Fast, highly sensitive and label free detection of small genetic sequence difference of DNA using novel Surface-Enhanced Raman Spectroscopy nanostructured sensor

Gaidi, Mounir; Daoudi, Kais; Tlili, Abdelaziz; Columbus, Soumya; Leblanc-Lavoie, Joël; Ramachandran, Krithikadevi; Suleiman, Bashir M.; Alhazaa, Abdulaziz; Khakani, My Alì El

doi:10.1016/j.sbsr.2021.100406

Cited by 12 publications

(8 citation statements)

References 42 publications

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“…We can easily note that both viruses (COVID19 and H1N1) have distinguished Raman spectra. We previously report that this technique (SERS) is able to detect small difference between two DNAs genetic sequences [48] . This technique could possibly be developed with functionalization of SERS substrates with specific labels to target the viral proteins, nucleic acids precisely.…”

Section: Resultsmentioning

confidence: 99%

Ultra-sensitive and fast optical detection of the spike protein of the SARS-CoV-2 using AgNPs/SiNWs nanohybrid based sensors

Daoudi

Ramachandran

Alawadhi

et al. 2021

Surfaces and Interfaces

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Severe acute respiratory syndrome SARS-CoV-2 virus led to notable challenges amongst researchers in view of development of new and fast detecting techniques. In this regard, surface-enhanced Raman spectroscopy (SERS) technique, providing a fingerprint characteristic for each material, would be an interesting approach. The current study encompasses the fabrication of a SERS sensor to study the SARS-CoV-2 S1 (RBD) spike protein of the SARS-CoV-2 virus family. The SERS sensor consists of a silicon nanowires (SiNWs) substrate decorated with plasmonic silver nanoparticles (AgNPs). Both SiNWs fabrication and AgNPs decoration were achieved by a relatively simple wet chemical processing method. The study deliberately projects the factors that influence the growth of silicon nanowires, uniform decoration of AgNPs onto the SiNWs matrix along with detection of Rhodamine-6G (R6G) to optimize the best conditions for enhanced sensing of the spike protein. Increasing the time period of etching process resulted in enhanced SiNWs’ length from 0.55 to 7.34 µm. Furthermore, the variation of the immersion time in the decoration process of AgNPs onto SiNWs ensued the optimum time period for the enhancement in the sensitivity of detection. Tremendous increase in sensitivity of R6G detection was perceived on SiNWs etched for 2 min (length=0.90 µm), followed by 30s of immersion time for their optimal decoration by AgNPs. These SiNWs/AgNPs SERS-based sensors were able to detect the spike protein at a concentration down to 9.3 × 10 −12 M. Strong and dominant peaks at 1280, 1404, 1495, 1541 and 1609 cm −1 were spotted at a fraction of a minute. Moreover, direct, ultra-fast, facile, and affordable optoelectronic SiNWs/AgNPs sensors tuned to function as a biosensor for detecting the spike protein even at a trace level (pico molar concentration). The current findings hold great promise for the utilization of SERS as an innovative approach in the diagnosis domain of infections at very early stages.

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Section: Resultsmentioning

confidence: 99%

Ultra-sensitive and fast optical detection of the spike protein of the SARS-CoV-2 using AgNPs/SiNWs nanohybrid based sensors

Daoudi

Ramachandran

Alawadhi

et al. 2021

Surfaces and Interfaces

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“…For the mentioned process the SiNWs having higher surface to volume ratio hosts higher quanta of analyte as well the silver nanoparticles for efficient light trapping and confinement with its length and area. The denser hotspots of silver nanoparticles interact with the DNA chemical moity by tying on its surface owing to adsorption process gives rise to an effective and sensitive detection [11,6]. The interaction process and plausible mechanism is presented in Fig 3b.…”

Section: Mechanism Of Dna Sensing In Sersmentioning

confidence: 99%

“…The experimental process followed the MACE process for the fabrication of SiNWs and its functionalization is followed with PLD process (5000 NLP laser ablations) which is detailed as in our earlier reports [11]. The fabricated NA sensor morphology is depicted in Fig 1.…”

Section: Morphological Features Of Na Sensormentioning

confidence: 99%

Dual phenomenon of surface plasmon and laser optics induced EM enhancement for rapid DNA detection with semiconductor nanostructures (SiNWs/AgNPs)

Ramachandran

Dauodi²,

Columbus³

et al. 2022

J. Phys.: Conf. Ser.

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Recently exploring bioanalytical instrumentation principles emphasized with combination of optics and EM fields in surface enhanced Raman spectroscopy (SERS). The principles favour the rapid detection of DNA with proper fabrication of SERS sensor. 1D semiconductor nanostructures (SiNWs) functionalization with plasmonic silver nanoparticles are fabricated by PLD process and exploited for SERS detection of DNA. The DNA nucleotide bands are indexed with reference to their Raman shift as Adenine (A), Guanine (G), Cytosine (C), Thymine (T) at Raman spectral regions of 1352 cm-1, 676 cm-1, 1625 cm-1, 1441 cm-1 respectively. The finest conditions for sensitive detection of DNA were investigated and their interaction mechanism are presented. The point-to-point reproducibility measurements imprinted higher degree of concordancy. The designed SERS sensor will be definitely helpful almost in all application fields with portable handheld Raman spectrophotometer in near future.

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“…The significant differences in structural properties of cancerous DNA are due to the pattern of methylations, strongly affecting the DNA adsorption [ 117 ], and resulting in enhanced adenine SERS spectra. Many tunable plasmonic nanostructures sensors as nanowires, nano-stars, nano-shells, nano-spheres, nano-flowers, and three dimensional SERS hotspot matrixes were successfully used for the evaluation of DNA mutation and methylation [ 118 , 119 , 120 , 121 , 122 ]. Recently, the direct SERS detection of nucleic acids was coupled with polymerase chain reaction (PCR) to detect ct-DNA mutations by using spermine-functionalized Ag NP as a plasmonic substrate able reduce noise by minimizing the adsorption of aspecific molecules and interfering signals [ 113 ].…”

Section: Insights Into Double Helix Structure and Analysis: Spectroscopic Approachesmentioning

confidence: 99%

DNA Studies: Latest Spectroscopic and Structural Approaches

et al. 2021

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This review looks at the different approaches, techniques, and materials devoted to DNA studies. In the past few decades, DNA nanotechnology, micro-fabrication, imaging, and spectroscopies have been tailored and combined for a broad range of medical-oriented applications. The continuous advancements in miniaturization of the devices, as well as the continuous need to study biological material structures and interactions, down to single molecules, have increase the interdisciplinarity of emerging technologies. In the following paragraphs, we will focus on recent sensing approaches, with a particular effort attributed to cutting-edge techniques for structural and mechanical studies of nucleic acids.

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Fast, highly sensitive and label free detection of small genetic sequence difference of DNA using novel Surface-Enhanced Raman Spectroscopy nanostructured sensor

Cited by 12 publications

References 42 publications

Ultra-sensitive and fast optical detection of the spike protein of the SARS-CoV-2 using AgNPs/SiNWs nanohybrid based sensors

Ultra-sensitive and fast optical detection of the spike protein of the SARS-CoV-2 using AgNPs/SiNWs nanohybrid based sensors

Dual phenomenon of surface plasmon and laser optics induced EM enhancement for rapid DNA detection with semiconductor nanostructures (SiNWs/AgNPs)

DNA Studies: Latest Spectroscopic and Structural Approaches

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