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

Overview of Chakraborty S. et al.

AuthorsChakraborty S., Sharma S., Maiti P.K., Krishnan Y.
AffiliationNational Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bangalore 560065, Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India  
JournalNucleic Acids Research
Year 2009

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.