1
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Percot A, Maurel MC, Lambert JF, Zins EL. New insights into the surface Enhanced Raman Scattering (SERS) response of adenine using chemometrics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 314:124177. [PMID: 38554690 DOI: 10.1016/j.saa.2024.124177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/15/2024] [Accepted: 03/18/2024] [Indexed: 04/02/2024]
Abstract
The SERS response of adenine is one of the most studied, due to its outstanding exaltation. However, the spectra obtained strongly differ according to the experimental conditions and still remain not well understood. To be able to search for the presence of this molecule in complex environments, it is essential to better understand the SERS response of adenine alone. After a brief presentation of the literature on the subject, we present results suggesting that the experimental spectra would result from the overlap of different spectroscopic signatures, that may probably be due to different non-covalent interactions or different electromagnetic fields experienced by adenine molecules. An independent component analysis is reported. Our results underline the difficulty to precisely analyze the experimental data, the need to continue this research and to constitute data banks that would allow comparing the spectra obtained in different laboratories according to the experimental conditions.
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Affiliation(s)
- A Percot
- Sorbonne Université, CNRS, MONARIS, UMR8233, F-75005 Paris, France.
| | - M C Maurel
- Sorbonne Université, Muséum National d'Histoire Naturelle, CNRS,MNHN, UMR7205, ISYEB, F-75005 Paris, France
| | - J F Lambert
- Sorbonne Université, CNRS, LAMS, UMR8220, F-75005 Paris, France
| | - E L Zins
- Sorbonne Université, CNRS, MONARIS, UMR8233, F-75005 Paris, France
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2
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Cheng HW, Tsai HM, Wang YL. Exploiting Purine as an Internal Standard for SERS Quantification of Purine Derivative Molecules Released by Bacteria. Anal Chem 2023; 95:16967-16975. [PMID: 37931018 PMCID: PMC10666080 DOI: 10.1021/acs.analchem.3c03259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/08/2023]
Abstract
Surface-enhanced Raman scattering (SERS) is a highly sensitive technique used in diverse biomedical applications including rapid antibiotic susceptibility testing (AST). However, signal fluctuation in SERS, particularly the widespread of signals measured from different batches of SERS substrates, compromises its reliability and introduces potential errors in SERS-AST. In this study, we investigate the use of purine as an internal standard (IS) to recalibrate SERS signals and quantify the concentrations of two important purine derivatives, adenine and hypoxanthine, which are the most important biomarkers used in SERS-AST. Our findings demonstrate that purine IS effectively mitigates SERS signal fluctuations and enables accurate prediction of adenine and hypoxanthine concentrations across a wide range (5 orders of magnitude). Calibrations with purine as an IS outperform those without, exhibiting a 10-fold increase in predictive accuracy. Additionally, the calibration curve obtained from the first batch of SERS substrates remains effective for 64 additional substrates fabricated over a half-year period. Measurements of adenine and hypoxanthine concentrations in bacterial supernatants using SERS with purine IS closely align with the liquid chromatography-mass spectrometry results. The use of purine as an IS offers a simple and robust platform to enhance the speed and accuracy of SERS-AST, while also paving the way for in situ SERS quantification of purine derivatives released by bacteria under various stress conditions.
