Development of RNA G-quadruplex (rG4)-targetingl-RNA aptamers by rG4-SELEX

Mubarak I. Umar, Chun-Yin Chan, Chun Kit Kwok

Published: 2022-04-19 DOI: 10.1038/s41596-022-00679-6

RNA G-quadruplex

rG4-SELEX

l-RNA aptamers

aptamer secondary structure

nucleic acid motifs

AI 解读

Supplementary information

Reporting Summary

Generation of mouse–human chimeric embryos

Genome-wide quantification of transcription factor binding at single-DNA-molecule resolution using methyl-transferase footprinting

Generation of CRISPR–Cas9-mediated genetic knockout human intestinal tissue–derived enteroid lines by lentivirus transduction and single-cell cloning

A puromycin-dependent activity-based sensing probe for histochemical staining of hydrogen peroxide in cells and animal tissues

Decoding personal biotic and abiotic airborne exposome

A clinically relevant model of focal embolic cerebral ischemia by thrombus and thrombolysis in rhesus monkeys

Bioengineering human intestinal mucosal grafts using patient-derived organoids, fibroblasts and scaffolds

Biomimetic tail-to-head terpene cyclizations using the resorcin[4]arene capsule catalyst

Neuroscience robotics for controlled induction and real-time assessment of hallucinations

