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DNA adsorption at functionalized Si/buffer interfaces studied by x-ray reflectivity
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Image of FIG. 1.
FIG. 1.

Si(111). A miscut of angle in the direction between the macroscopic surface-normal unit-vector and the [111] direction yields a surface of dense atomic planes with regular steps of height and width . Top: Schema and bottom: Hydrogen-terminated, atomic-scale model.

Image of FIG. 2.
FIG. 2.

Multistep protocol for the covalent anchoring of an amine-functionalized molecular monolayer on a surface. (a) Grafting of ester-functionalized alkyl chains, (b) hydrolysis of ester groups, and [(c) and (d)] activation of acid groups and coupling of ethyldiamine.

Image of FIG. 3.
FIG. 3.

Molecular models of (a) dodecanoic acid and (b) dodecanamide, -(2-aminoethyl) (with a surface silicon atom of the crystalline lattice replacing the terminal methyl groups). Fully extended (top) and disordered (bottom) conformations. Red. oxygen, blue: Nitrogen, black: Carbon and white: Hydrogen. The cylinders represent volumes of and , respectively, occupied on average by each molecule, as determined by the x-ray reflectivity measurements (Sec. III B).

Image of FIG. 4.
FIG. 4.

Molecular-scale model representation of the functionalized silicon surface. Red: Oxygen, blue: Nitrogen, black: Carbon, and white: Hydrogen. The model is drawn with a random surface coverage of 44% of the available bonding sites [and an arbitrarily chosen in-plane nematic order parameter for the azimuthal carbon-chain tilt direction of ].

Image of FIG. 5.
FIG. 5.

AFM images of (a) a bare and (b) an amine-terminated Si(111) functionalized surfaces measured in air (Ref. 33). The step width of corresponds to a miscut of 0.2°.

Image of FIG. 6.
FIG. 6.

A composite energy-dispersive reflectivity spectra of an amine-functionalized sample, as shown in Fig. 5, measured in air (black) and under buffer (red). The solid line shows the expected reflectivity according to the structural model fit to the data obtained at the ESRF, as will be presented below (see Fig. 9). The insert shows the data measured in air by fixed incidence angle: Black: 0.0405°, blue: 0.063°, red: 0.097°, green: 0.18°, yellow: 0.26°, cyan: 0.36°, magenta: 0.49°, and brown: 0.63°.

Image of FIG. 7.
FIG. 7.

PTFE sample cell. The horizontal silicon wafer is covered by the buffer solution whose meniscus against the thin copolymer windows can be seen in the photograph.

Image of FIG. 8.
FIG. 8.

Acid-terminated functionalized silicon sample. Top: Reflectivity and bottom: Normalized to the Fresnel step reflectivity (Black: In air and red: Under buffer solution). The insert shows the real-space density profiles as continuous lines that describe the data shown in reciprocal space. The molecular model in real space (see Fig. 3) is drawn schematically for illustration. The series of continual (green) traces present a succession of fairly rapid (about ), reflectivity curves measured under buffer solution and showing sample degradation under irradiation.

Image of FIG. 9.
FIG. 9.

Amine-terminated functionalized silicon sample. Top: Reflectivity and bottom: Normalized to the Fresnel step reflectivity (Black: In air, red: Under buffer solution, and blue: Under buffer after DNA adsorption). The (red- and black-)filled symbols are the results of rocking curves recorded for each angle of incidence and the open symbols are direct reflectivity scans (a few black-filled symbols can be seen to overlie the black open symbols). The insert shows the real-space density profiles as continuous lines that describe the data shown in reciprocal space. The molecular model in real space (see Fig. 3) is drawn schematically for illustration. The continual (green, olive, and orange) traces are an intermediate state following the addition of increasing concentrations of DNA to the buffer solution: , , and , respectively. The (blue) data (lowest lying curves) were recorded at this last concentration after the first introduction of DNA to the cell. The (blue) solid lines show a model density profile (insert) describing this data. The (cyan) traces show the reproducibility of this profile following the addition of a much greater quantity of DNA .

