The role of Project 1 is to develop and test new chemistries to analyze mutation deletion and mrna expression by hybridization in the 96 well microarray format.
Specific aim 1 is focused on oligonucleotide probe chemistry, to enhance the selectivity and affinity of target binding. We emphasize new chemistries which we have begun to develop: peptide- probe chimera and probes employing branched AAP backbone chemistry.
This aim relies on modeling of mismatched duplex domains by Project 2.
Specific Aim 2 is focused on systematic (combinatorial) variation of surface chemistry, so as to exploit ling range interactions between the hybridization surface and solution state nucleic acid targets. This work is driven by collaboration with the surface modeling group of Project 2.
Specific Aim 3 will implement published fluorescence and chemiluminescent labeling methods, and will develop new lanthanide based fluorescence approaches which are matched to the special characteristics of the proximal CCD detection method od Project 3. In collaboration with Cores A&B, Specific Aim 3 also involves investigation of methods to achieve MRNA and DNA amplification especially those methods which can be automated.
Specific Aim 4 is focused on the development of quantitative high molecular weight target binding assays, employing RNA and DNA from well characterized tumor cell lines. We will use these assays to evaluate probe, surface and labeling chemistry improvements, on the workstations of Core A.
In Specific Aims 5 &6, we will analyze RNA and DNA from the highly characterized, nearly homogenous, library of lung tumor samples obtained from Core B. Core A facilities will be used to test advancements in probe, surface, labeling and detection, on RBA and DNA from those Core B tumor samples. These two aims involve identifying gene targets to be used as models for analysis of point mutation, LOH, mRNA expression and splicing as lung tumor biomarkers. The choice of these model loci and the process of designing the corresponding oligonucleotide probe sets ( for fabrication as microarrays in Core A) is performed in very close collaboration with the molecular biologists of Core B.
