Study of the DNA structure and orientation using SERS: Influence of the hybridisation and mismatches

In this article we study the structure and the orientation of DNA strands by Surface Enhanced Raman Scattering (SERS). We study the influence of two parameters on the structure of strands containing 20 adenines: the hybridization with the complementary strand and the presence of mismatch within the sequence. By varying the concentration of complementary strands, we show that hybridisation induces a change in strand orientation and loss of flexibility, indicating that the formation of the double helix freezes the conformation of DNA strand. The introduction of a mismatch has the same effects on strand orientation and flexibility but also induces hybridisation defects in the formation of the double helix. We therefore highlight the presence of non-hybridized adenine bases, this effect being all the more visible when the mismatch is close to the centre of the strand. We also highlight spectral markers of these structural changes and of the evolution of hybridisation. For example, we observe the main band shift of the adenine from 734 to 747 cm^-1 indicating a reorientation of the base during hybridisation from a perpendicular configuration to a configuration parallel to the surface.