A Small-molecule Fluorescence Probe ANP77 for Sensing RNA Internal Loop of C, U and A/CC Motifs and Their Binding Molecules

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2021 Aug 6

PMID 34358308

Citations 5

Authors

Bimolendu Das

Asako Murata

Kazuhiko Nakatani

Affiliations

Soon will be listed here.

Abstract

Small-molecules interacting with particular RNAs and modulating their functions are vital tools for RNA-targeting drug discovery. Considering the substantial distribution of the internal loops involving two contiguous cytosines opposite to a single-nucleotide base (Y/CC; Y = C, U or A) within the biologically significant functional RNAs, developing small-molecule probes targeting Y/CC sites should provide profound insight into their functions and roles in biochemical processes. Herein, we report ANP77 as the small-molecule probe for sensing RNA internal loop of Y/CC motifs and molecules binding to the motifs. The Y/CC motifs interact with ANP77 via the formation of a 1:1 complex and quench the fluorescence of ANP77. The flanking sequence-dependent binding to C/CC and U/CC sites was assessed by fluorometric screening, provided the binding heat maps. The quenching phenomena of ANP77 fluorescence was confirmed with intrinsic potential drug target pre-miR-1908. Finally, the binding-dependent fluorescence quenching of ANP77 was utilized in the fluorescence indicator displacement assay to demonstrate the potential of ANP77 as an indicator by using the RNA-binding drugs, risdiplam and branaplam.

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References

Kozomara A, Birgaoanu M, Griffiths-Jones S . miRBase: from microRNA sequences to function. Nucleic Acids Res. 2018; 47(D1):D155-D162. PMC: 6323917. DOI: 10.1093/nar/gky1141. View

Shibata T, Nakatani K . Fluorescence Probe for Detecting CCG Trinucleotide Repeat DNA Expansion and Slip-Out. Chembiochem. 2016; 17(18):1685-8. DOI: 10.1002/cbic.201600200. View

Kobori A, Horie S, Suda H, Saito I, Nakatani K . The SPR sensor detecting cytosine[bond]cytosine mismatches. J Am Chem Soc. 2004; 126(2):557-62. DOI: 10.1021/ja037947w. View

Xia X, Li Y, Wang W, Tang F, Tan J, Sun L . MicroRNA-1908 functions as a glioblastoma oncogene by suppressing PTEN tumor suppressor pathway. Mol Cancer. 2015; 14:154. PMC: 4534015. DOI: 10.1186/s12943-015-0423-0. View

Ratni H, Ebeling M, Baird J, Bendels S, Bylund J, Chen K . Discovery of Risdiplam, a Selective Survival of Motor Neuron-2 ( SMN2) Gene Splicing Modifier for the Treatment of Spinal Muscular Atrophy (SMA). J Med Chem. 2018; 61(15):6501-6517. DOI: 10.1021/acs.jmedchem.8b00741. View

Meyer S, Hergenrother P . Small molecule ligands for bulged RNA secondary structures. Org Lett. 2009; 11(18):4052-5. PMC: 4975938. DOI: 10.1021/ol901478x. View

Nakatani K, Natsuhara N, Mori Y, Mukherjee S, Das B, Murata A . Synthesis of Naphthyridine Dimers with Conformational Restriction and Binding to DNA and RNA. Chem Asian J. 2017; 12(23):3077-3087. DOI: 10.1002/asia.201701293. View

Wicks S, Hargrove A . Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA. Methods. 2019; 167:3-14. PMC: 6756977. DOI: 10.1016/j.ymeth.2019.04.018. View

Jayaraj G, Nahar S, Maiti S . Nonconventional chemical inhibitors of microRNA: therapeutic scope. Chem Commun (Camb). 2014; 51(5):820-31. DOI: 10.1039/c4cc04514a. View

10.

Li Y, Kowdley K . MicroRNAs in common human diseases. Genomics Proteomics Bioinformatics. 2012; 10(5):246-53. PMC: 3611977. DOI: 10.1016/j.gpb.2012.07.005. View

11.

Zhang , Chung , OLDENBURG . A Simple Statistical Parameter for Use in Evaluation and Validation of High Throughput Screening Assays. J Biomol Screen. 2000; 4(2):67-73. DOI: 10.1177/108705719900400206. View

12.

Thomas J, Hergenrother P . Targeting RNA with small molecules. Chem Rev. 2008; 108(4):1171-224. DOI: 10.1021/cr0681546. View

13.

Murata A, Harada Y, Fukuzumi T, Nakatani K . Fluorescent indicator displacement assay of ligands targeting 10 microRNA precursors. Bioorg Med Chem. 2013; 21(22):7101-6. DOI: 10.1016/j.bmc.2013.09.007. View

14.

Zhang J, Takei F, Nakatani K . Emission of characteristic fluorescence from the ligand-cytosine complex in U_A/ACU bulged RNA duplex. Bioorg Med Chem. 2007; 15(14):4813-7. DOI: 10.1016/j.bmc.2007.05.007. View

15.

Warner K, Hajdin C, Weeks K . Principles for targeting RNA with drug-like small molecules. Nat Rev Drug Discov. 2018; 17(8):547-558. PMC: 6420209. DOI: 10.1038/nrd.2018.93. View

16.

Zhang J, Umemoto S, Nakatani K . Fluorescent indicator displacement assay for ligand-RNA interactions. J Am Chem Soc. 2010; 132(11):3660-1. DOI: 10.1021/ja100089u. View

17.

Otabe T, Nagano K, Kawai G, Murata A, Nakatani K . Inhibition of pre-miRNA-136 processing by Dicer with small molecule BzDANP suggested the formation of ternary complex of pre-miR-136-BzDANP-Dicer. Bioorg Med Chem. 2019; 27(10):2140-2148. DOI: 10.1016/j.bmc.2019.03.031. View

18.

Childs-Disney J, Yildirim I, Park H, Lohman J, Guan L, Tran T . Structure of the myotonic dystrophy type 2 RNA and designed small molecules that reduce toxicity. ACS Chem Biol. 2013; 9(2):538-550. PMC: 3944380. DOI: 10.1021/cb4007387. View

19.

Di Giorgio A, Duca M . Synthetic small-molecule RNA ligands: future prospects as therapeutic agents. Medchemcomm. 2019; 10(8):1242-1255. PMC: 6748380. DOI: 10.1039/c9md00195f. View

20.

Umemoto S, Im S, Zhang J, Hagihara M, Murata A, Harada Y . Structure-activity studies on the fluorescent indicator in a displacement assay for the screening of small molecules binding to RNA. Chemistry. 2012; 18(32):9999-10008. DOI: 10.1002/chem.201103932. View