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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.

SUBMITTER: Chakraborty S

PROVIDER: S-EPMC2685084 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature

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

Chakraborty Saikat S Sharma Suruchi S Maiti Prabal K PK Krishnan Yamuna Y

Nucleic acids research 20090311 9

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 ...[more]

PMID: 19279188

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