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Nucleic Acids Research Advance Access published online on March 11, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp133
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structural Biology

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

Saikat Chakraborty1, Suruchi Sharma1, Prabal K. Maiti2 and Yamuna Krishnan1,*

1National Centre for Biological Sciences, TIFR, GKVK, Bellary Road, Bangalore 560065 and 2Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India

*To whom correspondence should be addressed. Tel: +91 80 23666180; Fax: +91 80 23636462; Email: yamuna{at}ncbs.res.in

Received December 16, 2008. Revised February 16, 2009. Accepted February 17, 2009.

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.


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