Transcription factors as molecular targets: molecular mechanisms of decoy ODN and their design

Recent progress in cellular and molecular research has provided a new technique to inhibit target gene expression based on DNA technology such as antisense oligonucleotides (ODN) or decoy ODN. Especially, application of an antisense strategy to regulate the transcription of disease-related genes in vivo has important therapeutic potential to treat or cure a variety of diseases and abnormal physiological conditions. On the other hand, recently, a successful ODN-based approach termed decoy ODN has used synthetic ODN containing an enhancer element that can penetrate cells, to bind to sequence-specific DNA-binding proteins and interfere with transcription in vitro and in vivo. Transfection of cis-element double-stranded decoy ODN has been reported as a new powerful tool in a new class of anti-gene strategies to treat various diseases as gene therapy or as a research tool to examine the molecular mechanisms of expression of a specific gene. Transfection of double-stranded ODN corresponding to the cis-sequence will result in attenuation of the authentic cis-trans interaction, leading to removal of trans-factors from the endogenous cis-elements with subsequent modulation of gene expression. To date, we have chosen several target transcription factors such as NFkappaB (nuclear factor-kappaB) and E2F to prevent the progression of diseases, and negative regulatory element (NRE) for the renin gene and angiotensinogen gene-activating element (AGE) for the angiotensinogen gene to examine the molecular mechanisms of gene expression. In this section, we introduce the principles of the decoy strategy and how to design decoy ODN.