PubMed · 13249358
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D M BROWN, A R TODD. 1955. Nucleic acids.. https://doi.org/10.1146/annurev.bi.24.070155.001523
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We report a new theoretical approach to optimize the performance and quantify the results of gene expression oligonucleotide microarrays which are widely used in biomedical research. An on-array hybridization isotherm that takes into account the screened Coulomb repulsion between the assayed nucleic acid target and the layer of surface tethered oligonucleotide probes is presented. The hybridization efficiency is found as a function of the genomic target (sequence, length, and concentration), array parameters (probe sequence and length, surface probe density), and hybridization conditions (temperature and buffer ionic strength). We present simple relations for the hybridization signal maximum and the linear dynamic detection range and show explicit criteria for optimization. The approach is based on an extension of our recently published theory (Vainrub, A.; Pettitt, B. M. Phys. Rev. E 2002, 66, art. no.-041905) which we generalize here for the cases of target depletion effects and arbitrary target length.
The IR absorption spectra of protein, DNA, RNA, and phospholipid films as a function of the water content are reported. We find that the hydration of protein films affects the peak intensity of amide I and amide II bands and the shape of the amide III band. For nucleic acids, the symmetric (nu(S) PO(2) (-)) and antisymmetric (nu(AS) PO(2) (-)) stretching vibrations of the phosphate linkage are the most affected by hydration, because both intensity changes and frequency shifts are observed. The spectra of phospholipid films are also sensitive to hydration, and they exhibit changes in the peak intensities and frequencies of both nu(S) PO(2) (-) and nu(AS) PO(2) (-) vibrations. We interpret the spectral differences between water saturated and dried films both in terms of structural changes and the change in the local dielectric in the vicinity of the polar and solvent exposed groups. In addition, we observe that the most significant change in the absorption intensity, frequency, and shape of the water sensitive vibrations occurs at high hydration levels. The principal component analysis of hydration results and the kinetics of water removal from sample films are also discussed. In addition, protein spectra acquired using film and KBr pellet sampling techniques are compared.
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