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Nucleic Acids Research Advance Access originally published online on March 26, 2009
Nucleic Acids Research 2009 37(10):3332-3341; doi:10.1093/nar/gkp178
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Nucleic Acids Research, 2009, Vol. 37, No. 10 3332-3341
© 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.

Nucleic Acid Enzymes

Elucidating the mechanism of DNA-dependent ATP hydrolysis mediated by DNA-dependent ATPase A, a member of the SWI2/SNF2 protein family

Macmillan Nongkhlaw1, Popy Dutta1, Joel W. Hockensmith2, Sneha Sudha Komath1,* and Rohini Muthuswami1,*

1School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India and 2University of Virginia, Charlottesville, VA 22908, USA

*To whom correspondence should be addressed. Tel: +91 11 2670 4154; Fax: +91 11 2671 7586; Email: rohini{at}mail.jnu.ac.in

Correspondence may also be addressed to Sneha Sudha Komath. Tel: +91 11 2670 4502; Fax: +91 11 2671 7586; Email: sskomath{at}mail.jnu.ac.in

Received September 1, 2008. Revised February 22, 2009. Accepted March 4, 2009.

The active DNA-dependent ATPase A domain (ADAAD), a member of the SWI2/SNF2 family, has been shown to bind DNA in a structure-specific manner, recognizing DNA molecules possessing double-stranded to single-stranded transition regions leading to ATP hydrolysis. Extending these studies we have delineated the structural requirements of the DNA effector for ADAAD and have shown that the single-stranded and double-stranded regions both contribute to binding affinity while the double-stranded region additionally plays a role in determining the rate of ATP hydrolysis. We have also investigated the mechanism of interaction of DNA and ATP with ADAAD and shown that each can interact independently with ADAAD in the absence of the other. Furthermore, the protein can bind to dsDNA as well as ssDNA molecules. However, the conformation change induced by the ssDNA is different from the conformational change induced by stem-loop DNA (slDNA), thereby providing an explanation for the observed ATP hydrolysis only in the presence of the double-stranded:single-stranded transition (i.e. slDNA).


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