Independent control of grafting density and conformation of single-stranded DNA brushes

Opdahl et al. 10.1073/pnas.0608568103.

Supporting Figures

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Supporting Figure 10
Supporting Figure 11




Fig. 10. Comparison of the surface densities of adenine nucleotides (dA) obtained from the XPS data for "urea-treated" films of d(T25-An) oligos and for (dA) homo-oligo films. Deposition conditions for the d(T25-An) films were as follows: 3 mM ssDNA, 1 M CaCl2 (pH 7), 1´ TE at 35°C for 2,400 min followed by a 30-min exposure to an 8 M urea-denaturing solution. Deposition conditions for the (dA) films were as follows: 1 mM ssDNA, 1 M NaCl (pH 7), 1´ TE at room temperature for 1,200 min; deposition of (dA) homo-oligos in 1 M CaCl2 buffers resulted in <25% changes in respective surface densities.





Fig. 11. Quantitative analysis of the d(Tm-An) grafting density using XPS. (a) XPS data in the N 1s region are decomposed into contributions from thymine (green) and adenine (red) nucleotides. (b) The N 1s fits are constrained by the known stoichiometry of the d(Tm-An) oligo (thymine contains 2 N atoms,adenine contains 5 N atoms). (c) The N 1s XPS signal is generated and attenuated throughout the total thickness t of the DNA film (green and red) with effective attenuation length (EAL) LN = 3.116 nm. The DNA film also attenuates the XPS signal from the gold substrate (yellow) with EAL LAu = 3.858 nm. EAL values are from ref. 1. (d) The intensity of the XPS signal measured from the bare gold substrate combined with the attenuated intensity from c provides the total DNA film thickness. (e) The intensities I of the dT and dA components of N 1s XPS peaks correspond to the respective nitrogen atomic densities (relative to Au) of the two DNA components NN. For simplicity, in this calculation both components are assumed to be uniformly distributed throughout the DNA film, i.e., the same (average) attenuation length LN is used for N 1s signal from both components. The experimental and material parameters in the second term have been extensively discussed in refs. 1 and 2. Note that the DNA surface densities obtained this way are consistent with those calculated using an explicit two-layer model of the DNA where tA is fixed at »1 nm. (f) Surface density (amount of substance) of nitrogen atoms qN is obtained by multiplying the nitrogen atomic density NN by the total layer thickness t (1). The corresponding surface density of nucleotides and DNA grafting density can be calculated based on the known stoichiometry of oligonucleotides.

1. Petrovykh DY, Kimura-Suda H, Tarlov MJ, Whitman LJ (2004) Langmuir 20:429-440.

2. Petrovykh DY, Kimura-Suda H, Opdahl A, Richter LJ, Tarlov MJ, Whitman LJ (2006) Langmuir 22:2578-2587.

This Article

  1. Published online before print December 26, 2006, doi: 10.1073/pnas.0608568103 PNAS January 2, 2007 vol. 104 no. 1 9-14
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