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Study of the Inhibitory Effect of Fatty Acids on the Interaction between DNA and Polymerase β

Jun Yang1*, Jing Yang1,2†, Zheng-Qin Yin3*, Jing Xu1, Ning Hu1, I. Svir4, Min Wang1, Yuan-Yi Li1, Lei Zhan1, Song Wu1, and Xiao-Lin Zheng1

1Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education; Bioengineering College, Chongqing University, Chongqing 400030, China; fax: 86-23-6511-1931; E-mail: yjun1999@hotmail.com; bioyangjun@cqu.edu.cn

2Department of Information Engineering, Chongqing Communication College, Chongqing 400035, China

3Southwest Eye Hospital, Southwest Hospital, Third Military Medical University, Chongqing 400038, China; fax: 86-23-6546-0711; E-mail: qinzyin@yahoo.com.cn

4Kharkov National University of Radioelectronics, UA-61166 Kharkov, Ukraine

These authors contributed equally.

* To whom correspondence should be addressed.

Received October 6, 2008; Revision received November 24, 2008
The binding of human DNA polymerase β (pol β) to DNA template–primer duplex and single-stranded DNA in the absence or presence of pol β inhibitors has been studied using a surface plasmon resonance biosensor. Two fatty acids, linoleic acid and nervonic acid, were used as potent pol β inhibitors. In the interaction between pol β and DNA, pol β could bind to ssDNA in a single binding mode, but bound to DNA template–primer duplexes in a parallel mode. Both pol β inhibitors prevented the binding of pol β to the single strand overhang and changed the binding from parallel to single mode. The affinities of pol β to the template–primer duplex region in the presence of nervonic acid or linoleic acid were decreased by 20 and 5 times, respectively. The significant inhibitory effect of nervonic acid on the pol β–duplex interaction was due to both a 2-fold decrease in the association rate and a 9-fold increase in the dissociation rate. In the presence of linoleic acid, no significant change of association rate was observed, and the decrease in binding affinity of pol β to DNA was mainly due to 7-fold increase in the dissociation rate.
KEY WORDS: DNA polymerase β, surface plasmon resonance, fatty acid, inhibition, SPR biosensor

DOI: 10.1134/S0006297909070165