We have identified a new class of molecular receptors amenable to drug targeting to modulate gene expression. Modulation of gene expression has broad applications in molecular therapeutics, including cancer, heart disease, inflammation, neurodegeneration, endocrinology, asthma, and diabetes. The scientific community affected by this discovery is very broad and includes basic as well as translational scientists. These molecular targets comprise secondary DNA structures (G- quadruplexes and i-motifs) found frequently in the promoter elements of a wide variety of genes including c-Myc, Bcl-2, VEGF, Hif-1a, PDGF-A, and RET. Proof of principle exists that stabilization of these secondary DNA structures with small molecules results in repression of gene expression in cells and this repression is dependent on an intact G-quadruplex in the promoter region. Quarfloxin, a drug originating from the PI's laboratory, is a first-in-class G-quadruplex-interactive drug that targets G-quadruplexes in ribosomal DNA and is in phase II clinical trials. The selectivity and corresponding lack of any serious toxicity in the clinical trials is partially dependent on the selective uptake into the nucleolus of cancer cells along with the 400-fold selectivity of Quarfloxin for the parallel-type G-quadruplex found in rDNA over duplex DNA. The objective of this proposal is to provide structural insight into silencer elements consisting of a G- quadruplex and i-motif within a duplex region that corresponds to the silencer elements. Herein lies the challenge because the i-motif is only normally generated under the negative superhelicity found in a plasmid supercoiled state or as a consequence of transcriptional runoff. We have proposed a solution to this problem along with techniques to provide a structure-based approach and development of a high-throughput assay for screening for compounds that interact with this composite structure. The ability to form the composite i-motif/G-quadruplex structure within a duplex molecule will permit us to identify small molecules that have enhanced target selectivity. The challenge addressed in this proposal is to design a system in which we can externally control the production of genes in cells. This technology, if successful, will have applications in the treatment of cancer, heart disease, and Alzheimer's disease.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM085585-03
Application #
7893865
Study Section
Special Emphasis Panel (ZGM1-GDB-7 (EU))
Program Officer
Tompkins, Laurie
Project Start
2008-08-01
Project End
2012-07-31
Budget Start
2010-08-01
Budget End
2011-07-31
Support Year
3
Fiscal Year
2010
Total Cost
$299,970
Indirect Cost
Name
University of Arizona
Department
Type
Organized Research Units
DUNS #
806345617
City
Tucson
State
AZ
Country
United States
Zip Code
85721
Kendrick, Samantha; Kang, Hyun-Jin; Alam, Mohammad P et al. (2014) The dynamic character of the BCL2 promoter i-motif provides a mechanism for modulation of gene expression by compounds that bind selectively to the alternative DNA hairpin structure. J Am Chem Soc 136:4161-71
Kang, Hyun-Jin; Kendrick, Samantha; Hecht, Sidney M et al. (2014) The transcriptional complex between the BCL2 i-motif and hnRNP LL is a molecular switch for control of gene expression that can be modulated by small molecules. J Am Chem Soc 136:4172-85
Cui, Yunxi; Koirala, Deepak; Kang, HyunJin et al. (2014) Molecular population dynamics of DNA structures in a bcl-2 promoter sequence is regulated by small molecules and the transcription factor hnRNP LL. Nucleic Acids Res 42:5755-64
Yu, Zhongbo; Gaerig, Vanessa; Cui, Yunxi et al. (2012) Tertiary DNA structure in the single-stranded hTERT promoter fragment unfolds and refolds by parallel pathways via cooperative or sequential events. J Am Chem Soc 134:5157-64
Brown, Robert V; Hurley, Laurence H (2011) DNA acting like RNA. Biochem Soc Trans 39:635-40
Brown, Robert V; Danford, Forest L; Gokhale, Vijay et al. (2011) Demonstration that drug-targeted down-regulation of MYC in non-Hodgkins lymphoma is directly mediated through the promoter G-quadruplex. J Biol Chem 286:41018-27
Balasubramanian, Shankar; Hurley, Laurence H; Neidle, Stephen (2011) Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nat Rev Drug Discov 10:261-75
Brooks, Tracy A; Hurley, Laurence H (2010) Targeting MYC Expression through G-Quadruplexes. Genes Cancer 1:641-649
Gonzalez, Veronica; Hurley, Laurence H (2010) The c-MYC NHE III(1): function and regulation. Annu Rev Pharmacol Toxicol 50:111-29
Qin, Yong; Fortin, Jessica S; Tye, Denise et al. (2010) Molecular cloning of the human platelet-derived growth factor receptor beta (PDGFR-beta) promoter and drug targeting of the G-quadruplex-forming region to repress PDGFR-beta expression. Biochemistry 49:4208-19

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