Structural Biology Meets Nanoscience at the Interface: the Nanoscale Structure of DNA and the Interactions of Single Molecules of DNA with Surfaces.

DNA has been selected by millennia of evolution as the primary molecule that carries, preserves and uses information for the great majority of the living organisms. The structure of DNA is the basis for the astonishingly complex functions that DNA accomplishes very efficiently. A sugar-phosphate backbone solubilizes a double helix of paired and stacked aromatic bases that are so shielded by the aqueous environment. In this hydrophobic environment, bases also find the specific interactions that are the foundation of the chemical recognition between the two chains, the essential informational content for the replication of life itself, the other major discovery of James Watson and Francis Crick’s, together with the unveiling of the helical structure. The chemical specificity of the DNA recognition code is so stringent that is can be used to prepare artificial constructs that take advantage of the information code to easily and purposely auto-assemble structures of unprecedented complexity. Nanoscale objects of very complex topology and geometry have been prepared by mastering the art of oligonucleotide sequence selection and design; the recognition process has been used as an add-in feature to drive recognition processes in systems that would not display it, and so achieve self-assembly, proximity, order. The pairing of DNA bases into a double helix, and the additional recognition properties that DNA normally employs in the living cell has been shown to be valuable for the assembly of electronic circuit elements, possibly a starting step towards a totally new electronic architecture.[1] On a size-scale that is one order of magnitude larger than that relevant for base-pairing and recognition, a DNA double-helix displays a whole new set of properties, derived from the chemical inhomogeneity along the chain, and from the helical nature itself. These properties have been the object of the studies of our group in the last years. With scanning force microscopy experiments, we have directly measured how a double-stranded DNA helix can be intrinsically curved, though being fairly flexible, and how its flexibility can be modulated along the chain.[2,3] We have shown that the dynamics of the different sections of the chain can be studied directly, and we have found them to depend on the sequence too.[4] These Nanoscale properties of DNA are known to have a paramount effect on DNA-protein interactions in the living organisms. We have recently shown that they can also affect the way DNA also interacts with non-biological objects, like crystalline surfaces, all the way to the point of representing an example of nanoscale recognition between DNA and non-biological objects.[5] The understanding of these long-range nanoscale properties of DNA could lay the groundwork of a new generation of recognition processes that might be used in nanoscience. 1. Keren, K., Krueger, M., Gilad, R., Ben-Yoseph, G., Sivan, U., and Braun, E., Science 297, 72-75 (2002). 2. Zuccheri, G., Scipioni, A., Cavaliere, V., Gargiulo, G., De Santis, P., and Samorì, B., Proc. Natl. Acad. Sci. USA 98, 3074-3079. (2001). 3. Scipioni, A., Anselmi, C., Zuccheri, G., Samorì, B., and De Santis, P., Biophys. J. 83, 2408-2418 (2002). 4. Scipioni, A., Zuccheri, G., Anselmi, C., Bergia, A., Samorì, B., and De Santis, P., Chemistry & Biology 9, 1315-1321 (2002). 5. Sampaolese, B., Bergia, A., Scipioni, A., Zuccheri, G., Savino, M., Samorì, B., and De Santis, P., Proc Natl. Acad. Sci. USA 99, 13566-13570 (2002).