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Nucleic Acids Research Advance Access originally published online on June 12, 2007
Nucleic Acids Research 2007 35(12):4086-4093; doi:10.1093/nar/gkm445
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Nucleic Acids Research, 2007, Vol. 35, No. 12 4086-4093
© 2007 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.

Molecular Biology

Regulation of DNA nucleases by molecular crowding

Yoshiharu Sasaki1,2, Daisuke Miyoshi1 and Naoki Sugimoto1,3,*

1Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501, 2Fine Co., Ltd., 5-7-8 Shimoshinjo, Higashiyodogawa-ku, Osaka, 533-0021 and 3Department of Chemistry, Faculty of Science and Engineering, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe 658-8501

*To whom correspondence should be addressed. Tel: +078 435 2497; Fax: +078 435 2539; Email: sugimoto{at}konan-u.ac.jp

Received February 15, 2007. Revised May 17, 2007. Accepted May 18, 2007.

Here, we examined the effects of molecular crowding on the function, structure and stability of nucleases. We found that the hydrolysis of a 29-mer double-stranded DNA by the endonucleases DNase I and S1 nuclease was substantially enhanced by molecular crowding using polyethylene glycol (PEG); however, molecular crowding had little effect on hydrolysis by exo III and exo I exonucleases. Moreover, kinetic analysis showed that the maximum velocity for the reaction of DNase I at 25°C was increased from 0.1 to 2.7 µM/min by molecular crowding with 20% (w/v) PEG, whereas that of exonuclease I at 37°C decreased from 2.2 to 0.4 µM/min. In contrast, molecular crowding did not significantly affect the Michaelis constant of DNase I or exonuclease I. These results indicate that molecular crowding has different effects on the catalytic activities of exonucleases and endonucleases.


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