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Affiliation(s)
- Ho-Wen Cheng
- Molecular
Science and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei 106319, Taiwan
- International
Graduate Program of Molecular Science and Technology, National Taiwan University, Taipei 106319, Taiwan
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106319, Taiwan
| | - Hsin-Mei Tsai
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106319, Taiwan
| | - Yuh-Lin Wang
- Institute
of Atomic and Molecular Sciences, Academia Sinica, Taipei 106319, Taiwan
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3
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Liu F, Wu T, Tian A, He C, Bi X, Lu Y, Yang K, Xia W, Ye J. Intracellular metabolic profiling of drug resistant cells by surface enhanced Raman scattering. Anal Chim Acta 2023; 1279:341809. [PMID: 37827617 DOI: 10.1016/j.aca.2023.341809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Intracellular metabolic profiling reveals real-time metabolic information useful for the study of underlying mechanisms of cells in particular conditions such as drug resistance. However, mass spectrometry (MS), one of the leading metabolomics technologies, usually requires a large number of cells and complex pretreatments. Surface enhanced Raman scattering (SERS) has an ultrahigh detection sensitivity and specificity, favorable for metabolomics analysis. However, some targeted SERS methods focus on very limited metabolite without global bioprofiling, and some label-free approaches try to fingerprint the metabolic response based on whole SERS spectral classification, but comprehensive interpretation of biological mechanisms was lacking. (95) RESULTS: We proposed a label-free SERS technique for intracellular metabolic profiling in complex cellular lysates within 3 min. We first compared three kinds of cellular lysis methods and sonication lysis shows the highest extraction efficiency of metabolites. To obtain comprehensive metabolic information, we collected a spectral set for each sample and further qualified them by the Pearson correlation coefficient (PCC) to calculate how many spectra should be acquired at least to gain the adequate information from a statistical and global view. In addition, according to our measurements with 10 pure metabolites, we can understand the spectra acquired from complex cellular lysates of different cell lines more precisely. Finally, we further disclosed the variations of 22 SERS bands in enzalutamide-resistant prostate cancer cells and some are associated with the androgen receptor signaling activity and the methionine salvage pathway in the drug resistance process, which shows the same metabolic trends as MS. (149) SIGNIFICANCE: Our technique has the capability to capture the intracellular metabolic fingerprinting with the optimized lysis approach and spectral set collection, showing high potential in rapid, sensitive and global metabolic profiling in complex biosamples and clinical liquid biopsy. This gives a new perspective to the study of SERS in insightful understanding of relevant biological mechanisms. (54).
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Affiliation(s)
- Fugang Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Tingyu Wu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Ao Tian
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Chang He
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Xinyuan Bi
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Yao Lu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Kai Yang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Weiliang Xia
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China; State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, PR China.
| | - Jian Ye
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China; State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, PR China; Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China.
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4
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Chia ZC, Chen YL, Chuang CH, Hsieh CH, Chen YJ, Chen KH, Huang TC, Chen MC, Huang CC. Polyphenol-assisted assembly of Au-deposited polylactic acid microneedles for SERS sensing and antibacterial photodynamic therapy. Chem Commun (Camb) 2023; 59:6339-6342. [PMID: 37186113 DOI: 10.1039/d3cc00733b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
3D SERS microneedles with self-assembled AuNPs were fabricated with tannic acid (chemical glue and reductant) on polylactic acid microneedles for in-depth chemical and biomolecular analysis, with LOD values below 200 ppb for small molecules and 102 CFU cm-2 for bacteria. The MB/Au-microneedles were used for photodynamic therapy with SERS-monitored photosensitizer degradation.
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Affiliation(s)
- Zi-Chun Chia
- Department of Photonics, National Cheng Kung University, Tainan 70101, Taiwan
| | - Yi-Lun Chen
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
| | - Cheng-Hsun Chuang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
| | - Chou-Hsun Hsieh
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
| | - Ya-Jyun Chen
- Department of Photonics, National Cheng Kung University, Tainan 70101, Taiwan
| | - Kuan-Hsu Chen
- Department of Photonics, National Cheng Kung University, Tainan 70101, Taiwan
| | - Tzu-Chi Huang
- Department of Photonics, National Cheng Kung University, Tainan 70101, Taiwan
| | - Mei-Chin Chen
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
| | - Chih-Chia Huang
- Department of Photonics, National Cheng Kung University, Tainan 70101, Taiwan
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan 70101, Taiwan.
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5
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Pan X, Qian C, Chow A, Wang L, Kamenetska M. Atomically precise binding conformations of adenine and its variants on gold using single molecule conductance signatures. J Chem Phys 2022; 157:234201. [PMID: 36550043 DOI: 10.1063/5.0103642] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We demonstrate single molecule conductance as a sensitive and atomically precise probe of binding configurations of adenine and its biologically relevant variants on gold. By combining experimental measurements and density functional theory (DFT) calculations of single molecule-metal junction structures in aqueous conditions, we determine for the first time that robust binding of adenine occurs in neutral or basic pH when the molecule is deprotonated at the imidazole moiety. The molecule binds through the donation of the electron lone pairs from the imidazole nitrogen atoms, N7 and N9, to the gold electrodes. In addition, the pyrimidine ring nitrogen, N3, can bind concurrently and strengthen the overall metal-molecule interaction. The amine does not participate in binding to gold in contrast to most other amine-terminated molecular wires due to the planar geometry of the nucleobase. DFT calculations reveal the importance of interface charge transfer in stabilizing the experimentally observed binding configurations. We demonstrate that biologically relevant variants of adenine, 6-methyladenine and 2'-deoxyadenosine, have distinct conductance signatures. These results lay the foundation for biosensing on gold using single molecule conductance readout.
