Sun, D., & Hurley, L. H. (1995). TBP binding to the TATA box induces a specific downstream unwinding site that is targeted by pluramycin. Chemistry and Biology, 2(7), 457-469.
PMID: 9383448;Abstract:
Background: The TATA-binding protein (TBP) is one of the major components of the human TFIID multiprotein complex. It is important in directing the initiation of RNA transcription at a site immediately downstream of the TATA sequence (TATA box) found in many eukaryotic promoters. The crystal structure of TBP complexed with an oligonucleotide containing the TATA box revealed a protein with an approximate two-fold symmetry which apparently has symmetrical interactions with DNA. It is not known how an asymmetric effect involving downstream activation can be produced by an apparent symmetric complex. We set out to examine the state of DNA in the TBP-DNA complex using pluramycin, a small molecular weight probe of DNA accessibility. Results: Binding of TBP to the TATA box facilitates intercalation of pluramycin at a defined site immediately downstream of the TATA sequence through an apparent transient unwinding of the DNA. Pluramycin adducts are detected by the production of DNA strand breakage products upon heating. Incubation of pluramycin with the TBP-DNA complex facilitates the trapping of the specific complex by intercalation. Gel mobility shift and circularization assays reveal that the binding of pluramycin on the 3′-side of the TATA box region considerably stabilizes the TBP-DNA complex. Conclusions: We propose that the TBP-DNA-pluramycin ternary complex is a 'specific' binding mode in which TBP and pluramycin make compensatory alterations in DNA, accounting for the improved stability of the ternary complex. We also propose a model of the ternary complex that explains the observed asymmetric effect of TBP binding to the TATA box.
Thurston, D. E., & Hurley, L. H. (1983). A rational basis for development of antitumor agents in the pyrrolo[1,4]benzodiazepine group. Drugs of the Future, 8(11), 957-971.
Kaiser, C. E., Van Ert, N. A., Agrawal, P., Chawla, R., Yang, D., & Hurley, L. H. (2017). Insight into the Complexity of the i-Motif and G-Quadruplex DNA Structures Formed in the KRAS Promoter and Subsequent Drug-Induced Gene Repression. Journal of the American Chemical Society, 139(25), 8522-8536.
Activating KRAS mutations frequently occur in pancreatic, colorectal, and lung adenocarcinomas. While many attempts have been made to target oncogenic KRAS, no clinically useful therapies currently exist. Most efforts to target KRAS have focused on inhibiting the mutant protein; a less explored approach involves targeting KRAS at the transcriptional level. The promoter element of the KRAS gene contains a GC-rich nuclease hypersensitive site with three potential DNA secondary structure-forming regions. These are referred to as the Near-, Mid-, and Far-regions, on the basis of their proximity to the transcription start site. As a result of transcription-induced negative superhelicity, these regions can open up to form unique DNA secondary structures: G-quadruplexes on the G-rich strand and i-motifs on the C-rich strand. While the G-quadruplexes have been well characterized, the i-motifs have not been investigated as thoroughly. Here we show that the i-motif that forms in the C-rich Mid-region is the most stable and exists in a dynamic equilibrium with a hybrid i-motif/hairpin species and an unfolded hairpin species. The transcription factor heterogeneous nuclear ribonucleoprotein K (hnRNP K) was found to bind selectively to the i-motif species and to positively modulate KRAS transcription. Additionally, we identified a benzophenanthridine alkaloid that dissipates the hairpin species and destabilizes the interaction of hnRNP K with the Mid-region i-motif. This same compound stabilizes the three existing KRAS G-quadruplexes. The combined effect of the compound on the Mid-region i-motif and the G-quadruplexes leads to downregulation of KRAS gene expression. This dual i-motif/G-quadruplex-interactive compound presents a new mechanism to modulate gene expression.
Seaman, F. C., & Hurley, L. H. (1999). 31P-Nmr as a probe for drug-nucleic acid interactions. Phosphorus, Sulfur and Silicon and Related Elements, 144-146, 297-300.
Abstract:
The structural impact of covalent and noncovalent interactions of drugs with DNA is an important component for understanding the biochemical and biological consequences of DNA damage. Work in this laboratory has focused on a number of potentially therapeutically important drugs that distort DNA by unwinding, bending DNA into the major or minor groove. These lead to enhanced recognition of DNA by proteins involved in transcription and replication. In this paper, we will present the structures of one of these complexes and show how 31P-NMR can be used to monitor these distortive effects.
Hurley, L., Brown, R. V., & Hurley, L. -. (2011). DNA acting like RNA. Biochemical Society transactions, 39(2).
Over the last decade or so, secondary non-B-DNA structures such as G-quadruplexes and i-motifs have come into focus as biologically functioning moieties that are potentially involved in telomeric interactions and the control of gene expression. In the present short review, we first describe the structural and dynamic parallels with complex RNA structures, including the importance of sequence and ions in folding, and then we describe the biological consequences of the folded structures. We conclude that there are considerable parallels between secondary and tertiary structures in RNA and DNA from both the folding and the biological perspectives.
