Functionalizing gold with single strand DNA: novel insight into optical properties <i>via</i> combined spectroscopic ellipsometry and nanolithography measurements

Pinto, Giulia; Parisse, Pietro; Solano, Ilaria; Canepa, Paolo; Canepa, M.; Casalis, Loredana; Cavalleri, Ornella

doi:10.1039/c8sm02589d

Cited by 14 publications

(15 citation statements)

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“…A 100% MCH SAM was then deposited on that same substrate and fit to a Cauchy layer, using the weak Lorentz peaks around 368 nm and 508 nm. This experimental data was normalized to the literature thickness of 1 nm, similar to what has been demonstrated previously [35]. Fresh gold substrates exposed to 1 µM aptamer and varying concentrations of MCH were then measured and fit to a Cauchy layer for a total thickness.…”

Section: Ellipsometry Measurementsmentioning

confidence: 99%

Impact of Self-Assembled Monolayer Design and Electrochemical Factors on Impedance-Based Biosensing

Brothers

Moore

Lawrence

et al. 2020

Sensors

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Real-time sensing of proteins, especially in wearable devices, remains a substantial challenge due to the need to convert a binding event into a measurable signal that is compatible with the chosen analytical instrumentation. Impedance spectroscopy enables real-time detection via either measuring electrostatic interactions or electron transfer reactions while simultaneously being amenable to miniaturization for integration into wearable form-factors. To create a more robust methodology for optimizing impedance-based sensors, additional fundamental studies exploring components influencing the design and implementation of these sensors are needed. This investigation addresses a sub-set of these issues by combining optical and electrochemical characterization to validate impedance-based sensor performance as a function of (1) biorecognition element density, (2) self-assembled monolayer chain length, (3) self-assembled monolayer charge density, (4) the electrochemical sensing mechanism and (5) the redox reporter selection. Using a pre-existing lysozyme aptamer and lysozyme analyte combination, we demonstrate a number of design criteria to advance the state-of-the-art in protein sensing. For this model system we demonstrated the following: First, denser self-assembled monolayers yielded substantially improved sensing results. Second, self-assembled monolayer composition, including both thickness and charge density, changed the observed peak position and peak current. Third, single frequency measurements, while less informative, can be optimized to replace multi-frequency measurements and in some cases (such as that with zwitterionic self-assembled monolayers) are preferred. Finally, various redox reporters traditionally not used in impedance sensing should be further explored. Collectively, these results can help limit bottlenecks associated with device development, enabling realization of next-generation impedance-based biosensing with customize sensor design for the specific application.

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Section: Ellipsometry Measurementsmentioning

confidence: 99%

Impact of Self-Assembled Monolayer Design and Electrochemical Factors on Impedance-Based Biosensing

Brothers

Moore

Lawrence

et al. 2020

Sensors

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“…As can be observed in Figure 4 ,

values in the NIR (far from molecular resonances) and

values in the near UV are definitely larger for C 6 -ssDNA SAMs deposited in 1 M NaCl buffer with respect to SAMs deposited in 1 mM NaCl buffer. According to previous reports [ 45 , 58 ], these features are associated to the film optical thickness, a quantity depending on refractive index and thickness, that is higher for 1 M NaCl C 6 -ssDNA samples.…”

Section: Resultsmentioning

confidence: 84%

“…We note that in Pinto et al [ 45 ], SE spectra, accidentally referred to as 1 M NaCl data, were actually 1 mM NaCl data. Therefore, those spectra must not be directly compared with the ones presented in this paper.…”

Section: Resultsmentioning

confidence: 90%

“…To this end, we previously coupled SE analysis with Electrochemical Impedance Spectroscopy to investigate alkanethiol and protein monolayers [ 61 ]. In the present study, nanoshaving experiments have been advantageously exploited to disentangle this correlation: assuming the SAM thickness values obtained from AFM, it is possible to obtain an estimation of the refractive index through a comparison between ellipsometric data and simulated curves, following the approach described in Pinto et al [ 45 ].…”

Section: Resultsmentioning

confidence: 99%

“…For ultrathin films, the thickness and refractive index are correlated parameters. We exploit the thickness data obtained from AFM nanolithography measurements to disentangle this correlation [ 40 , 45 ]. Indeed, the cross-fertilization between the two methods (scanning probe microscopy and Spectroscopic Ellipsometry) can be advantageously employed to obtain quantitative and consistent data on thickness and refractive index of monomolecular films, once a proper optical model of the system is provided.…”