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Affiliation(s)
- Xiaoyun Pan
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, Massachusetts 02215, USA
| | - Cheng Qian
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, USA
| | - Amber Chow
- Department of Physics, Boston University, 590 Commonwealth Ave., Boston, Massachusetts 02215, USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, New Jersey 08854, USA
| | - Maria Kamenetska
- Department of Chemistry, Boston University, 590 Commonwealth Ave., Boston, Massachusetts 02215, USA
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6
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Cho NH, Kim YB, Lee YY, Im SW, Kim RM, Kim JW, Namgung SD, Lee HE, Kim H, Han JH, Chung HW, Lee YH, Han JW, Nam KT. Adenine oligomer directed synthesis of chiral gold nanoparticles. Nat Commun 2022; 13:3831. [PMID: 35780141 PMCID: PMC9250518 DOI: 10.1038/s41467-022-31513-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/21/2022] [Indexed: 12/30/2022] Open
Abstract
Precise control of morphology and optical response of 3-dimensional chiral nanoparticles remain as a significant challenge. This work demonstrates chiral gold nanoparticle synthesis using single-stranded oligonucleotide as a chiral shape modifier. The homo-oligonucleotide composed of Adenine nucleobase specifically show a distinct chirality development with a dissymmetric factor up to g ~ 0.04 at visible wavelength, whereas other nucleobases show no development of chirality. The synthesized nanoparticle shows a counter-clockwise rotation of generated chiral arms with approximately 200 nm edge length. The molecular dynamics and density functional theory simulations reveal that Adenine shows the highest enantioselective interaction with Au(321)R/S facet in terms of binding orientation and affinity. This is attributed to the formation of sequence-specific intra-strand hydrogen bonding between nucleobases. We also found that different sequence programming of Adenine-and Cytosine-based oligomers result in chiral gold nanoparticles' morphological and optical change. These results extend our understanding of the biomolecule-directed synthesis of chiral gold nanoparticles to sequence programmable deoxyribonucleic acid and provides a foundation for programmable synthesis of chiral gold nanoparticles.
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Affiliation(s)
- Nam Heon Cho
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Young Bi Kim
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Yoon Young Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang Won Im
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Ryeong Myeong Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jeong Won Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seok Daniel Namgung
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hye-Eun Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hyeohn Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jeong Hyun Han
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hye Won Chung
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yoon Ho Lee
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jeong Woo Han
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, 37673, Republic of Korea.
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea.
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7
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Stefancu A, Moisoiu V, Desmirean M, Iancu SD, Tigu AB, Petrushev B, Jurj A, Cozan RG, Budisan L, Fetica B, Roman A, Dobie G, Turcas C, Zdrenghea M, Teodorescu P, Pasca S, Piciu D, Dima D, Bálint Z, Leopold N, Tomuleasa C. SERS-based DNA methylation profiling allows the differential diagnosis of malignant lymphadenopathy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120216. [PMID: 34364036 DOI: 10.1016/j.saa.2021.120216] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/12/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
This study highlights the potential of surface-enhanced Raman scattering (SERS) to differentiate between B-cell lymphoma (BCL), T-cell lymphoma (TCL), lymph node metastasis of melanoma (Met) and control (Ctr) samples based on the specific SERS signal of DNA extracted from lymph node tissue biopsy. Differences in the methylation profiles as well as the specific interaction of malignant and non-malignant DNA with the metal nanostructure are captured in specific variations of the band at 1005 cm-1, attributed to 5-methylcytosine and the band at 730 cm-1, attributed to adenine. Thus, using the area ratio of these two SERS marker bands as input for univariate classification, an area under the curve (AUC) of 0.70 was achieved in differentiating between malignant and non-malignant DNA. In addition, DNA from the BCL and TCL groups exhibited differences in the area of the SERS band at 730 cm-1, yielding an AUC of 0.84 in differentiating between these two lymphadenopathies. Lastly, using multivariate data analysis techniques, an overall accuracy of 94.7% was achieved in the differential diagnosis between the BCL, TCL, Met and Ctr groups. These results pave the way towards the implementation of SERS as a novel tool in the clinical setting for improving the diagnosis of malignant lymphadenopathy.
