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Structure and Binding Properties of DNA on Graphite and Carbon Nanotubes

Anand Jagota Lehigh University, Chemical Engineering & Bioengineering

DNA adsorbs strongly on graphene, graphite, and single wall carbon nanotubes (SWCNTs), forming strong non-covalently associated hybrids. In the case of carbon nanotubes, these hybrids allow easy dispersion in aqueous medium. Recently, we have found that certain short DNA oligomers ( 10-20 bases in length) recognize corresponding carbon nanotubes, allowing separation of the latter from a mixture. By allowing SWCNTs to be purified, these hybrids are enabling many fundamental studies and applications, for example in biomedical sensing and imaging. In this presentation, we will present studies of the structure and binding properties of DNA on graphite and carbon nanotubes. To measure directly the binding free energy of DNA on graphite, we have used AFM-based single molecule force spectroscopy to peel single strands of DNA off graphite. We find that binding strengths are quite strong, about 10 kT per DNA base, and depend on the type of base and DNA sequence. To explain the recognition of SWCNTs by short ssDNA oligomers, we have proposed novel secondary structures analogous to the protein beta-sheet and beta-barrels. Molecular dynamics simulations support the idea that these novel adsorbed structures are stabilized by non-Watson-Crick base pairs. By surfactant exchange, we have studied how ssDNA sequence affects binding. We find that activation energies for removal of DNA by a surfactant correlates strongly with recognition ability. Together, these findings point to the existence of a new class of surface-adsorption stabilized secondary structures of ssDNA by means of which it can recognize nanomaterials.