Thymine/adenine diblock-oligonucleotide monolayers and hybrid brushes on gold: a spectroscopic study

Howell, Caitlin; Hamoudi, Hicham; Zharnikov, Michael

doi:10.1186/1559-4106-8-6

Cited by 11 publications

(6 citation statements)

References 44 publications

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“…[78] Copyright 2012, American Chemical Society. not affected by the procedure and the EG3/A25SH templates exhibited a proper hybridization ability with respect to the complementary ssDNA strand, with the extent of hybridization increasing, as expected, [88][89][90] with the decreasing A25SH density. [87] Combination of the IPER approach with EBL allows the fabrication of complex EG3/ssDNA patterns, with a representative example shown in Figure 13c.…”

Section: Lithography With Single-stranded Dnasupporting

confidence: 69%

“…[ 87 ] By application of IPER, with the dose varying from 0 to 1 mC cm −2 , the content of ssDNA in the binary EG3/A25SH SAMs, normalized to the density of the single‐component A25SH monolayer, could be gradually tuned from 0% to ≈70% (Figure 13b). As shown by the dedicated spectroscopic experiments, the electronic structure of both EG3 and A25SH molecules was not affected by the procedure and the EG3/A25SH templates exhibited a proper hybridization ability with respect to the complementary ssDNA strand, with the extent of hybridization increasing, as expected, [ 88–90 ] with the decreasing A25SH density. [ 87 ]…”

Section: Lithography With Single‐stranded Dnamentioning

confidence: 54%

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Electron‐Irradiation Promoted Exchange Reaction as a Tool for Surface Engineering and Chemical Lithography

Terfort

Zharnikov

2021

Adv Materials Inter

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tacting solutions, what, for example, is of relevance for the protection of materials from oxidation and degradation. Even more important, this assembly can modify or even redefine completely the chemical, physical, and biological properties of the substrate surface, adapting it to a specific task or an application. Finally, such a supported assembly can be functional on its own, for example, as an element of molecular or organic electronics [4][5][6][7] or a molecular sensor array. [8] A particular advantage of SAMs is the flexibility of their design. The SAMforming molecules consist generally of three major building blocks, videlicet the docking group mentioned above, the terminal tail group building the SAM-ambient interface, and the molecular backbone connecting the docking and tail groups and mediating the self-assembly. [1][2][3] Depending on a particular goal or a specific application, these buildings blocks can be flexibly selected and combined together as well as individually designed, for example, by the introduction of functional groups into the molecular backbone. [9,10] The resulting SAMs can be further modified by physical tools, such as ultra-violet light, electron irradiation, X-rays, and ions. Among these tools, electron irradiation is probably the most versatile one, as it gives the largest flexibility and provides the highest possible lateral resolution. It serves in particular well for tuning SAM properties, [11] fixation of metal films at the SAMambient interface, [12,13] SAM-based lithography and related nanofabrication, [14][15][16][17][18][19][20][21][22][23] as well as preparation of SAM-based carbon nanomembranes (CNMs). [24][25][26][27][28] All these applications rely on the specific effects of electron irradiation on the SAM-forming molecules and the SAMs as a whole. The major irradiationinduced processes include cleavage of individual chemical bonds within the SAM-forming molecules or between the docking groups and the substrate, desorption of the released molecules and their fragments, formation of new chemical groups as a result of reactions between electron-activated moieties, and cross-linking of the molecular fragments. [29][30][31] The occurrence, extent, and rates of the above processes as well as the balance between them depend on the electron energy, identity of the substrate, length of the molecular backbone, and packing density of a SAM but, above all, on the character of the molecular backbone. [31][32][33][34][35] Whereas the scission of nearly all bonds (CH, CC, Self-assembled monolayers (SAMs) can serve as versatile resist/template materials for surface engineering and electron beam lithography (EBL), making possible a new type of lateral patterning: chemical lithography (CL). Whereas CL has been well established for aromatic SAMs, it is hardly possible for aliphatic monolayers, because of extensive irradiation-induced damage excluding selective modification of specific chemical groups. Turning this drawback into an advantage, the irradiation-promoted exchange reactio...

