. We focus on the study of the restriction enzyme reactions (DpnII) within DNA nanostructures on flat gold films by atomic force microscopy (AFM). Typically we work with a few patches of DNA self assembled monolayers (SAMs) that are hundred nm in size and are lithographically fabricated within alkylthiol SAMs by AFM nanografting. We start by nanografting a few patches of a single-stranded DNA (ssDNA) molecule of 44 base pairs (bps) with a 4 bps recognition sequence (specific for DpnII) in the middle. Afterwards, reaction-ready DNA nanopatches are obtained by hybridization with a complementary 44bps ssDNA sequence. The enzymatic reactions were carried out over nanopatches with different density. By carrying out AFM height measurements, we are able to show that the capability of the DpnII enzyme to reach and react at the recognition site is easily varied by controlling the DNA packing in the nanostructures. We have found strong evidence that inside our ordered DNA nanostructures the enzyme (that works as a dimer) can operate down to the limit in which the space between adjacent DNA molecules is equal to the size of the DNA/enzyme complex. Similar experiments were carried out with a DNA sequence without the recognition site, clearly finding that in that case the enzymatic reaction did not lead to digestion of the molecules. These findings suggest that it is possible to tune the efficiency of an enzymatic reaction on a surface by controlling the steric hindrance inside the DNA nanopatches without vary any further physical or chemical variable. These findings are opening the door to novel applications in both the fields of biosensing and fundamental biophysics.
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Affiliation(s)
- Matteo Castronovo
- Sincrotrone Trieste S.C.p.A., S.S. 14 Km 163.5, 34012 Basovizza, Trieste, Italy
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47
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Peled D, Daube SS, Naaman R. Selective enzymatic labeling to detect packing-induced denaturation of double-stranded DNA at interfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:11842-11846. [PMID: 18800816 DOI: 10.1021/la801437n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The adsorption of DNA on surfaces is a widespread procedure and is a common way for fabrication of biosensors, DNA chips, and nanoelectronic devices. Although the biologically relevant and prevailing in vivo structure of DNA is its double-stranded (dsDNA) conformation, the characterization of DNA on surfaces has mainly focused on single-stranded DNA (ssDNA). Studying the structure of dsDNA on surfaces is of invaluable importance to microarray performance since their effectiveness relies on the ability of two DNA molecules to hybridize and remain stable. In addition, many of the enzymatic transactions performed on DNA require dsDNA, rather than ssDNA, as a substrate. However, it is not established that adsorbed dsDNA remains in its structure and does not denature. Here, two methodologies have been developed for distinguishing between surface-adsorbed single- and double-stranded DNA. We demonstrate that, upon formation of a dense monolayer, the nonthiolated strand comprising the dsDNA is released and the monolayer consists of mostly ssDNA. The fraction of dsDNA within the ssDNA monolayer depends on the length of the oligomers. A likely mechanism leading to this rearrangement is discussed.
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Affiliation(s)
- Dana Peled
- Department of Chemical Physics and Chemical Research Support, Weizmann Institute, Rehovot 76100, Israel
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48
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Sensitive detection of lip genes by electrochemical DNA sensor and its application in polymerase chain reaction amplicons from Phanerochaete chrysosporium. Biosens Bioelectron 2008; 24:1474-9. [PMID: 19010661 DOI: 10.1016/j.bios.2008.09.031] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2008] [Revised: 09/21/2008] [Accepted: 09/24/2008] [Indexed: 11/23/2022]
Abstract
An electrochemical DNA sensor based on the sandwich hybridization recognition of target sequence of lignin peroxidase (lip) genes on a gold electrode was developed. A monolayer of thiolated capture probe was formed on a gold electrode through self-assembling. Following hybridizations with target nucleic acid and biotinylated detection probe, streptavidin-horseradish peroxidase (HRP) conjugate was applied to the electrode. The DNA conformation and surface coverage on electrode were characterized by impedance spectroscopy and square wave voltammetry. The experimental variables were optimized to maximize the hybridization efficiency, detection sensitivity and speed up the assay time. The amperometric current response to HRP-catalyzed reaction was linearly related to the natural logarithm of the target nucleic acid concentration in the range from 0.6 to 30 nM, with the correlation coefficient of 0.9722. The detection limit was 0.03 nM. Synthesized oligonucleotide as well as Phanerochaete chrysosporium lip gene fragments amplified using polymerase chain reaction and digested by restriction endonucleases were tested. The DNA sensor exhibited good precision, stability, sensitivity, and selectivity, and discriminated satisfactorily against mismatched nucleic acid samples of similar lengths.
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49
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Tison CK, Milam VT. Manipulating DNA probe presentation via enzymatic cleavage of diluent strands. Biomacromolecules 2008; 9:2468-76. [PMID: 18715032 DOI: 10.1021/bm800497g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We previously reported a system for the controlled redispersion of DNA-linked aggregates using secondary, competitive hybridization events and found that complete redispersion is contingent upon dilution of the active 20 base-long probe strands with 20 base-long nonhybridizing strands. Here, to reduce the steric interference of nonhybridizing or diluent strands on probe activity, we investigate the effect of shorter diluent strands on the hybridization activity of immobilized probes using the following two approaches: (1) simultaneously coupling shorter diluent strands and longer probe strands to microspheres and (2) simultaneously coupling diluent and probe strands of the same base length to microspheres and then clipping diluent strands with the restriction endonuclease AluI. Results indicate that one can reduce the duplex density down by 50-70% of its initial value, depending on the location of the recognition motif along the hybridization segment. In addition, tighter control over the number of probe-target duplexes is achieved with the enzyme-based approach.
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Affiliation(s)
- Christopher K Tison
- School of Materials Science and Engineering, Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, 771 Ferst Drive NW, Atlanta, Georgia 30332-0245, USA
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50
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Cederquist KB, Golightly RS, Keating CD. Molecular beacon-metal nanowire interface: effect of probe sequence and surface coverage on sensor performance. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:9162-71. [PMID: 18624416 PMCID: PMC2677025 DOI: 10.1021/la703854x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We report the effect of surface coverage and sequence on the performance of 5' thiolated, 3' fluorophore-labeled DNA hairpin probes bound to Au/Ag striped ("barcoded") metal nanowires. Coverage was controlled by varying probe concentration, buffer ionic strength, and by addition of short hydroxy-terminated alkanethiol diluent molecules during probe assembly onto the nanowire surface. Surface dilution of the surface-bound probes with a omega-hydroxyl alkanethiol, a commonly accepted practice in the surface-bound DNA literature, did not appreciably improve sensor performance as compared to similar probe coverages without hydroxyalkanethiol diluents; this finding underscores the differences between the molecular beacon probes used here and more traditional nonfluorescent, random coil probes. We found that intermediate probe coverage of approximately 10 (12) molecules/cm (2) gave the best discrimination between presence and absence of a target sequence. Because we are interested in multiplexed assays, we also compared several beacon probe sequences having different stabilities for secondary structure formation in solution; we found that both probe surface coverage and sensor performance varied for different probe sequences. When five different molecular beacon probes, each bound to barcoded nanowires, were used in a multiplexed, wash-free assay for target oligonucleotides corresponding to viral nucleic acid sequences, these differences in probe performance did not prevent accurate target identification. We anticipate that the findings described here will also be relevant to other applications involving molecular beacons or other structured nucleic acid probes immobilized on metal surfaces.
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Affiliation(s)
- Kristin B. Cederquist
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | | | - Christine D. Keating
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
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