Estimation of statistical binding properties of ligand population during in vitro selection based on population dynamics theory.
During in vitro selection process, it is very valuable to monitor the binding properties of the ligand population in real time, particularly the population average of the association constant in the population. If this monitoring can be realized, the selection process can be controlled in a rational way. In this paper, we present a simple method to estimate the binding properties of the ligand population during in vitro selection. The framework of the method is as follows. First, the number of all the collected ligand molecules, which are eluted after incubation and washing, is measured. Ideally, this number corresponds to the number of all the ligand molecules bound with the target-receptor or other materials in a test tube. This measurement is performed through several successive rounds of selection. Second, the measured numbers of molecules are subjected to a theoretical analysis, based on the mathematical theory of population dynamics in the selection process. Then, we can estimate the probability density of the binding free energy in the ligand population. The validity of our method was confirmed by several computer simulations based on a physicochemical model.
Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan. Electronic address: taita@mail.saitama-u.ac.jp.
Takuyo
T
Aita
Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan.
Koichi
K
Nishigaki
Innovation Research Organization, Saitama University, 255 Shimo-okubo, Saitama 338-8570, Japan.
Yuzuru
Y
Husimi
D003198:Computer Simulation; D066298:In Vitro Techniques / Q000379:methods*; D008024:Ligands; D008956:Models, Chemical; D010455:Peptides / Q000737:chemistry*; D013816:Thermodynamics
D008024:Ligands; D010455:Peptides
Aptamer; Binding constant; Directed evolution; In vitro evolution; Monitoring method; SELEX