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Affiliation(s)
- Andrei Stefancu
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Vlad Moisoiu
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Minodora Desmirean
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Pathology, Constantin Papilian Military Hospital, Cluj-Napoca, Romania
| | - Stefania D Iancu
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Adrian B Tigu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Bobe Petrushev
- Department of Pathology, Octavian Fodor Gastroenterology Institute, Cluj-Napoca, Romania
| | - Ancuta Jurj
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ramona G Cozan
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Liviuta Budisan
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Bogdan Fetica
- Department of Pathology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Andrei Roman
- Department of Radiology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Radiology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Gina Dobie
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cristina Turcas
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihnea Zdrenghea
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Hematology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Patric Teodorescu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Hematology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Sergiu Pasca
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Department of Hematology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Doina Piciu
- Department of Nuclear Medicine, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Delia Dima
- Department of Hematology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
| | - Zoltán Bálint
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - Nicolae Leopold
- Faculty of Physics, Babeș-Bolyai University, Cluj-Napoca, Romania; Biomed Data Analytics SRL, Cluj-Napoca, Romania.
| | - Ciprian Tomuleasa
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania; Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Hematology, "Prof. Dr. Ion Chiricuță" Institute of Oncology, Cluj-Napoca, Romania
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8
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Yoshimoto T, Seki M, Okabe H, Matsuda N, Wu DY, Futamata M. Three distinct adsorbed states of adenine on gold nanoparticles depending on pH in aqueous solutions. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Harroun SG, Zhang Y, Chen TH, Chang HT, Vallée-Bélisle A. Silver oxide model surface improves computational simulation of surface-enhanced Raman spectroscopy on silver nanoparticles. Phys Chem Chem Phys 2021; 23:15480-15484. [PMID: 34263277 DOI: 10.1039/d1cp01498f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Surface-enhanced Raman spectroscopy (SERS) coupled with density functional theory (DFT) computations can characterise the adsorption orientation of a molecule on a nanoparticle surface. When using DFT to simulate SERS on a silver surface, one typically employs an atom (Ag), ion (Ag+), or cluster (Agx or Agx+) as the model surface. Here, by examining the nucleobase 2,6-diaminopurine (2,6-DAP) and then generalising our strategy to three other molecules, we show that employing silver oxide (Ag2O) as the model surface can quantitatively improve the accuracy of simulated SERS.
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Affiliation(s)
- Scott G Harroun
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, Montréal, QC H3C 3J7, Canada.
| | - Yaoting Zhang
- Department of Chemistry, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Tzu-Heng Chen
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan. and Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Huan-Tsung Chang
- Department of Chemistry, National Taiwan University, Taipei, 10617, Taiwan.
| | - Alexis Vallée-Bélisle
- Laboratory of Biosensors & Nanomachines, Département de Chimie, Université de Montréal, Montréal, QC H3C 3J7, Canada. and Département de Biochimie et Médicine Moléculaire, Université de Montréal, Montréal, QC, H3C 3J7, Canada
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10
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Si NT, Nhung NTA, Bui TQ, Nguyen MT, Nhat PV. Gold nanoclusters as prospective carriers and detectors of pramipexole. RSC Adv 2021; 11:16619-16632. [PMID: 35479146 PMCID: PMC9031969 DOI: 10.1039/d1ra02172a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
Pramipexole (PPX) is known in the treatment of Parkinson's disease and restless legs syndrome. We carried out a theoretical investigation on pramipexole-Au cluster interactions for the applications of drug delivery and detection. Three Au N clusters with sizes N = 6, 8 and 20 were used as reactant models to simulate the metallic nanostructured surfaces. Quantum chemical computations were performed in both gas phase and aqueous environments using density functional theory (DFT) with the PBE functional and the cc-pVDZ-PP/cc-pVTZ basis set. The PPX drug is mainly adsorbed on gold clusters via its nitrogen atom of the thiazole ring with binding energies of ca. -22 to -28 kcal mol-1 in vacuum and ca. -18 to -24 kcal mol-1 in aqueous solution. In addition to such Au-N covalent bonding, the metal-drug interactions are further stabilized by electrostatic effects, namely hydrogen-bond NH⋯Au contributions. Surface-enhanced Raman scattering (SERS) of PPX adsorbed on the Au surfaces and its desorption process were also examined. In comparison to Au8, both Au6 and Au20 clusters undergo a shorter recovery time and a larger change of energy gap, being possibly conducive to electrical conversion, thus signaling for detection of the drug. A chemical enhancement mechanism for SERS procedure was again established in view of the formation of nonconventional hydrogen interactions Au⋯H-N. The binding of PPX to a gold cluster is expected to be reversible and triggered by the presence of cysteine residues in protein matrices or lower-shifted alteration of environment pH. These findings would encourage either further theoretical probes to reach more accurate views on the efficiency of pramipexole-Au interactions, or experimental attempts to build appropriate gold nanostructures for practical trials, harnessing their potentiality for applications.
