  From a nanoscience perspective, cellular processes and their reduced in vitro
imitations provide extraordinary examples for highly robust few or single
molecule reaction pathways. A prime example are biochemical reactions involving
DNA molecules, and the coupling of these reactions to the physical
conformations of DNA. In this review, we summarise recent results on the
following phenomena: We investigate the biophysical properties of DNA-looping
and the equilibrium configurations of DNA-knots, whose relevance to biological
processes are increasingly appreciated. We discuss how random DNA-looping may
be related to the efficiency of the target search process of proteins for their
specific binding site on the DNA molecule. And we dwell on the spontaneous
formation of intermittent DNA nanobubbles and their importance for biological
processes, such as transcription initiation. The physical properties of DNA may
indeed turn out to be particularly suitable for the use of DNA in nanosensing
applications.
