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: email@example.com
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