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Affiliation(s)
- Nguyen Thanh Si
- Computational Chemistry Research Group, Ton Duc Thang University Ho Chi Minh City Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University Ho Chi Minh City Vietnam
| | | | - Thanh Q Bui
- Department of Chemistry, University of Sciences, Hue University Hue Vietnam
| | - Minh Tho Nguyen
- Institute for Computational Science and Technology (ICST) Ho Chi Minh City Vietnam
| | - Pham Vu Nhat
- Department of Chemistry, Can Tho University Can Tho Vietnam
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11
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Tzeng Y, Lin BY. Silver-Based SERS Pico-Molar Adenine Sensor. BIOSENSORS-BASEL 2020; 10:bios10090122. [PMID: 32932787 PMCID: PMC7559806 DOI: 10.3390/bios10090122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 11/22/2022]
Abstract
Adenine is an important molecule for biomedical and agricultural research and applications. The detection of low concentration adenine molecules is thus desirable. Surface-enhanced Raman scattering (SERS) is a promising label-free detection and fingerprinting technique for molecules of significance. A novel SERS sensor made of clusters of silver nanostructures deposited on copper bumps in valleys of an etched silicon substrate was previously reported to exhibit a low and reproducible detection limit for a 10−11 M neutral adenine aqueous solution. Reflection of laser illumination from the silicon surface surrounding a valley provides additional directions of laser excitation to adenine molecules adsorbing on a silver surface for the generation of enhanced SERS signal strength leading to a low detection limit. This paper further reports a concentration dependent shift of the ring-breathing mode SERS adenine peak towards 760 cm−1 with decreasing concentration and its pH-dependent SERS signal strength. For applications, where the pH value can vary, reproducible detection of 10−12 M adenine in a pH 9 aqueous solution is feasible, making the novel SERS structure a desirable pico-molar adenine sensor.
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12
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Nguyen PHL, Hong B, Rubin S, Fainman Y. Machine learning for composition analysis of ssDNA using chemical enhancement in SERS. BIOMEDICAL OPTICS EXPRESS 2020; 11:5092-5121. [PMID: 33014602 PMCID: PMC7510872 DOI: 10.1364/boe.397616] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 05/05/2023]
Abstract
Surface-enhanced Raman spectroscopy (SERS) is an attractive method for bio-chemical sensing due to its potential for single molecule sensitivity and the prospect of DNA composition analysis. In this manuscript we leverage metal specific chemical enhancement effect to detect differences in SERS spectra of 200-base length single-stranded DNA (ssDNA) molecules adsorbed on gold or silver nanorod substrates, and then develop and train a linear regression as well as neural network models to predict the composition of ssDNA. Our results indicate that employing substrates of different metals that host a given adsorbed molecule leads to distinct SERS spectra, allowing to probe metal-molecule interactions under distinct chemical enhancement regimes. Leveraging this difference and combining spectra from different metals as an input for PCA (Principal Component Analysis) and NN (Neural Network) models, allows to significantly lower the detection errors compared to manual feature-choosing analysis as well as compared to the case where data from single metal is used. Furthermore, we show that NN model provides superior performance in the presence of complex noise and data dispersion factors that affect SERS signals collected from metal substrates fabricated on different days.
