University of Washington
Grant: $71,372 - National Institutes of Health - May. 19, 2009
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Award Description: DNA microarrays are in principle particularly well suited for real-time identification of known or related species. Microarrays are inherently parallel, as hundreds to thousands of nucleic acid signatures can be probed for in a single hybridization assay. Their potential for integration into microfluidic lab-on-a-chip automated portable devices makes microarrays an attractive alternative to expensive and time-consuming cloning and sequencing. We hypothesize that a comprehensive mathematical model of microarray hybridization will serve as a valuable tool for testing the applicability of different analysis algorithms in systems of varying complexity, and has the hitherto untapped potential to guide the development of new data analysis algorithms. Model development will be carried out in parallel with experimental studies in nucleic acid hybridization kinetics for model validation, utilizing a novel microfluidic gel-based hybridization platform for real-time imaging with temperature control. This type of model could serve as a tool for systematic evaluation of analysis algorithms and/or experimental designs for a large variety of sample compositions, and guide the development of methods to further discriminate between hybridizations by similar targets.
Project Description: In the first quarter, we have worked on the 1st Specific Aim: developing a finite element computational model of DNA hybridization in a gel-based microfluidic microarray. We have developed a model using the finite element modeling package COMSOL MultiphysicsTM. The current version of the model incorporates the following physical processes: target diffusion in the finite volume of solution (confined by the geometry of the experimental hybridization chamber), diffusion into and inside three-dimensional gel elements, and hybridization onto and dissociation from the gel-immobilized probe molecules. In the hybridization chamber, we model four different gel elements with probes of different affinities embedded in them. Diffusion in solution and within the gel elements was described by Fick's Law, hybridization and dissociation were described by a two-state reversible kinetic model. In the first phase, hybridization and dissociation of a single target with three different probe sequences was considered: perfect-match probe, one-base mismatch probe, and partial match probe. For thermal dissociation modeling, we used the thermodynamic software program MeltCalc to calculate the changes in enthalpy and entropy for our specific sequences, and used these values to calculate the Gibbs free energy and equilibrium constant as a function of temperature. The temperature-dependent equilibrium constant was used to calculate temperature-dependent dissociation constant. Preliminary validation of the model gave good qualitative agreement between the simulations and experimental data. We have also built a model of hybridization of targets onto planar two-dimensional binding elements, utilizing the same kinetic constants and relationships between thermodynamic parameters and temperature as in the three-dimensional model, both with and without considering surface diffusion of targets. In the next report quarter, we will finish Aim#1 and start work on Specific Aim #2.
Jobs Summary: PREDOCTORAL RESEARCH ASSOCIATE 2-Engage in research on sponsored projects under general supv of faculty/research staff. May include independent research under the guidance of a faculty member. Normally a doctoral candidate. (Total jobs reported: 0)
Project Status: Less Than 50% Completed
This award's data was last updated on May. 19, 2009. Help expand these official descriptions using the wiki below.
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