Single-stranded DNA adsorption characteristics by hollow spherule allophane nano-particles: pH dependence and computer simulation

Abstract Clay mineral surfaces have been important for the prebiotic organization and protection of nucleic acids. The morphological observation to provide insight into the adsorption structure and characteristics of single-stranded DNA (ss-DNA) by natural allophane particles was presented. The molecular orbital (MO) computer simulation has been used to probe the interaction of ss-DNA and/or adenosine 5′-monophosphate and allophane with active sites. Our simulations predicted that the strand undergoes some extent of the elongation, which induces the alteration of the conformation of the phosphate backbone, base–base distance and excluded volume correlation among bases. This work demonstrates the ss-DNA adsorption by the allophane particles with novel insights into the morphological features and detailed molecular level information. The overall results support a general adsorption mechanism for the ss-DNA/allophane complexation.