Single-stranded DNA oligomer brush structure is dominated by intramolecular interactions mediated by the ion environment

Gil, Phwey S.; Lacks, Daniel J.; Parisse, Pietro; Casalis, Loredana; Ngavouka, Maryse D. Nkoua

doi:10.1039/c8sm01743c

Cited by 8 publications

(9 citation statements)

References 25 publications

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“…A thicker, higher coverage SAM formed by almost upright molecules is obtained in these conditions. This picture ( Figure 3 ) is in agreement with the observation, for a set SAM molecular density, of elongated DNA strands at low ionic strength and mushroom-like strands at high ionic strength [ 50 , 51 ].…”

Section: Resultssupporting

confidence: 90%

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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Section: Resultssupporting

confidence: 90%

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

et al. 2020

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“…Response of the ssDNA Brush to Ion Environments. Recent studies have shown that the DNA structure is highly dependent on its surrounding aqueous environment, 50 which is of high importance in sensor applications of surface-attached ssDNA brushes. 51 Especially, the presence of specific cation species causes changes in inter-nucleotide distances 52 and can strongly affect the grafting density 53,54 and hybridization regimes of DNA on solid supports.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…Recent studies have shown that the DNA structure is highly dependent on its surrounding aqueous environment, which is of high importance in sensor applications of surface-attached ssDNA brushes . Especially, the presence of specific cation species causes changes in inter-nucleotide distances and can strongly affect the grafting density , and hybridization regimes of DNA on solid supports. , Figure a shows a schematic of the effect of increasing ionic strength on the DNA brush, which leads to its compression or expansion.…”

Section: Resultsmentioning

confidence: 99%

In Situ Monitoring of Rolling Circle Amplification on a Solid Support by Surface Plasmon Resonance and Optical Waveguide Spectroscopy

Lechner

Hageneder

Schmidt

et al. 2021

ACS Appl. Mater. Interfaces

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The growth of surface-attached single-stranded deoxyribonucleic acid (ssDNA) chains is monitored in situ using an evanescent wave optical biosensor that combines surface plasmon resonance (SPR) and optical waveguide spectroscopy (OWS). The "grafting-from" growth of ssDNA chains is facilitated by rolling circle amplification (RCA), and the gradual prolongation of ssDNA chains anchored to a gold sensor surface is optically tracked in time. At a sufficient density of the polymer chains, the ssDNA takes on a brush architecture with a thickness exceeding 10 μm, supporting a spectrum of guided optical waves traveling along the metallic sensor surface. The simultaneous probing of this interface with the confined optical field of surface plasmons and additional more delocalized dielectric optical waveguide modes enables accurate in situ measurement of the ssDNA brush thickness, polymer volume content, and density gradients. We report for the first time on the utilization of the SPR/OWS technique for the measurement of the RCA speed on a solid surface that can be compared to that in bulk solutions. In addition, the control of ssDNA brush properties by changing the grafting density and ionic strength and post-modification via affinity reaction with complementary short ssDNA staples is discussed. These observations may provide important leads for tailoring RCA toward sensitive and rapid assays in affinity-based biosensors.

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“…In queste condizioni si ottiene un SAM più spesso e con una copertura maggiore formata da molecole quasi "in piedi". Questa interpretazione è in accordo con l'osservazione, su SAM di densità molecolare fissata, di filamenti allungati a bassa forza ionica e filamenti ripiegati ad alta forza ionica [39]. [38].…”

Section: Fig 3 Esperimenti DI Shaving Su Sam Di Dna Preparati a Bassa Forza Ionica (A-c) E Ad Alta Forza Ionica (D-f) Immagini Afm Acquisunclassified

<em>SELF-ASSEMBLY</em> DI DNA SU SUPERFICIE: UNO STUDIO COMBINATO NANOLITOGRAFIA/SPETTROSCOPIA OTTICA

Cavalleri¹

2020

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The self-assembly of organic molecules and biomolecules on inorganic surfaces is a complex process which results from the interplay between different interactions: molecule/molecule, molecule/surface, and molecule/solvent interactions. The interest in the study of molecular self-assembly derives from the possibility to obtain functionalized surfaces that exhibit the functional properties of the deposited (bio) molecules. Self-Assembled Monolayers (SAMs) are indeed widely used in biosensing. SAMs of organosulphur compounds on gold are among the most widely studied SAMs. In the following, a combined approach that couples scanning probe microscopy and spectroellipsometry is discussed and applied to the study of the morphological, mechanical and optical properties of SAMs of DNA single strands. DNA SAMs are a widely investigated system since they can be exploited for the design of DNA microarrays based on the hybridization between complementary DNA strands.

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Single-stranded DNA oligomer brush structure is dominated by intramolecular interactions mediated by the ion environment

Abstract: Single-stranded DNA (ssDNA) brushes, in which ssDNA oligomers are tethered to surfaces in dense monolayers, are being investigated for potential biosensing applications.

Cited by 8 publications

References 25 publications

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

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

In Situ Monitoring of Rolling Circle Amplification on a Solid Support by Surface Plasmon Resonance and Optical Waveguide Spectroscopy

<em>SELF-ASSEMBLY</em> DI DNA SU SUPERFICIE: UNO STUDIO COMBINATO NANOLITOGRAFIA/SPETTROSCOPIA OTTICA

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