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Factors that control the gold nanoparticles' aggregation induced by adenine molecules: New insights through a combined experimental and theoretical study. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113136] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Tzeng Y, Lin BY. Silver SERS Adenine Sensors with a Very Low Detection Limit. BIOSENSORS-BASEL 2020; 10:bios10050053. [PMID: 32429203 PMCID: PMC7277772 DOI: 10.3390/bios10050053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 01/10/2023]
Abstract
The detection of adenine molecules at very low concentrations is important for biological and medical research and applications. This paper reports a silver-based surface-enhanced Raman scattering (SERS) sensor with a very low detection limit for adenine molecules. Clusters of closely packed silver nanoparticles on surfaces of discrete ball-like copper bumps partially covered with graphene are deposited by immersion in silver nitrate. These clusters of silver nanoparticles exhibit abundant nanogaps between nanoparticles, where plasmonic coupling induces very high local electromagnetic fields. Silver nanoparticles growing perpendicularly on ball-like copper bumps exhibit surfaces of large curvature, where electromagnetic field enhancement is high. Between discrete ball-like copper bumps, the local electromagnetic field is low. Silver is not deposited on the low-field surface area. Adenine molecules interact with silver by both electrostatic and functional groups and exhibit low surface diffusivity on silver surface. Adenine molecules are less likely to adsorb on low-field sensor surface without silver. Therefore, adenine molecules have a high probability of adsorbing on silver surface of high local electric fields and contribute to the measured Raman scattering signal strength. We demonstrated SERS sensors made of clusters of silver nanoparticles deposited on discrete ball-like copper bumps with very a low detection limit for detecting adenine water solution of a concentration as low as 10−11 M.
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Detection of Biological Bricks in Space. The Case of Adenine in Silica Aerogel. LIFE (BASEL, SWITZERLAND) 2019; 9:life9040082. [PMID: 31717814 PMCID: PMC6958507 DOI: 10.3390/life9040082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/15/2019] [Accepted: 10/24/2019] [Indexed: 11/16/2022]
Abstract
Space missions using probes to return dust samples are becoming more frequent. Dust collectors made of silica aerogel blocks are used to trap and bring back extraterrestrial particles for analysis. In this work, we show that it is possible to detect traces of adenine using surface-enhanced Raman spectroscopy (SERS). The method was first optimized using adenine deposition on glass slides and in glass wells. After this preliminary step, adenine solution was injected into the silica aerogel. Finally, gaseous adenine was successfully trapped in the aerogel. The presence of traces of adenine was monitored by SERS through its characteristic bands at 732, 1323, and 1458 cm-1 after the addition of the silver Creighton colloid. Such a method can be extended in the frame of Tanpopo missions for studying the interplanetary transfer of prebiotic organic compounds of biological interest.
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Mamián-López MB, Temperini MLA. On the Cooperativity Effect in Watson and Crick and Wobble Pairs for a Halouracil Series and Its Potential Quantitative Application Studied through Surface-Enhanced Raman Spectroscopy. Anal Chem 2018; 90:14165-14172. [PMID: 30457840 DOI: 10.1021/acs.analchem.8b02188] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The nature of the cooperativity effect of hydrogen bonds in Watson and Crick and wobble base pairs formed with thymine, uracil, and its 5-halogenated derivatives (5-fluoro, -chloro, and -bromouracil) has been studied through SERS and by using chemometric tools to process data and extract relevant information. Remarkable differences between the two kinds of pairs were clearly observed, and the behavior correlated to the withdrawing character of different substituents at the 5-position of uracil was verified. Multivariate analyses have also unveiled information about the pair's stability, and a stronger cooperativity effect seems to rule the Watson and Crick pairs when compared to wobble pairs. Defined patterns in the behavior of Watson and Crick pairs allowed the design of an indirect methodology for quantifying 5-bromouracil using a partial least squares (PLS) method with variable selection. Limit of detection (LOD) values of 0.037 and 0.112 mmol L-1 in the absence and presence of structurally similar interferences were reached, while its direct surface-enhanced Raman spectroscopy (SERS) quantification is only possible at ∼45 mmol L-1.
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Affiliation(s)
- Mónica B Mamián-López
- Department of Fundamental Chemistry, Institute of Chemistry , University of São Paulo , São Paulo 03178-200 , Brazil
| | - Marcia L A Temperini
- Department of Fundamental Chemistry, Institute of Chemistry , University of São Paulo , São Paulo 03178-200 , Brazil
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