Abstract
New methods to identify RNA-binding small molecules open yet unexplored opportunities for the pharmacological modulation of RNA-driven biology and disease states. One such approach is the use of small molecule microarrays (SMMs). Typically, SMMs are generated by spatially arraying and covalently linking a library of small molecules to a glass surface. Next, incubation of the arrays with a fluorescently labeled RNA reveals binding interactions that are detected upon slide imaging. The relative ease with which SMMs are manufactured enables the screening of multiple oligonucleotides in parallel against tens of thousands of small molecules, providing information about both binding and selectivity of identified RNA–small molecule interactions. This approach is useful for screening a broad variety of structurally and functionally diverse RNAs. Here, we present a general method for the preparation and use of SMMs to rapidly identify small molecules that selectively bind to an RNA of interest.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsSpringer Nature is developing a new tool to find and evaluate Protocols. Learn more
References
Cooper TA, Wan LL, Dreyfuss G (2009) RNA and disease. Cell 136(4):777–793
Sztuba-Solinska J et al (2014) Identification of biologically active, HIV TAR RNA-binding small molecules using small molecule microarrays. J Am Chem Soc 136(23):8402–8410
Hergenrother PJ, Depew KM, Schreiber SL (2000) Small-molecule microarrays: covalent attachment and screening of alcohol-containing small molecules on glass slides. J Am Chem Soc 122(32):7849–7850
Koehler AN, Shamji AF, Schreiber SL (2003) Discovery of an inhibitor of a transcription factor using small molecule microarrays and diversity-oriented synthesis. J Am Chem Soc 125(28):8420–8421
Kawasumi M et al (2005) Small molecule microarrays to discover compounds that modulate cell cycle checkpoint function. J Invest Dermatol 124(4):A39–A39
Miao H et al (2007) Ring-opening and ring-closing reactions of a shikimic acid-derived substrate leading to diverse small molecules. J Comb Chem 9(2):245–253
Vegas AJ et al (2007) Fluorous-based small-molecule microarrays for the discovery of histone deacetylase inhibitors. Angew Chem Int Ed Engl 46(42):7960–7964
Stanton BZ et al (2009) A small molecule that binds Hedgehog and blocks its signaling in human cells. Nat Chem Biol 5(3):154–156
Aminova O, Paul DJ, Childs-Disney JL, Disney MD (2008) Two-dimensional combinatorial screening identifies specific 6′-acylated kanamycin A- and 6′-acylated neamine-RNA hairpin interactions. Biochemistry 47(48):12670–12679
Disney MD et al (2008) Two-dimensional combinatorial screening identifies specific aminoglycoside – RNA internal loop partners. J Am Chem Soc 130(33):11185–11194
Velagapudi SP, Gallo SM, Disney MD (2014) Sequence-based design of bioactive small molecules that target precursor microRNAs. Nat Chem Biol 10(4):291–297
Luo Y, Disney MD (2014) Bottom-up design of small molecules that stimulate exon 10 skipping in mutant MAPT pre-mRNA. Chembiochem 15(14):2041–2044
Chirayil S, Chirayil R, Luebke KJ (2009) Discovering ligands for a microRNA precursor with peptoid microarrays. Nucleic Acids Res 37(16):5486–5497
Diaz JP et al (2014) Association of a peptoid ligand with the apical loop of pri-miR-21 inhibits cleavage by Drosha. RNA 20(4):528–539
Bradner JE et al (2006) A robust small-molecule microarray platform for screening cell lysates. Chem Biol 13(5):493–504
Bradner JE, McPherson OM, Koehler AN (2006) A method for the covalent capture and screening of diverse small molecules in a microarray format. Nat Protoc 1(5):2344–2352
Baell JB, Holloway GA (2010) New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem 53(7):2719–2740
Campbell CT, Zhang Y, Gildersleeve JC (2010) Construction and use of glycan microarrays. Curr Protoc Chem Biol 2(1):37–53
Hartmann RK (2009) Handbook of RNA biochemistry. Wiley-VCH, Weinheim, p 931, 1st student Ed, pp xliii
Childs-Disney JL, Wu ML, Pushechnikov A, Aminova O, Disney MD (2007) A small molecule microarray platform to select RNA internal loop-ligand interactions. ACS Chem Biol 2(11):745–754
Wu H, Ge J, Uttamchandani M, Yao SQ (2011) Small molecule microarrays: the first decade and beyond. Chem Commun (Camb) 47(20):5664–5670
Lee HY, Park SB (2010) Small molecule microarray: functional-group specific immobilization of small molecules. Methods Mol Biol 669:23–42
Acknowledgment
This Research was supported by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media New York
About this protocol
Cite this protocol
Connelly, C.M., Abulwerdi, F.A., Schneekloth, J.S. (2017). Discovery of RNA Binding Small Molecules Using Small Molecule Microarrays. In: Uttamchandani, M., Yao, S. (eds) Small Molecule Microarrays. Methods in Molecular Biology, vol 1518. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6584-7_11
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6584-7_11
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6582-3
Online ISBN: 978-1-4939-6584-7
eBook Packages: Springer Protocols