Biochip Dna Hybridization Dynamics Simulation

The gene chip technology is a booming sector of biology detection technologieswhich provides improvements in bioanalytical methods for purposes such as DNAsequencing, mutations detection and analysis of gene expression map. It immobilizesDNA molecules with known sequences on a solid surface, and unscrambles the sequenceinformation of DNA sample relying on highly selective nucleic acid hybridizationcharacteristic. General theoretical and numerical models of heterogeneous hybridizationkinetics are required in order to design and optimize such biochips, build up stableexperimental system and to develop a quantitative method for online interpretation ofexperimental results.A mathematical model based on receptor-ligand interactions at a cell surface hadbeen modified and further developed to represent heterogeneous DNA-DNAhybridization on a solid surface. In this work an existing general kinetic modeling ofheterogeneous hybridization is modified and a new modeling is obtained for the case ofwell-spaced, noninteracting surface-bound molecules. In this model the immobilizedDNA molecules are called probes, and the DNA molecules in solution with unknownsequences are called targets. The model shows that the probability of successfulhybridization between probe and target is not a constant. Along with progressing of thehybridization process, the experiment environment is variational. Therefore the resultindicates that the probability of successful hybridization is a conditional probability,varying according to the experiment conditions. Its mathematical expression is obtainedby fitting.The heterogeneous hybridization processes ought to keep to the laws ofthermodynamics, the thermodynamic stability of the target-probe complex is governed bythe Gibbs free energy of binding. A thermodynamics criterion about stability is fixedthrough the analysis in the work. In addition, it is discussed how the hybridization statusis in the cases of the temperature T in cyclic variation and asymmetric probe densities.The results indicate that there is a good correlation between the new model and theexperimental data, and the different reaction systems have corresponding hybridizationmodels.