RNA binding properties of novel gene silencing pyrrole-imidazole polyamides.

Pyrrole-imidazole (PI) polyamides are a novel group of gene-silencing compounds, which bind to a minor groove of double stranded (ds)DNA in a sequence-specific manner. To explore the RNA binding properties of PI polyamides targeting rat transforming growth factor-ß1 (TGF-ß1 Polyamide) and influenza A virus (PA polyamide), we designed dsRNAs with an identical sequence to the target DNA and analyzed RNA binding properties of the polyamide. Biacore assay showed fast binding of TGF-ß1 Polyamide to the dsRNA, whereas mismatch polyamide did not bind to the dsRNA. Dissociation equilibrium constant (KD) value was 6.7×10(-7) of the target dsRNA. These results indicate that PI polyamide could bind to RNA with a 2 log lower binding affinity than its DNA-binding affinity. We designed a PI polyamide targeting the panhandle stem region of influenza A virus. KD value of the PI polyamide to dsRNA targeting influenza A virus was 4.6×10(-7). Gel-shift assay showed that TGF-ß1 and PA polyamides bound to the appropriate dsDNA, whereas these PI polyamides did not show obvious gel-shift with the appropriate dsRNA. Structural modeling suggests that PI polyamide binds to the appropriate B-form dsDNA in the minor groove, whereas it does not fit in the minor groove to dsRNA. Thus PI polyamides have a lower binding affinity with target dsRNA than they do with dsDNA. The distinct binding properties of PI polyamides to dsRNA and dsDNA may be associated with differences of secondary structure and chemical binding properties between target RNA and DNA.

Development of a chimeric DNA-RNA hammerhead ribozyme targeting SARS virus.

OBJECTIVE: Severe acute respiratory syndrome (SARS) is a severe pulmonary infectious disease caused by a novel coronavirus. To develop an effective and specific medicine targeting the SARS-coronavirus (CoV), a chimeric DNA-RNA hammerhead ribozyme was designed and synthesized using a sequence homologous with the mouse hepatitis virus (MHV). METHOD: Chimeric DNA-RNA hammerhead ribozyme targeting MHV and SARS-CoV were designed and synthesized.To confirm its activity, in vitro cleavage reactions were performed with the synthesized ribozyme. Effects of the chimeric ribozyme were evaluated on multiplication of MHV. Effects of the chimeric ribozyme on expression of SARS-CoV were evaluated in cultured 3T3 cells. RESULT: The synthetic ribozyme cleaved the synthetic target MHV and SARS-CoV RNA into fragments of predicted length. The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited multiplication of MHV in DBT cells by about 60%. The chimeric DNA-RNA hammerhead ribozyme targeting SARS-CoV significantly inhibited the expression of SARS-CoV RNA in 3T3 cells transfected with the recombinant plasmid. The chimeric DNA-RNA ribozyme targeting SARS-CoV significantly inhibited MHV viral activity and expression of recombinant SARS RNA in vitro. CONCLUSION: These findings indicate that the synthetic chimeric DNA-RNA ribozyme could provide a feasible treatment for SARS.

The latent membrane protein 1 (LMP1) encoded by Epstein-Barr virus induces expression of the putative oncogene Bcl-3 through activation of the nuclear factor-kappaB.

The Epstein-Barr virus (EBV)-encoded oncoprotein latent membrane protein 1 (LMP1) has an essential role in B-lymphocyte transformation by the virus and is expressed in certain EBV-associated tumors and lymphoproliferative disorders. By using the Flp-In/TREx-inducible expression system, we introduced LMP1 into two human cell lines, Jurkat and HEK-293, and found that in both of them the putative cellular oncogene Bcl-3 is rapidly induced following the expression of LMP1. Bcl-3 was also induced in Ramos cells after in vitro EBV infection and after transfection with an LMP1 expression vector. This LMP1-induced Bcl-3 expression is considered to be mediated by the transcription factor NF-kappaB, because (1) deletion of a critical NF-kappaB-binding site in the Bcl-3 promoter abolished its responsiveness to LMP1, (2) an IkappaB mutant that specifically inhibits NF-kappaB activity suppressed the LMP1-induced activation of the Bcl-3 promoter, and (3) an LMP1 mutant lacking its effector domain CTAR2, required for the activation of NF-kappaB, is severely impaired in its ability to induce Bcl-3. Western blot analyses showed that all EBV-infected and LMP1-expressing lymphoid cell lines express Bcl-3. These results suggest the possibility that Bcl-3 is involved in the pathogenesis of certain EBV-associated malignancies and lymphoproliferative disorders.