The broad, long-term objectives of this proposal are to develop and maintain a software package dedicated to the design of oligonucleotides to make DNA microarrays for gene expression and genotyping analysis. This package will be built on the latest knowledge of the thermodynamics of DNA hybridization on chips.
The specific aims are 1) enhance our current software designing oligonucleotides for expression analysis 2) add to this package new software designing oligonucleotides for splicing variant and single nucleotide polymorphisms detection, 3) pursue the development of an oligonucleotide database related to the design software and 4) maintain and distribute broadly these packages. The health relatedness of this project is to provide to Biologist powerful but easy to use software to design oligonucleotides for DNA microarray experiments. There is a broad range of research fields relying on DNA microarrays. Some examples include gene expression profiling of tumors to adapt treatments to specific kind of cancer, or detection of single mutation in genes pre-disposing to some diseases. The research plan will consist in first determining experimentally the thermodynamic parameters of the hybridization on chips to then accurately simulating such phenomena in our software. The experimental approach will involve to measure the melting curve of thousands of perfectly and non-perfectly matched DNA duplexes on parallel on DNA chips in order to assign a thermodynamic value to every single base-pair and mismatches in a given sequence environment. These values will be applied to the existing Nearest Neighbor model to predict hybridization on chips. Based on this knowledge, we will not only improve our existing algorithms but also design new ones to strongly enhance the capability of our software, specially regarding the design of oligonucleotides to detect splicing variants of a given gene or single nucleotide polymorphisms. The implementation will be modular to facilitate further modification or reuse of some libraries. All the code writing, including comments, will be done aiming a broad portability across existing platforms and an open source distribution to facilitate further developments. We will also implement and distribute a complete database and related tools for in house storage of oligonucleotides sequence and associated data generated by end-users.
| Ozel, Ayse Bilge; Srivannavit, Onnop; Rouillard, Jean-Marie et al. (2012) Target concentration dependence of DNA melting temperature on oligonucleotide microarrays. Biotechnol Prog 28:556-66 |
| Markham, Nicholas R; Zuker, Michael (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol 453:3-31 |
| O-Charoen, Sirimon; Srivannavit, Onnop; Gulari, Erdogan (2007) Simulation and visualization of flow pattern in microarrays for liquid phase oligonucleotide and peptide synthesis. Biotechnol Prog 23:755-61 |
| Le Brigand, Kevin; Russell, Roslin; Moreilhon, Chimene et al. (2006) An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. Nucleic Acids Res 34:e87 |