Image of FIG. 10.
FIG. 10.

Molecular model of 294 bp double-stranded DNA fragments adsorbed on a solid surface.

Image of FIG. 11.
FIG. 11.

Embedding of the adsorbed DNA molecules. Black circles: DNA, light gray: Surface monomolecular layer, and dark gray: Silicon monocrystalline substrate. (a) 100% coverage , (b) 50% coverage , and (c) 31% coverage .

Image of FIG. 12.
FIG. 12.

Molecular model of an isolated double-stranded DNA molecule adsorbed on the positively charged, amine-functionalized surface.

Image of FIG. 13.
FIG. 13.

Single-stranded DNA on an amine-terminated functionalized silicon surface. Top: Reflectivity and bottom: Normalized to the Fresnel step reflectivity. The open symbols are direct reflectivity scans. The insert shows the real-space density profiles used to model the data. The solid lines are the result of a fit to the data and the dashed lines are the profiles and corresponding reflectivities from Fig. 9. (Black: In air and red: Under buffer solution). The lighter symbols (green, orange, cyan, and blue) parallel those of Fig. 9.

Image of FIG. 14.
FIG. 14.

Schematic construction of the wavevector transfer of specular reflectivity [, , ]. (a) Fixed wavelength, variable angle of incidence and (b) fixed angle of incidence, variable wavelength. (c) The (blue/green) shaded regions schematize the incident/detector divergences and , (d) Resolution volume around the scattering vector. The (red) region around shows a section of the convoluted resolution volume. , the intersection of this volume with the axis, is the instrumental resolution for pure specular reflectivity and is independent of the angular resolution of the detector; is the projection of the extended volume with this axis and corresponds to the full width at half maximum of the resolution for the diffuse scattering around the specular axis; is the corresponding projection perpendicular to this axis in the scattering plane yielding the in-plane resolution. The divergences in the third dimension, out of the incidence plane, are not shown for clarity.

Image of FIG. 15.
FIG. 15.

Schema of the measurement of the direct-beam (with the sample lowered out of the figure) and rocking-curve profiles.

Image of FIG. 16.
FIG. 16.

Resolution function. Dashed line: Gaussian, solid lines: Eq. (A5)-(“softest” to sharpest), black: (Lorentzian), blue: , red: , green: , and gray: Ideal trapezoidal slit function with .

Image of FIG. 17.
FIG. 17.

Kinematics of a (a) “rocking curve” and (b) “detector scan” . .

Image of FIG. 18.
FIG. 18.

Measured rocking curves for the acid-terminated sample in air (black) and under buffer solution (red). The background scattering (as seen in the lower envelope of the scans), modulated as for the specular reflectivity, arises from the surface roughness. Under buffer, this background is constant except for very grazing angles of incidence and is due to diffuse scattering from density fluctuations in the aqueous solution. Notice the anomalous surface reflections or Yoneda (Ref. 66) peaks (arrow) around (and by reciprocity).

Image of FIG. 19.
FIG. 19.

Schema of the spreading upon reflection by a curved surface. The beam footprint is , where is the beam height. The spreading angle, , where is the radius of curvature, is a function of this footprint and, thus, would decrease with increasing incidence angle.


Generic image for table
Table I.

Parameters of the models used to describe the data. IR indicates the results of surface infrared spectroscopy quantification (see, for example, Ref. 40). The numerical surface densities are found to be less than half that of binding sites on the Si(111) surface . The area/molecule for the grafted monomolecular layer is the inverse of the numeric surface density and is to be compared to that of a dense alkyl chain: for liquid paraffins (Ref. 69), for monolayers of fatty acids (Ref. 70) and for crystalline -hydrocarbons (Ref. 71).

Generic image for table
Table II.

294 bp double-stranded DNA.

Generic image for table
Table III.

146 base single-stranded DNA.


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: DNA adsorption at functionalized Si/buffer interfaces studied by x-ray reflectivity