In this project, we use small molecule microarrays to identify RNA- and DNA- binding small molecules. We have assembled a library of 65,000 small molecules that may be screened in the microarray format. In each case, molecules are printed on to glass slides using a microarrayer robot and covalently linked to the surface. Next, fluorescently labeled oligonucleotides with defined structures (such as hairpins or quadruplexes) are incubated on array surfaces. Spots that increase in fluorescence intensity are scored as binding. Once hit molecules of interest are identified from the screen, they are characterized through chemical synthesis, biochemical and biophysical analyses, and if possible in cellular assays to confirm biological activity as well as binding to the oligonucleotide. In this project, we place an interest in RNA and DNA structures involved in regulating gene expression.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Investigator-Initiated Intramural Research Projects (ZIA)
Project #
1ZIABC011585-02
Application #
9153994
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
2
Fiscal Year
2015
Total Cost
Indirect Cost
Name
Basic Sciences
Department
Type
DUNS #
City
State
Country
Zip Code
Calabrese, David R; Chen, Xiang; Leon, Elena C et al. (2018) Chemical and structural studies provide a mechanistic basis for recognition of the MYC G-quadruplex. Nat Commun 9:4229
Moon, Michelle H; Hilimire, Thomas A; Sanders, Allix M et al. (2018) Measuring RNA-Ligand Interactions with Microscale Thermophoresis. Biochemistry 57:4638-4643
Connelly, Colleen M; Boer, Robert E; Moon, Michelle H et al. (2017) Discovery of Inhibitors of MicroRNA-21 Processing Using Small Molecule Microarrays. ACS Chem Biol 12:435-443
Connelly, Colleen M; Abulwerdi, Fardokht A; Schneekloth Jr, John S (2017) Discovery of RNA Binding Small Molecules Using Small Molecule Microarrays. Methods Mol Biol 1518:157-175
Abulwerdi, Fardokht A; Shortridge, Matthew D; Sztuba-Solinska, Joanna et al. (2016) Development of Small Molecules with a Noncanonical Binding Mode to HIV-1 Trans Activation Response (TAR) RNA. J Med Chem 59:11148-11160
Connelly, Colleen M; Moon, Michelle H; Schneekloth Jr, John S (2016) The Emerging Role of RNA as a Therapeutic Target for Small Molecules. Cell Chem Biol 23:1077-1090
Felsenstein, Kenneth M; Saunders, Lindsey B; Simmons, John K et al. (2016) Small Molecule Microarrays Enable the Identification of a Selective, Quadruplex-Binding Inhibitor of MYC Expression. ACS Chem Biol 11:139-48
Abulwerdi, Fardokht A; Schneekloth Jr, John S (2016) Microarray-based technologies for the discovery of selective, RNA-binding molecules. Methods 103:188-95
Sztuba-Solinska, Joanna; Shenoy, Shilpa R; Gareiss, Peter et al. (2014) Identification of biologically active, HIV TAR RNA-binding small molecules using small molecule microarrays. J Am Chem Soc 136:8402-10