ABSTRACT
The binding of human DNA polymerase beta (pol beta) to DNA template-primer duplex and single-stranded DNA in the absence or presence of pol beta inhibitors has been studied using a surface plasmon resonance biosensor. Two fatty acids, linoleic acid and nervonic acid, were used as potent pol beta inhibitors. In the interaction between pol beta and DNA, pol beta could bind to ssDNA in a single binding mode, but bound to DNA template-primer duplexes in a parallel mode. Both pol beta inhibitors prevented the binding of pol beta to the single strand overhang and changed the binding from parallel to single mode. The affinities of pol beta 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 beta-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 beta to DNA was mainly due to 7-fold increase in the dissociation rate.
Subject(s)
DNA Polymerase beta/metabolism , DNA, Single-Stranded/metabolism , Fatty Acids, Monounsaturated/pharmacology , Linoleic Acid/pharmacology , Base Sequence , DNA Polymerase beta/chemistry , DNA Polymerase beta/genetics , DNA, Single-Stranded/chemistry , DNA, Single-Stranded/genetics , Fatty Acids/metabolism , Humans , Kinetics , Molecular Sequence Data , Nucleic Acid Conformation , Protein Binding/drug effectsABSTRACT
In this work, we present a theoretical analysis of diffusion processes at arrays of recessed microelectrodes and evaluate the dependence of these processes on the main geometrical parameters (distance between electrodes in the array and slope of side walls of conical recesses) of this complex system. To allow for faster computation time and excellent accuracy, numerical simulations were performed upon transforming the real space allowed for diffusion using a quasi-conformal mapping introduced for this array geometry in our previous work (Amatore, C., Oleinick, A. I. and Svir, I. J. Electroanal. Chem. 2006, 597, 77-85). The applied quasi-conformal mapping is perfectly suited to the considered microelectrode array geometry and ensures that the abrupt change of boundary conditions reflecting the contorted geometries of the considered microelectrode array are treated efficiently and precisely in the simulations.
ABSTRACT
A new software package, 'KINFITSIM', for fitting and simulating kinetic data is presented. The main goals of the KINFITSIM package are to obtain the best-fit parameters-rate constants, amplitudes and others-to a user specified chemical mechanism, plots of the calculated and experimental absorbance versus time, and a report to the user with the results. The KINFITSIM package can be used in either chemical research or for educational purposes.
ABSTRACT
The chemical transformations of electrogenerated ion-radicals of a number of complex organic compounds may be accompanied by emission of photons. An electrogenerated chemiluminescence (ECL) quantum contains information both on the kinetics of the heterogeneous electrode processes and on the subsequent homogeneous chemical reactions in the solution. Application of ECL to solution analysis provides advantages in comparison to electrochemical methods. We demonstrate a new approach for numerical simulation of the microdisc problem in spherical co-ordinates and apply it to ECL homogeneous analysis under non-steady state electrolysis.
