title: 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 (dA(15)) 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 dA(15). The pH-triggered transition between the two defined helical forms of dA(15) 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 dA(15) represents a new molecular building block for the construction of quick-response, pH-switchable architectures in structural DNA nanotechnology.
authors.affiliation: National Centre for Biological Sciences, TIFR, GKVK, Bangalore, India.
authors.forename: Saikat
authors.initials: S
authors.lastname: Chakraborty
authors.forename: Suruchi
authors.initials: S
authors.lastname: Sharma
authors.forename: Prabal K
authors.initials: PK
authors.lastname: Maiti
authors.forename: Yamuna
authors.initials: Y
authors.lastname: Krishnan
mesh_terms: D002942:Circular Dichroism; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D019281:Dimerization; D004591:Electrophoresis, Polyacrylamide Gel; D006863:Hydrogen-Ion Concentration; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011061:Poly A / Q000737:chemistry*; D012965:Sodium Chloride / Q000737:chemistry; D013050:Spectrometry, Fluorescence; D013696:Temperature
chemical_list: D011061:Poly A; C015465:poly(dA); D012965:Sodium Chloride; D004247:DNA