Atomic Force Microscopy and Spectroscopic Ellipsometry combined analysis of Small Ubiquitin-like Modifier adsorption on functional monolayers

Solano, Ilaria; Parisse, Pietro; Gramazio, Federico; Ianeselli, Luca; Medagli, Barbara; Cavalleri, Ornella; Casalis, Loredana; Canepa, M.

doi:10.1016/j.apsusc.2016.10.195

Cited by 8 publications

(4 citation statements)

References 49 publications

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“…Simple inspection of the SE data, applying the well-established difference spectra method, may provide some impressive snapshots of film-related processes. [38][39][40][41][42][43][44] Modeling of the optical system (substrate/film/ ambient) can be performed for a more in-depth interpretation of the data. [36,45] Much useful to feed optical modeling of ultrathin organic films, ancillary analyses such as those based on imaging methods can provide independent estimates of thickness.…”

Section: Introductionmentioning

confidence: 99%

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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Section: Introductionmentioning

confidence: 99%

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

Pinto

Dante

Rotondi

et al. 2022

Adv Materials Inter

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“…In recent years, we have developed a multi-technique analytical approach to evaluate the sensing properties of hybrid interfaces by coupling AFM, SE, EIS, and QCM [7,[25][26][27][28]. We focused on the study of self-assembled monolayers (SAMs) of thiolterminated molecules on gold, from simple alkanethiols to DNA strands and proteins.…”

Section: Introductionmentioning

confidence: 99%

DNA Sensing Platforms: Novel Insights into Molecular Grafting Using Low Perturbative AFM Imaging

Rotondi

Canepa

Angeli

et al. 2023

Sensors

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By using AFM as a nanografting tool, we grafted micrometer-sized DNA platforms into inert alkanethiol SAMs. Tuning the grafting conditions (surface density of grafting lines and scan rate) allowed us to tailor the molecular density of the DNA platforms. Following the nanografting process, AFM was operated in the low perturbative Quantitative Imaging (QI) mode. The analysis of QI AFM images showed the coexistence of molecular domains of different heights, and thus different densities, within the grafted areas, which were not previously reported using contact AFM imaging. Thinner domains corresponded to low-density DNA regions characterized by loosely packed, randomly oriented DNA strands, while thicker domains corresponded to regions with more densely grafted DNA. Grafting with densely spaced and slow scans increased the size of the high-density domains, resulting in an overall increase in patch height. The structure of the grafted DNA was compared to self-assembled DNA, which was assessed through nanoshaving experiments. Exposing the DNA patches to the target sequence produced an increase in the patch height, indicating that hybridization was accomplished. The relative height increase of the DNA patches upon hybridization was higher in the case of lower density patches due to hybridization leading to a larger molecular reorganization. Low density DNA patches were therefore the most suitable for targeting oligonucleotide sequences.

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“…Scanning probe nanolithography methods are versatile tools that allow for a precision patterning of ultrathin organic monolayers [ 31 , 32 ]. Since the first reports by Liu and coworkers [ 33 , 34 ], scanning probe nanolithography has been successfully employed to produce patterned organic/inorganic interfaces for the precise immobilization of nano-objects (from nanoparticles to biomolecules) [ 35 ] as well as to develop sensing platforms that are able to detect molecular recognition events [ 36 , 37 , 38 ].…”

Section: Introductionmentioning

confidence: 99%

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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Atomic Force Microscopy and Spectroscopic Ellipsometry combined analysis of Small Ubiquitin-like Modifier adsorption on functional monolayers

Cited by 8 publications

References 49 publications

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

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

DNA Sensing Platforms: Novel Insights into Molecular Grafting Using Low Perturbative AFM Imaging

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

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