Computational approach to design potential siRNA for CDKN2A gene silencing in melanoma through RNA interference

Melanoma is one of the most important cancers of the skin, accounting 75% of mortality rates worldwide and 8.9% in Khyber Pakhtunkhwa Pakistan. It begins to develop within melanocytes of skin. Its incidence rate is higher in males (35%) than females (20%). The very first sign of the disease the appearance of an ugly black mole on the skin. Up till now, cyclin dependent kinase inhibitor 2A (CDKN2A) has been reported the major gene responsible for the disease. Different treatment options are available for melanoma including chemotherapy, immunotherapy, targeted therapy, and surgical resection, etc. In the present study, a computational method is used to design efficient siRNA against CDKN2A. RNA silencing mechanism control gene at the transcriptional level by means of RNA interference technology. For this purpose, mRNA sequences of CDKN2A are retrieved, tandem repeats and UTR's motifs are predicted and removed, target sites for each siRNA are identified and 19–20 mer siRNAs are designed. There is efficient siRNA that is complementary to the target mRNA designed, based on the probability ratio >70% with minimum free energy, and low GC content to influence gene silencing. This computational method of designing siRNA is capable of silencing CDKN2A and is suggested for further in vitro exploration to confirm its efficacy.