The stereochemistry of the interaction and recognition processes of DNA has been traditionally described in the Ångström scale. DNA can also provide recognition processes whose selectivity and stringency can be modulated along different scale lengths, as it takes place in direct and indirect read-out mechanisms between DNA and proteins. Embedded in DNA are informational codes that control its recognition processes also in the nanoscale. These recognition processes can exploit multiple layers of information to drive self-assembly amongst biological and non-biological molecules (1). They are based on the nanoscale superstructural and mechanical properties that are modulated along the DNA chain by its sequence. Atomic Force Microscopy by imaging single DNA molecules makes it possible: a) to translate the linear information of the base sequences into these functional elements, and to “sequence” those properties (2-4); b) to monitor the length-scale and also the time-scale of the equilibration processes in the dynamics of a single DNA chain (5). Those nanoscale properties of DNA are capable to control gene expression (6) and to lead to recognition processes between a crystal surface and the sequence of the DNA (7). These recognition processes are studied also with the Single Molecule Force Spectroscopy approach (8,9). (1) B. Samorì & G. Zuccheri, Angew. Chem. Int. Ed. Engl., 44 (8): 1166-81 (2005). (2) G. Zuccheri, A. Scipioni, G. Gargiulo, V. Cavaliere, G. De Santis, B. Samorì, Proc. Natl. Acad. Sci. (USA), 98; 3074-3079 (2001). (3) A. Scipioni, G. Zuccheri, M. Savino, B. Samorì, P. De Santis, Biophys. J., 83 (5): 2408-18 (2002). (4) G. Zuccheri and B. Samorì, Methods in Cell Biology 68: 357-395 (2002). (5) A. Scipioni, G. Zuccheri, C. Anselmi, A. Bergia, B. Samorì, P. De Santis, Chem Biol., 9 (12): 1315-21 (2002). (6) M. Barna, M. Branford, A. Bergia, B. Samori, and P. P. Pandolfi, Developmental Cell, 3: 499-510 (2002). (7) B. Sampaolese, A. Bergia, A. Scipioni, G. Zuccheri, M. Savino, B. Samorì,. P. De Santis, Proc. Natl. Acad. Sci. (USA) 99: 13566-13570 (2002). (8) F. Grandi, G. Zuccheri, B. Samorì (to be published) (9) Y. Bustanji, C. Arciola, M. Conti, E. Mandello, L. Montanaro, B. Saporì, Proc. Natl. Acad. Sci. (USA), 100: 13292-13297 (2003).