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Schuknecht F, Kołątaj K, Steinberger M, Liedl T, Lohmueller T. Accessible hotspots for single-protein SERS in DNA-origami assembled gold nanorod dimers with tip-to-tip alignment. Nat Commun 2023; 14:7192. [PMID: 37938571 PMCID: PMC10632510 DOI: 10.1038/s41467-023-42943-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/27/2023] [Indexed: 11/09/2023] Open
Abstract
The label-free identification of individual proteins from liquid samples by surface-enhanced Raman scattering (SERS) spectroscopy is a highly desirable goal in biomedical diagnostics. However, the small Raman scattering cross-section of most (bio-)molecules requires a means to strongly amplify their Raman signal for successful measurement, especially for single molecules. This amplification can be achieved in a plasmonic hotspot that forms between two adjacent gold nanospheres. However, the small (≈1-2 nm) gaps typically required for single-molecule measurements are not accessible for most proteins. A useful strategy would thus involve dimer structures with gaps large enough to accommodate single proteins, whilst providing sufficient field enhancement for single-molecule SERS. Here, we report on using a DNA origami scaffold for tip-to-tip alignment of gold nanorods with an average gap size of 8 nm. The gaps are accessible to streptavidin and thrombin, which are captured at the plasmonic hotspot by specific anchoring sites on the origami template. The field enhancement achieved for the nanorod dimers is sufficient for single-protein SERS spectroscopy with sub-second integration times. This design for SERS probes composed of DNA origami with accessible hotspots promotes future use for single-molecule biodiagnostics in the near-infrared range.
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Affiliation(s)
- Francis Schuknecht
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539, Munich, Germany
| | - Karol Kołątaj
- Physics Department and CeNS, Ludwig-Maximilians-University Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
- Département de Physique, Université de Fribourg, Chemin du Musée 3, 1700, Fribourg, Switzerland
| | - Michael Steinberger
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539, Munich, Germany
| | - Tim Liedl
- Physics Department and CeNS, Ludwig-Maximilians-University Munich, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
| | - Theobald Lohmueller
- Chair for Photonics and Optoelectronics, Nano-Institute Munich, Department of Physics, Ludwig-Maximilians-Universität (LMU), Königinstraße 10, 80539, Munich, Germany.
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Myres GJ, Kitt JP, Harris JM. Raman Scattering Reveals Ion-Dependent G-Quadruplex Formation in the 15-mer Thrombin-Binding Aptamer upon Association with α-Thrombin. Anal Chem 2023; 95:16160-16168. [PMID: 37870982 DOI: 10.1021/acs.analchem.3c02751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The discovery of DNA aptamers that bind biomolecular targets has enabled significant innovations in biosensing. Aptamers form secondary structures that exhibit selective high-affinity interactions with their binding partners. The binding of its target by an aptamer is often accompanied by conformational changes, and sensing by aptamers often relies on these changes to provide readout signals from extrinsic labels to detect target association. Many biosensing applications involve aptamers immobilized to surfaces, but methods to characterize conformations of immobilized aptamers and their in situ response have been lacking. To address this challenge, we have developed a structurally informative Raman spectroscopy method to determine conformations of the 15-mer thrombin-binding aptamer (TBA) immobilized on porous silica surfaces. The TBA is of interest because its binding of α-thrombin depends on the aptamer forming an antiparallel G-quadruplex, which is thought to drive signal changes that allow thrombin-binding to be detected. However, specific metal cations also stabilize the G-quadruplex conformation of the aptamer, even in the absence of its protein target. To develop a deeper understanding of the conformational response of the TBA, we utilize Raman spectroscopy to quantify the effects of the metal cations, K+ (stabilizing) and Li+ (nonstabilizing), on G-quadruplex versus unfolded populations of the TBA. In K+ or Li+ solutions, we then detect the association of α-thrombin with the immobilized aptamer, which can be observed in Raman scattering from the bound protein. The results show that the association of α-thrombin in K+ solutions produces no detectable change in aptamer conformation, which is found in the G-quadruplex form both before and after binding its target. In Li+ solutions, however, where the TBA is unfolded prior to α-thrombin association, protein binding occurs with the formation of a G-quadruplex by the aptamer.
