The poly dA helix: A new structural motif for high performance DNA-based molecular switches

Abstract

We report a pH-dependent conformational transition in short, defined homopolymeric deoxyadenosines (dA₁₅) from a single helical structure with stacked nucleobases at neutral pH to a double-helical, parallel-stranded duplex held together by AH⁺-H⁺A base pairs at acidic pH. Using native PAGE, 2D NMR, circular dichroism (CD) and fluorescence spectroscopy, we have characterized the two different pH dependent forms of dA₁₅. The pH-triggered transition between the two defined helical forms of dA₁₅ is characterized by CD and fluorescence. The kinetics of this conformational switch is found to occur on a millisecond time scale. This robust, highly reversible, pH-induced transition between the two well-defined structured states of dA₁₅ represents a new molecular building block for the construction of quick-response, pH-switchable architectures in structural DNA nanotechnology.