DNA binding to crystalline silica characterized by Fourier-transform infrared spectroscopy.

Abstract

The interaction of DNA with crystalline silica in buffered aqueous solutions at physiologic pH has been investigated by Fourier-transform infrared spectroscopy (FT-IR). In aqueous buffer, significant changes occur in the spectra of DNA and silica upon coincubation, suggesting that a DNA-silica complex forms as silica interacts with DNA. As compared to the spectrum of silica alone, the changes in the FT-IR spectrum of silica in the DNA-silica complex are consistent with an Si-O bond perturbation on the surface of the silica crystal. DNA remains in a B-form conformation in the DNA-silica complex. The most prominent changes in the DNA spectrum occur in the 1225 to 1000 cm-1 region. Upon binding, the PO2- asymmetric stretch at 1225 cm-1 is increased in intensity and slightly shifted to lower frequencies; the PO2- symmetric stretch at 1086 cm-1 is markedly increased in intensity and the band at 1053 cm-1, representing either the phosphodiester or the C-O stretch of DNA backbone, is significantly reduced in intensity. In D2O buffer, the DNA spectrum reveals a marked increase in intensity of the peak at 1086 cm-1 and a progressive decrease in intensity of the peak at 1053 cm-1 when DNA is exposed to increasing concentrations of silica. The carbonyl band at 1688 cm-1 diminishes and shifts to slightly lower frequencies with increasing concentrations of silica. The present study demonstrates that crystalline silica binds to the phosphate-sugar backbone of DNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Mechanisms of carcinogenesis by crystalline silica in relation to oxygen radicals.

“…The FT-IR spectrum of quartz also showed modifications upon coincubation with DNA: the changes in the quartz spectrum were consistent with an Si-O bond perturbation on the surface of the quartz crystal (14). These FT-IR findings, obtained with two samples of quartz (min-U-sil 5 and Chinese standard) that gave similar results, are indicative of an effective hydrogen bonding interaction between surface silanol groups and the phosphate-sugar backbone of DNA.…”

“…Its advantages, compared to the BET method, include improved sensitivity, lack of requirement for specialized instrumentation, and the ability to make rapid simultaneous determinations on multiple samples. (14). Upon coincubation in aqueous buffer, alterations were observed in both DNA and quartz spectra, suggesting that a DNA-silica complex was formed as quartz interacted with DNA.…”

Mechanisms of crystalline silica-induced pulmonary toxicity revealed by global gene expression profiling

“…The bioinformatics analysis of the gene expression data in the silica exposed A549 cells and rat lungs, in addition to supporting the involvement of apoptosis in silica-induced pulmonary toxicity, provided novel insights into the mechanisms potentially underlying silica-induced apoptosis. The ability of silica to interact with DNA and, therefore, to result in DNA damage has been previously demonstrated (Mao et al, 1994). Even though it has been fairly well-established that silica exposure results in apoptosis indirectly through the generation of ROS (Santarelli et al, 2004;Hu et al, 2006), the apoptotic implication of direct DNA damage induced by silica, if any, is not known.…”

Soil Chemical Insights Provided through Vibrational Spectroscopy

“…Although, characterization of in situ soil bacteria is not possible, knowledge regarding the IR spectra of bacteria is very important for understanding processes of bacterial adhesion to mineral surfaces. A number of studies have used FTIR to characterize and study interactions of specific bacterial components including extracellular polymeric substances (EPS) (Badireddy et al, 2008;Beech et al, 1999;Eboigbodin and Biggs, 2008;Chorover, 2004, 2006;Wingender et al, 2001), lipopolysaccharides (LPS) (Brandenburg, 1993;Brandenburg et al, 2001Brandenburg et al, , 1997Brandenburg and Seydel, 1990;Kamnev et al, 1999;Chorover, 2007, 2008), phospholipids (Brandenburg et al, 1999;Brandenburg and Seydel, 1986;Cagnasso et al, 2010;Hübner and Blume, 1998), and DNA (Brewer et al, 2002;Falk et al, 1963;Mao et al, 1994;Pershina et al, 2009;Tsuboi, 1961;Zhou and Li, 2004). In addition, ATR-FTIR has emerged as a powerful tool for studying biofilm formation, composition, and structure (Beech et al, 2000;Cheung et al, 2000;Schmitt and Flemming, 1999;Spath et al, 1998).…”