This article analyzes the experience of identification and support of applied research in nanotechnology at the regional level. The models of technological dynamics and interaction of scientific and technological innovation with traditional technologies are developed and presented. Three types of nanotechnology developments functions (addition, substitution, environment-forming) are allocated. Methodological approaches to the assessment of synergistic effects of nanotechnology related to the construction of road maps, assessment of externalities, and introduction of real options valuation methods and the modified input-output are substantiated.