Section: Introductionmentioning

confidence: 99%

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Morphological and Mechanical Characterization of DNA SAMs Combining Nanolithography with AFM and Optical Methods

et al. 2020

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The morphological and mechanical properties of thiolated ssDNA films self-assembled at different ionic strength on flat gold surfaces have been investigated using Atomic Force Microscopy (AFM). AFM nanoshaving experiments, performed in hard tapping mode, allowed selectively removing molecules from micro-sized regions. To image the shaved areas, in addition to the soft contact mode, we explored the use of the Quantitative Imaging (QI) mode. QI is a less perturbative imaging mode that allows obtaining quantitative information on both sample topography and mechanical properties. AFM analysis showed that DNA SAMs assembled at high ionic strength are thicker and less deformable than films prepared at low ionic strength. In the case of thicker films, the difference between film and substrate Young’s moduli could be assessed from the analysis of QI data. The AFM finding of thicker and denser films was confirmed by X-Ray Photoelectron Spectroscopy (XPS) and Spectroscopic Ellipsometry (SE) analysis. SE data allowed detecting the DNA UV absorption on dense monomolecular films. Moreover, feeding the SE analysis with the thickness data obtained by AFM, we could estimate the refractive index of dense DNA films.

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Spectroscopic Ellipsometry Investigation of a Sensing Functional Interface: DNA SAMs Hybridization

Pinto

Dante

Rotondi

et al. 2022

Adv Materials Inter

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monitoring of therapeutic treatments. Many sensing concepts have been proposed and tested in recent years to achieve this challenging mix. For these purposes, hybrid interfaces, where a self-assembled monolayer (SAM) with the desired biofunctionality is immobilized on an inorganic substrate, represent a versatile, popular platform for effective biosensors.The impressive development regarding the fabrication of functionalized DNA strands have promoted these kinds of molecules as building blocks for the development of sensing platforms. [1][2][3] Selective and reversible hybridization between complementary strands can be exploited to detect specific biomarkers, from nucleic acid target sequences (such as miRNA, [4] ctDNA [5] or viral sequences [6] ) to proteins, by employing protein-DNA conjugates. [7][8][9][10] Clearly, the outbreak of the COVID-19 pandemic has boosted the urgent need for highly sensitive, inexpensive and rapid selective recognition of SARS-CoV-2 sequences and spurred research on DNA-based detection of viral sequences. [11,12] In this work, we analyze a DNA sensing concept that is implemented through a 3-step process (Figure 1). The process is initiated with the self-assembly of single-strand DNA (HS-pDNA, 22 bases) that binds to gold through a linker (hexanethiol, C6). According to well-defined protocols, [13] this SAM is exposed to mercaptohexanol (MCH), a thiol with the same alkyl chain length of the hexanethiol linker. It has been reported that MCH co-adsorption improves DNA film organization [14][15][16][17] and increases the efficiency of the final, hybridization step [18,19] that implements the recognition of the target sequence.Literature presents varieties of methods for the recognition of target sequences through the formation of double-strand DNA (dsDNA). Some approaches involve mass sensitive methods like Quartz Crystal Microbalance (QCM) [20][21][22][23][24] or electrochemical methods. [25][26][27][28] Optical methods have been proposed that exploit, among others, colorimetric detection, [29] Surface Plasmon Resonance phenomena (SPR) [22,23,30] or combined plasmonic photothermal effects and localized SPR. [31] SPR, in particular, has been valuably employed to study surface confined DNA hybridization on a system closely related to the one under investigation here. [32] Among optical methods, Spectroscopic Ellipsometry (SE) can be advantageously employed to track changes in film Here, a comprehensive study of a label-free detection platform for the recognition of oligonucleotide sequences based on hybridization of thioltethered DNA strands self-assembled on flat gold films is presented. The study exploits in-buffer spectroscopic ellipsometry (SE) measurements, a noninvasive method sensitive to monolayer films, supported by surface mass density change measurements (Quartz Crystal Microbalance with Dissipation, QCM-D) obtained under comparable experimental conditions. SE and QCM-D allow monitoring deposition of molecular precursors and DNA chain hybridization. Combining SE measurements wi...

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Functionalizing gold with single strand DNA: novel insight into optical properties via combined spectroscopic ellipsometry and nanolithography measurements

Abstract: We have studied the self-assembly of 22-base oligonucleotides bound by a short alkyl thiol linker (C6-ssDNA) on flat Au films.

Cited by 14 publications

References 37 publications

Impact of Self-Assembled Monolayer Design and Electrochemical Factors on Impedance-Based Biosensing

Impact of Self-Assembled Monolayer Design and Electrochemical Factors on Impedance-Based Biosensing

Morphological and Mechanical Characterization of DNA SAMs Combining Nanolithography with AFM and Optical Methods

Spectroscopic Ellipsometry Investigation of a Sensing Functional Interface: DNA SAMs Hybridization

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