Functionalization of silicon step arrays II: Molecular orientation of alkanes and DNA

Crain, Jason; Kirakosian, A.; Lin, Ja‐Chen; Gu, Yuedong; Shah, Rahul R.; Abbott, Nicholas L.; Himpsel, F. J.

doi:10.1063/1.1397297

Cited by 35 publications

(51 citation statements)

References 31 publications

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“…The spectra can be decomposed in two sharp and a broad peak transitions. The energy shift between and features is in agreement with previously published XANES spectra of DNA on gold surfaces [18]. The polarization of the synchrotron radiation with respect to the molecular orbital contributing to the signal could mask or enhance a particular transition.…”

supporting

confidence: 87%

Ordered Self-Assembled Monolayers of Peptide Nucleic Acids with DNA Recognition Capability

et al. 2004

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We report on the formation of ordered self-assembled monolayers (SAMs) of single-stranded peptide nucleic acids (ssPNA). In spite of their remarkable length (7 nm) thiolated PNAs assemble standing up on gold surfaces similarly to the SAMs of short alkanethiols. SAMs of ssPNA recognize complementary nucleic acids, acting as specific biosensors that discriminate even a point mutation in target ssDNA. These results are obtained by surface characterization techniques that avoid labeling of the target molecule: x-ray photoemission, x-ray absorption and atomic force microscopy.

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supporting

confidence: 87%

Ordered Self-Assembled Monolayers of Peptide Nucleic Acids with DNA Recognition Capability

et al. 2004

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“…Copyright © 2006 American Chemical Society) X-ray source with the aromatic nitrogen bonds that cause the 1s → π* transition at glancing incidence indicates that the DNA bases in a pure DNA fi lm were, on average, oriented more parallel to the surface. Similar trends have previously been observed with surface-bound double-stranded DNA oligomers on gold [ 39 ]. This indicates that on average the ssDNA chains had a slightly perpendicular orientation to the substrate.…”

Section: Assessing the Structure And Hybridization Properties Of Mixesupporting

confidence: 86%

Multi-technique Characterization of DNA-Modified Surfaces for Biosensing and Diagnostic Applications

Lee

Gamble

Harbers

et al. 2014

Surface Analysis and Techniques in Biology

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Complementary surface analysis techniques-X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fi ne structure (NEXAFS), time-offl ight secondary ion mass spectrometry (ToF-SIMS), and surface plasmon resonance (SPR)-were combined to characterize the structure and composition of DNAmodifi ed surfaces. Both model systems [thiolated single-stranded DNA (ssDNA) on gold surfaces] and commercial systems (ssDNA spotted onto microarray slides) were investigated. Pure thiolated 20-mer ssDNA assembles onto gold, with the ssDNA binding spontaneously to the surface via the thiol groups and nitrogen atoms

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“…27,29 The broader peak above 405 eV is attributed to the N 1s → σ* transition. 21,26 For the pure HS-ssDNA monolayer (Figure 2a, t = 0), the intensity of the π* peaks was slightly higher when the X-ray beam was at a glancing angle of incidence compared to that at normal incidence. At glancing incidence, the E vector of the polarized X-ray source is nearly perpendicular to the surface; therefore, the overlap of this E vector with the aromatic nitrogen bonds that cause the 1s → π* transition indicates that the DNA bases in a pure DNA film were, on average, oriented nominally parallel to the surface.…”

Section: Nexafs Orientation Studies Of Pure Dna and Mixed Dna/mcu Monmentioning

confidence: 95%

Surface Coverage and Structure of Mixed DNA/Alkylthiol Monolayers on Gold: Characterization by XPS, NEXAFS, and Fluorescence Intensity Measurements

et al. 2006

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Self-assembly of thiol-terminated single-stranded DNA (HS-ssDNA) on gold has served as an important model system for DNA immobilization at surfaces. Here, we report a detailed study of the surface composition and structure of mixed self-assembled DNA monolayers containing a short alkylthiol surface diluent [11-mercapto-1-undecanol (MCU)] on gold supports. These mixed DNA monolayers were studied with X-ray photoelectron spectroscopy (XPS), near-edge X-ray absorption fine structure spectroscopy (NEXAFS), and fluorescence intensity measurements. XPS results on sequentially adsorbed DNA/MCU monolayers on gold indicated that adsorbed MCU molecules first incorporate into the HS-ssDNA monolayer and, upon longer MCU exposures, displace adsorbed HSssDNA molecules from the surface. Thus, HS-ssDNA surface coverage steadily decreased with MCU exposure time. Polarization-dependent NEXAFS and fluorescence results both show changes in signals consistent with changes in DNA orientation after only 30 min of MCU exposure. NEXAFS polarization dependence (followed by monitoring the N 1s → π* transition) of the mixed DNA monolayers indicated that the DNA nucleotide base ring structures are oriented more parallel to the gold surface compared to DNA bases in pure HS-ssDNA monolayers. This indicates that HS-ssDNA oligomers reorient toward a more-upright position upon MCU incorporation. Fluorescence intensity results using end-labeled DNA probes on gold show little observable fluorescence on pure HSssDNA monolayers, likely due to substrate quenching effects between the fluorophore and the gold. MCU diluent incorporation into HS-ssDNA monolayers initially increases DNA fluorescence signal by densifying the chemisorbed monolayer, prompting an upright orientation of the DNA, and moving the terminal fluorophore away from the substrate. Immobilized DNA probe density and DNA target hybridization in these mixed DNA monolayers, as well as effects of MCU diluent on DNA hybridization in complex milieu (i.e., serum) were characterized by surface plasmon resonance (SPR) and 32 P-radiometric assays and reported in a related study Methods for surface-immobilizing single-strand nucleic acids that preserve their original hybridization specificity with minimized nonspecific interactions remain an important goal for improving the performance of DNA microarray and biosensor applications. As summarized in a recent review, 1 nucleic acid hybridization behavior observed between complementary probe and target DNA molecules in bulk solution differ from identical hybridization at a solid-liquid * Corresponding author. interface. In surface hybridization, nonspecific probe-surface interactions, electrostatic forces, and steric issues between adjacent DNA probes influence DNA target hybridization efficiency and capacity. For example, nucleotide primary amines on nonhybridized DNA segments can interact (e.g., covalently 2 or by acid-base adsorption) with the surface, becoming unavailable to hybridize with target DNA molecules. Effects of immobilized DNA p...

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Functionalization of silicon step arrays II: Molecular orientation of alkanes and DNA

Cited by 35 publications

References 31 publications

Ordered Self-Assembled Monolayers of Peptide Nucleic Acids with DNA Recognition Capability

Ordered Self-Assembled Monolayers of Peptide Nucleic Acids with DNA Recognition Capability

Multi-technique Characterization of DNA-Modified Surfaces for Biosensing and Diagnostic Applications

Surface Coverage and Structure of Mixed DNA/Alkylthiol Monolayers on Gold: Characterization by XPS, NEXAFS, and Fluorescence Intensity Measurements

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