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Affiliation(s)
- Grant J Myres
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Jay P Kitt
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Joel M Harris
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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Wu W, Yu C, Wang Q, Zhao F, He H, Liu C, Yang Q. Research advances of DNA aptasensors for foodborne pathogen detection. Crit Rev Food Sci Nutr 2019; 60:2353-2368. [PMID: 31298036 DOI: 10.1080/10408398.2019.1636763] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aptamers, referring to single-stranded DNA or RNA molecules can specifically recognize and bind to their targets. Based on their excellent specificity, sensitivity, high affinity, and simplicity of modification, aptamers offer great potential for pathogen detection and biomolecular screening. This article reviews aptamer screening technologies and aptamer application technologies, including gold-nanoparticle lateral flow assays, fluorescence assays, electrochemical assays, colorimetric assays, and surface-enhanced Raman assays, in the detection of foodborne pathogens. Although notable progress (more rapid, sensitive, and accurate) has been achieved in the field, challenges and drawbacks in their applications still remain to be overcome.
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Affiliation(s)
- Wei Wu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China.,State Key Laboratory of Bio-fibers and Eco-textiles, Institute of Biochemical Engineering, School of Materials Science and Engineering, Qingdao University, Qingdao, China
| | - Chundi Yu
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Qi Wang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Fangyuan Zhao
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Hong He
- Clinical Laboratory, Affiliated Hospital to Qingdao University, Qingdao, China
| | - Chunzhao Liu
- State Key Laboratory of Bio-fibers and Eco-textiles, Institute of Biochemical Engineering, School of Materials Science and Engineering, Qingdao University, Qingdao, China.,State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, China
| | - Qingli Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
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Raman Spectroscopy and Aptamers for a Label-Free Approach: Diagnostic and Application Tools. JOURNAL OF HEALTHCARE ENGINEERING 2019; 2019:2815789. [PMID: 31183028 PMCID: PMC6512054 DOI: 10.1155/2019/2815789] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/10/2019] [Indexed: 01/04/2023]
Abstract
Raman spectroscopy is a powerful optical technique based on the inelastic scattering of incident light to assess the chemical composition of a sample, including biological ones. Medical diagnostic applications of Raman spectroscopy are constantly increasing to provide biochemical and structural information on several specimens, being not affected by water interference, and potentially avoiding the constraint of additional labelling procedures. New strategies have been recently developed to overcome some Raman limitations related, for instance, to the need to deal with an adequate quantity of the sample to perform a reliable analysis. In this regard, the use of metallic nanoparticles, the optimization of fiber optic probes, and other approaches can actually enhance the signal intensity compared to spontaneous Raman scattering. Moreover, to further increase the potential of this investigation technique, aptamers can be considered as a valuable means, being synthetic, short, single, or double-stranded oligonucleotides (RNAs or DNAs) that fold up into unique 3D structures to specifically bind to selected molecules, even at very low concentrations, and thus allowing an early diagnosis of a possible disease. Due to the paramount relevance of the topic, this review focuses on the main Raman spectroscopy techniques combined with aptamer arrays in the label-free mode, providing an overview on different applications to support healthcare management.
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Pannico M, Calarco A, Peluso G, Musto P. Functionalized Gold Nanoparticles as Biosensors for Monitoring Cellular Uptake and Localization in Normal and Tumor Prostatic Cells. BIOSENSORS 2018; 8:E87. [PMID: 30287746 PMCID: PMC6316160 DOI: 10.3390/bios8040087] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/27/2018] [Accepted: 09/29/2018] [Indexed: 11/16/2022]
Abstract
In the present contribution the fabrication and characterization of functionalized gold nanospheres of uniform shape and controlled size is reported. These nano-objects are intended to be used as Surface Enhanced Raman Spectroscopy (SERS) sensors for in-vitro cellular uptake and localization. Thiophenol was used as molecular reporter and was bound to the Au surface by a chemisorption process in aqueous solution. The obtained colloidal solution was highly stable and no aggregation of the single nanospheres into larger clusters was observed. The nanoparticles were incubated in human prostatic cells with the aim of developing a robust, SERS-based method to differentiate normal and tumor cell lines. SERS imaging experiments showed that tumor cells uptake considerably larger amounts of nanoparticles in comparison to normal cells (up to 950% more); significant differences were also observed in the uptake kinetics. This largely different behaviour might be exploited in diagnostic and therapeutic applications.
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Affiliation(s)
- Marianna Pannico
- Institute for Polymers, Composites and Biomaterials, National Research Council of Italy, 80078 Pozzuoli, Italy.
| | - Anna Calarco
- Institute of Agro-environmental and Forest Biology, National Research Council of Italy, 80131 Naples, Italy.
| | - Gianfranco Peluso
- Institute of Agro-environmental and Forest Biology, National Research Council of Italy, 80131 Naples, Italy.
| | - Pellegrino Musto
- Institute for Polymers, Composites and Biomaterials, National Research Council of Italy, 80078 Pozzuoli, Italy.
