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Nucleic Acids Research 2004 32(19):e144; doi:10.1093/nar/gnh145
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Published online 26 October 2004

Nucleic Acids Research, Vol. 32 No. 19 © Oxford University Press 2004; all rights reserved

Reversibly switchable DNA nanocompartment on surfaces

Youdong Mao1,3, Chunxiong Luo1,3, Wei Deng6, Guangyin Jin2, Xiaomei Yu5, Zhaohui Zhang3, Qi Ouyang1,4,*, Runsheng Chen6 and Dapeng Yu2

1 Laboratory for Biotechnology, 2 Laboratory for Nanofabrication, 3 Department of Physics, 4 Center for Theoretical Biology and 5 Institute of Microelectronics, Peking University, Beijing 100871, China and 6 Laboratory for Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China

* To whom correspondence should be addressed. Tel: +86 10 62756943; Fax: +86 10 62751615; Email: qi{at}pku.edu.cn
Correspondence may also be addressed to Youdong Mao. Tel: +86 10 62528034; Fax: +86 10 62751615; Email: jackmao{at}water.pku.edu.cn

Received July 27, 2004; Revised September 21, 2004; Accepted October 6, 2004

Biological macromolecules have been used to fabricate many nanostructures, biodevices and biomimetics because of their physical and chemical properties. But dynamic nanostructure and biomachinery that depend on collective behavior of biomolecules have not been demonstrated. Here, we report the design of DNA nanocompartments on surfaces that exhibit reversible changes in molecular mechanical properties. Such molecular nanocompartments are used to encage molecules, switched by the collective effect of Watson–Crick base-pairing interactions. This effect is used to perform molecular recognition. Furthermore, we found that ‘fuel’ strands with single-base variation cannot afford an efficient closing of nanocompartments, which allows highly sensitive label-free DNA array detection. Our results suggest that DNA nanocompartments can be used as building blocks for complex biomaterials because its core functions are independent of substrates and mediators.


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