Toward an Effective Control of DNA’s Submolecular Conformation on a Surface

Abstract

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...