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Abstract
The electrochemical behavior of a synthetic oligonucleotide, thrombin-binding aptamer (TBA, 15-mer), was explored at a liquid-organogel microinterface array. TBA did not display any response when only background electrolytes were present in both phases. On the basis of literature reports that surfactants can influence nucleic acid detection, the response in the presence of cetyltrimethylammonium (CTA+) was examined. With both TBA and CTA+ in the aqueous phase, the transfer current for CTA+ was diminished, signifying the interaction of CTA+ with TBA. Experiments with CTA+ spiked into the organic phase revealed a sharp current peak, consistent with the interfacial formation of a CTA+-TBA complex. However, use of CTA+ as the organic phase electrolyte cation, as the salt with tetrakis(4-chlorophenyl)borate, greatly improved the response to TBA. In this case, a distinctive peak response (at ca. -0.25 V) was attributed to the transfer of CTA+ across the soft interface to complex with aqueous phase TBA. Employing this process as a detection step enabled a detection limit of 0.11 μM TBA (by cyclic voltammetry). Furthermore, the presence of magnesium cations at physiological concentration resulted in the disappearance of the TBA response because of Mg2+-induced folding of TBA. Also, the current response of TBA was decreased by the addition of thrombin, indicating TBA interacted with this binding partner. Finally, the interfacial surfactant-aptamer interaction was explored in a synthetic urine matrix that afforded a detection limit of 0.29 μM TBA. These results suggest that aptamer-binding interactions can be monitored by electrochemistry at aqueous-organic interfaces and open up a new possibility for detection in aptamer-binding assays.
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Affiliation(s)
- Bren Mark B Felisilda
- Curtin Institute for Functional Molecules and Interfaces, School of Molecular and Life Sciences , Curtin University , GPO Box U1987, Perth , Western Australia 6845 , Australia
| | - Damien W M Arrigan
- Curtin Institute for Functional Molecules and Interfaces, School of Molecular and Life Sciences , Curtin University , GPO Box U1987, Perth , Western Australia 6845 , Australia
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Meshik X, Xu K, Dutta M, Stroscio MA. Optical detection of lead and potassium ions using a quantum-dot-based aptamer nanosensor. IEEE Trans Nanobioscience 2014; 13:161-4. [PMID: 24771595 DOI: 10.1109/tnb.2014.2317315] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Quantum-dot (QD) based nanosensors can be used to detect a wide range of molecules. This study examined a nanosensor comprised of thrombin binding aptamer (TBA) with 700NC InGaP QD on the 5 (') terminus and an Au nanoparticle quencher on the 3 (') terminus. Both K(+) and Pb(2+) bind to TBA, resulting in a conformational change that brings the Au quencher closer to the QD. Photoluminescence measurements indicated a decrease in fluorescence corresponding to an increase in either K(+) or Pb(2+) concentration. For healthy blood serum K(+) concentrations (3.5-5 mM), the beacon exhibited 15-17% quenching efficiency. Pb(2+) concentration of 0.48 μM, the threshold for toxicity in serum, yielded 14% quenching. The beacon's ability to detect changes in ion levels in a critical range of concentrations can make it an effective diagnostic tool.
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Samanta A, Jana S, Das RK, Chang YT. Biocompatible surface-enhanced Raman scattering nanotags for in vivo cancer detection. Nanomedicine (Lond) 2014; 9:523-35. [DOI: 10.2217/nnm.13.222] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The advancement of surface-enhanced Raman scattering (SERS) is significantly increasing as an ultra-sensitive sensing technology in biomedical research. In this review, we focus on the most recent developments of biocompatible nanoprobes for cancer research. First, we discuss coating approaches to enhance the biocompatibility of SERS substrate and Raman reporters. Furthermore, interesting ligands such as antibodies, aptamers and polypeptides are attached to the surface of nanotags for targeting the cancerous cells in vitro. The unique multiplexing capabilities of the SERS technique have been applied for simultaneous multiple target recognition. Finally, these noninvasive, ultrasensitive tools are mostly highlighted for in vivo tumor detection. Potential application of SERS nanotags in therapeutic study and the possibility of SERS nanotags in biomedical applications are outlined briefly in this review.
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Affiliation(s)
- Animesh Samanta
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A *STAR), 11 Biopolis Way, 138667, Singapore
| | - Santanu Jana
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A *STAR), 11 Biopolis Way, 138667, Singapore
| | - Raj Kumar Das
- Department of Chemistry & MedChem Program for Life Sciences, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Young Tae Chang
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A *STAR), 11 Biopolis Way, 138667, Singapore
- Department of Chemistry & MedChem Program for Life Sciences, National University of Singapore, 3 Science Drive 3, 117543, Singapore
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