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Section: Lithography With Single-stranded Dnasupporting

confidence: 69%

Section: Lithography With Single‐stranded Dnamentioning

confidence: 54%

Electron‐Irradiation Promoted Exchange Reaction as a Tool for Surface Engineering and Chemical Lithography

Terfort

Zharnikov

2021

Adv Materials Inter

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“…NEXAFS spectroscopy in the condensed phase has been used to investigate the electronic and spatial structure of amino acids, peptides, and proteins − as well as nucleobases, nucleotides, and strands of deoxyribonucleic acid (DNA). − NEXAFS spectra for thin films of all standard amino acids are available for the carbon, nitrogen and oxygen K-edges. , The spectral changes caused by the formation of a peptide bond have been identified and characterized. , It has been proposed that, in a building block approach, NEXAFS spectra of polypeptides can be approximated from the spectra of their constituents. ,, Furthermore, calculations for neutral diglycine suggest that NEXAFS is sensitive toward the conformation of the peptide bond …”

Section: Introductionmentioning

confidence: 99%

Probing Structural Information of Gas-Phase Peptides by Near-Edge X-ray Absorption Mass Spectrometry

Dörner

Schwob

Atak

et al. 2021

J. Am. Soc. Mass Spectrom.

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Near-edge X-ray absorption mass spectrometry (NEXAMS) is an action-spectroscopy technique of growing interest for investigations into the spatial and electronic structure of biomolecules. It has been used successfully to give insights into different aspects of the photodissociation of peptides and to probe the conformation of proteins. It is a current question whether the fragmentation pathways are sensitive toward effects of conformational isomerism, tautomerism, and intramolecular interactions in gas-phase peptides. To address this issue, we studied the cationic fragments of cryogenically cooled gas-phase leucine enkephalin ([LeuEnk+H] + ) and methionine enkephalin ([MetEnk+H] + ) produced upon soft X-ray photon absorption at the carbon, nitrogen, and oxygen K-edges. The interpretation of the experimental ion yield spectra was supported by density-functional theory and restricted-open-shell configuration interaction with singles (DFT/ROCIS) calculations. The analysis revealed several effects that could not be rationalized based on the peptide's amino acid sequences alone. Clear differences between the partial ion yields measured for both peptides upon C 1s → π*(CC) excitations in the aromatic amino acid side chains give evidence for a sulfur−aromatic interaction between the methionine and phenylalanine side chain of [MetEnk+H] + . Furthermore, a peak associated with N 1s → π*(CN) transitions, linked to a tautomeric keto-to-enol conversion of peptide bonds, was only present in the photon energy resolved ion yield spectra of [MetEnk+H] + .

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“…This explains the role of the ionic strength in DNA conformation [ 15 , 16 ] and self-assembly [ 17 , 18 , 19 , 20 ], and motivates, for instance, the use of spacer molecules to promote the molecular organization of the DNA strands [ 17 , 21 , 22 ]. Different experimental approaches have been employed to investigate DNA self-assembly on gold, from electrochemical methods [ 18 , 22 , 23 , 24 ], to optical [ 20 , 25 , 26 ], infrared [ 22 , 27 , 28 ], and X-ray [ 17 , 28 , 29 ] spectroscopy. An aspect that has not been addressed so far is related to the mechanical properties of DNA Self-Assembled Monolayers (SAMs).…”

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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Thymine/adenine diblock-oligonucleotide monolayers and hybrid brushes on gold: a spectroscopic study

Cited by 11 publications

References 44 publications

Electron‐Irradiation Promoted Exchange Reaction as a Tool for Surface Engineering and Chemical Lithography

Electron‐Irradiation Promoted Exchange Reaction as a Tool for Surface Engineering and Chemical Lithography

Probing Structural Information of Gas-Phase Peptides by Near-Edge X-ray Absorption Mass Spectrometry

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

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