R.D. Kornberg and his colleagues have done extensive work on the process of transcription, specifically that of RNA polymerase II [2-5]. They have formed the structures at resolutions of RNAPII at less then 3 Å which can give an incredible amount of information. Since hydrogen bonding is around 3 Å, it allows us to study interactions between residues more clearly and really figure out the structure and how that relates to the mechanism. Morishita et al. could now benefit from the work that Kornberg has done. Though the work of Morishita et al. was published before Kornberg’s big discoveries, there were some lingering problems that could now be solved because of the extensive knowledge we have of RNAPII.
Transfection of cis-element ds oligodeoxynucleotides (ODN) has been shown to be a powerful tool that is a new type of anti-gene strategy for gene therapy and in the study of transcriptional factors [1]. Basically what it does is they use a decoy to treat diseases by controlling transcriptional regulation [1]. As was stated before, regulatory proteins known as transcription factors control what and when certain genes are transcribed. It would suggest that since a single factor can control transcription of some genes, should there be a mutation in the factor, it could be lethal. Morishita et al. hypothesize that using these decoy genes could bind transcription factors and block the genes that associate with some disease and thus prevent them. Basically, the decoy’s main role is to reduce promoter activity by inhibiting the binding of the transcription factor to the promoter region [1].
The work of Kornberg could really help to further this possible way of treating diseases. As of right now, the decoy genes just bind the promoter DNA and reduce the binding of RNAPII. This obviously will have its draw backs as the decoy may not work perfectly all the time and transcription could still occur. Since the work of Kornberg has given the insight on how exactly RNAPII functions and the structure of it, scientists can use that to their advantage when using these decoy ODNs. They can structure these decoy ODNs to not only prevent the binding of transcription factors, but in the event that they should bind, the decoys could be made so that they will disrupt the RNAPII structure and cause it to dissociate or at least prevent the formation of the mRNA. They could use the information of the RNAPII to better inhibit these factors and have more control over the regulation of transcription.
The work of Morishita et al. is quite promising as they have shown to inhibit HIV expression and replication by blocking the binding of the HIV regulatory protein Tat to the TAR region by using these decoy ODNs. This was in vitro however and it has been almost impossible in vivo. By using the information gathered by Kornberg et al. they may be able to find a way to construct a decoy ODN that would inhibit the association of the DNA with RNAPII but at the same time be able to use it in vivo to make huge medical strides.
[1] Morishita, R.; Higaki, J.; Tomita, N.; Ogihara, T. Application of Transcription Factor “Decoy” Strategy as Means of Gene Therapy and Study of Gene Expression in Cardiovascular Disease. Circ Res. 1998. 82, 1023-1028.
[2] Bushnell, D.A.; Cramer, P.; Kornberg, R.D. Structural basis of transcription: α-Amanitin-RNA polymerase II cocrystal at 2.8 Å resolution. PNAS. 5 February 2002. 99, 1218-1222.
[3] Cramer, P.; Bushnell, D.A.; Kornberg, R.D. Structural Basis of Transcription: RNA Polymerase II at 2.8 Ångstrom Resolution. Science. 8 June 2001. 292, 1863-1876.
[4] Gnatt, A.L; Cramer, P.; Fu, J.; Bushnell, D.A.; Kornberg, R.D. Structural Basis of Transcription: An RNA Polymerase II Elongation Complex at 3.3 Å Resolution. Science. 8 June 2001. 292, 1876-1882.
[5] Westover, K.D.; Bushnell, D.A.; Kornberg, R.D. Structural Basis of Transcription Nucleotide Selection by Rotation in the RNA Polymerase II Active Center. Cell. 12 November 2004. 119, 481-489.