Toward an Effective Control of DNA's Submolecular Conformation on a Surface
DNA adopts different conformations based on its environment. We reveal conditions that either preserve the DNA's physiological B conformation, even upon its placement in UHV, or lead to a partial B form to A form reorganization upon DNA's deposition on a surface. We use high resolution AFM to image DNA with a well defined number of base pairs deposited on mica. To enable the DNA's adhesion, we either add divalent cations to the DNA solution or functionalize the surface with a silane layer. The contour length of DNA on the silane is always in perfect agreement with the B form conformation, whereas cation deposited DNA is always, in some cases up to 20% shorter. We varied the equilibration time, the DNA length, and sequence and compared nicked to non nicked molecules, thus identifying several factors controlling the DNA's length. We performed TERS measurements confirming spectroscopically that cation deposited DNA undergoes a partial B form to A form conformational transition upon drying and pinpointed posi.