Objective: To design oligonucleotide probes for Cancer-testis (CT) genes for a microarray, which will be dedicated to a transcriptomic analysis of testis-specific genes in tumors and elucidation of the role of CT genes in the process of tumorigenesis.
Methods: The oligonucleotide probes for CT genes were designed through a combination of two probe designing tools available online, IDT and MEDIANTE. The "Oligonucleotide Properties Calculator" and "Oligo Analyzer 3.0" were applied to check the probe properties, including melting temperature, GC content and secondary structure forming possibilities etc.
Results: A total of 113 of 50 mer oligonucleotide probes were successfully designed for the 44 families of CT genes. The probes had a narrow range of Tm values between 63.2 degrees C and 67.5 degrees C and GC % contents between 35.3% and 51.5%.
Conclusion: The combinative use of the two probe designing tools, IDT and MEDIANTE, can successfully design oligonucleotide probes for cancer-testis genes.