Scanorama: integrating large and diverse single-cell transcriptomic datasets

Single-cell RNA sequencing (scRNA-seq)（单细胞RNA测序）

Data integration（数据集成）

Heterogeneity（异质性）

查看全部

Sections

Figures

References

Supplementary information

Davis, J. T. G-quartets 40 years later: from 5′-GMP to molecular biology and supramolecular chemistry. Angew. Chem. Int. Ed. 43, 668–698 (2004).
Neidle, S. & Balasubramanian, S. Quadruplex Nucleic Acids. Vol. 7 (Royal Society of Chemistry, 2006).
Kwok, C. K. & Merrick, C. J. G-quadruplexes: prediction, characterization, and biological application. Trends Biotechnol. 35, 997–1013 (2017).
Rhodes, D. & Lipps, H. J. G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res. 43, 8627–8637 (2015).
Valton, A. L. & Prioleau, M. N. G-quadruplexes in DNA replication: a problem or a necessity? Trends Genet. 32, 697–706 (2016).
Fay, M. M., Lyons, S. M. & Ivanov, P. RNA G-quadruplexes in biology: principles and molecular mechanisms. J. Mol. Biol. 429, 2127–2147 (2017).
Kwok, C. K., Marsico, G. & Balasubramanian, S. Detecting RNA G-quadruplexes (rG4s) in the transcriptome. Cold Spring Harb. Perspect. 10, a032284 (2018).
Varshney, D., Spiegel, J., Zyner, K., Tannahill, D. & Balasubramanian, S. The regulation and functions of DNA and RNA G-quadruplexes. Nat. Rev. Mol. Cell. Biol. 21, 459–474 (2020).
Lyu, K., Chow, E. Y., Mou, X., Chan, T. F. & Kwok, C. K. RNA G-quadruplexes (rG4s): genomics and biological functions. Nucleic Acids Res. 49, 5426–5450 (2021).
Metifiot, M., Amrane, S., Litvak, S. & Andreola, M. L. G-quadruplexes in viruses: function and potential therapeutic applications. Nucleic Acids Res. 42, 12352–12366 (2014).
Harris, L. M. & Merrick, C. J. G-quadruplexes in pathogens: a common route to virulence control? PLoS Pathog. 11, e1004562 (2015).
Hansel-Hertsch, R., Di Antonio, M. & Balasubramanian, S. DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential. Nat. Rev. Mol. Cell. Biol. 18, 279–284 (2017).
Ruggiero, E. & Richter, S. N. G-quadruplexes and G-quadruplex ligands: targets and tools in antiviral therapy. Nucleic Acids Res. 46, 3270–3283 (2018).
Cui, H. & Zhang, L. G-quadruplexes are present in human coronaviruses including SARS-CoV-2. Front. Microbiol. 11, 567317 (2020).
Zhao, C. et al. Targeting RNA G-quadruplex in SARS-CoV-2: a promising therapeutic target for COVID-19? Angew. Chem. Int. Ed. 60, 432–438 (2021).
Ruggiero, E. & Richter, S. N. Viral G-quadruplexes: new frontiers in virus pathogenesis and antiviral therapy. Annu. Rep. Med. Chem. 54, 101–131 (2020).
Ji, D. et al. Discovery of G-quadruplex-forming sequences in SARS-CoV-2. Brief. Bioinform. 22, 1150–1160 (2021).
Kosiol, N., Juranek, S., Brossart, P., Heine, A. & Paeschke, K. G-quadruplexes: a promising target for cancer therapy. Mol. Cancer 20, 40 (2021).
Sanchez-Martin, V., Soriano, M. & Garcia-Salcedo, J. A. Quadruplex ligands in cancer therapy. Cancers 13, (2021).
Young, B. E., Kundu, N. & Sczepanski, J. T. Mirror-image oligonucleotides: history and emerging applications. Chemistry 25, 7981–7990 (2019).
Nolte, A., Klussmann, S., Bald, R., Erdmann, V. A. & Furste, J. P. Mirror-design of l-oligonucleotide ligands binding to l-arginine. Nat. Biotechnol. 14, 1116–1119 (1996).
Kluszmann, S., Nolte, A., Bald, R., Erdmann, V. A. & Furste, J. P. Mirror-image RNA that binds d-adenosine. Nat. Biotechnol. 14, 1112–1115 (1996).
Tuerk, C. & Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505–510 (1990).
Ellington, A. D. & Szostak, J. W. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818–822 (1990).
Robertson, D. L. & Joyce, G. F. Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344, 467–468 (1990).
Vater, A. & Klussmann, S. Turning mirror-image oligonucleotides into drugs: the evolution of Spiegelmer® therapeutics. Drug Discov. Today 20, 147–155 (2015).
Sczepanski, J. T. & Joyce, G. F. Binding of a structured d-RNA molecule by an l-RNA aptamer. J. Am. Chem. Soc. 135, 13290–13293 (2013).
Sczepanski, J. T. & Joyce, G. F. Specific inhibition of microRNA processing using l-RNA aptamers. J. Am. Chem. Soc. 137, 16032–16037 (2015).
Lorenz, C., von Pelchrzim, F. & Schroeder, R. Genomic systematic evolution of ligands by exponential enrichment (Genomic SELEX) for the identification of protein-binding RNAs independent of their expression levels. Nat. Protoc. 1, 2204–2212 (2006).
Chan, C. Y. & Kwok, C. K. Specific binding of a d-RNA G-quadruplex structure with an l-RNA aptamer. Angew. Chem. Int. Ed. 59, 5293–5297 (2020).
Umar, M. I. & Kwok, C. K. Specific suppression of d-RNA G-quadruplex–protein interaction with an l-RNA aptamer. Nucleic Acids Res. 48, 10125–10141 (2020).
Ji, D., Lyu, K., Zhao, H. & Kwok, C. K. Circular l-RNA aptamer promotes target recognition and controls gene activity. Nucleic Acids Res. 49, 7280–7291 (2021).
Tolnai, Z. J. et al. Spiegelmer-based sandwich assay for cardiac troponin I detection. Int. J. Mol. Sci. 21, 4963 (2020).
Staple, D. W. & Butcher, S. E. Pseudoknots: RNA structures with diverse functions. PLoS Biol. 3, e213 (2005).
Benabou, S., Aviñó, A., Eritja, R., González, C. & Gargallo, R. Fundamental aspects of the nucleic acid i-motif structures. RSC Adv. 4, 26956–26980 (2014).
Williams, G. D., Chang, R. Y. & Brian, D. A. A phylogenetically conserved hairpin-type 3′ untranslated region pseudoknot functions in coronavirus RNA replication. J. Virol. 73, 8349–8355 (1999).
Brierley, I., Pennell, S. & Gilbert, R. J. Viral RNA pseudoknots: versatile motifs in gene expression and replication. Nat. Rev. Microbiol. 5, 598–610 (2007).
Romilly, C., Lippegaus, A. & Wagner, E. G. H. An RNA pseudoknot is essential for standby-mediated translation of the tisB toxin mRNA in Escherichia coli. Nucleic Acids Res. 48, 12336–12347 (2020).
Theimer, C. A., Blois, C. A. & Feigon, J. Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function. Mol. Cell 17, 671–682 (2005).
Chen, J. L. & Greider, C. W. Functional analysis of the pseudoknot structure in human telomerase RNA. Proc. Natl Acad. Sci. USA. 102, 8080–8085 (2005). discussion 8077-8089.
Mihalusova, M., Wu, J. Y. & Zhuang, X. Functional importance of telomerase pseudoknot revealed by single-molecule analysis. Proc. Natl Acad. Sci. USA. 108, 20339–20344 (2011).
Wang, Y., Yesselman, J. D., Zhang, Q., Kang, M. & Feigon, J. Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human. Proc. Natl Acad. Sci. USA. 113, E5125–E5134 (2016).
Dzatko, S. et al. Evaluation of the stability of DNA i-motifs in the nuclei of living mammalian cells. Angew. Chem. Int. Ed. 57, 2165–2169 (2018).
Zeraati, M. et al. I-motif DNA structures are formed in the nuclei of human cells. Nat. Chem. 10, 631–637 (2018).
Abou Assi, H., Garavis, M., Gonzalez, C. & Damha, M. J. i-Motif DNA: structural features and significance to cell biology. Nucleic Acids Res. 46, 8038–8056 (2018).
Donlic, A. & Hargrove, A. E. Targeting RNA in mammalian systems with small molecules. Wiley Interdiscip. Rev. RNA 9, e1477 (2018).
Falese, J. P., Donlic, A. & Hargrove, A. E. Targeting RNA with small molecules: from fundamental principles towards the clinic. Chem. Soc. Rev. 50, 2224–2243 (2021).
Monchaud, D. & Teulade-Fichou, M. P. A hitchhiker’s guide to G-quadruplex ligands. Org. Biomol. Chem. 6, 627–636 (2008).
Asamitsu, S., Bando, T. & Sugiyama, H. Ligand design to acquire specificity to intended G-quadruplex structures. Chemistry 25, 417–430 (2019).
Spiegel, J., Adhikari, S. & Balasubramanian, S. The structure and function of DNA G-quadruplexes. Trends Chem. 2, 123–136 (2020).
Umar, M. I., Ji, D., Chan, C. Y. & Kwok, C. K. G-quadruplex-based fluorescent turn-on ligands and aptamers: from development to applications. Molecules 24, 2416 (2019).
Collie, G. W. & Parkinson, G. N. The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem. Soc. Rev. 40, 5867–5892 (2011).
Chen, X. C. et al. Tracking the dynamic folding and unfolding of RNA G-quadruplexes in live cells. Angew. Chem. Int. Ed. 57, 4702–4706 (2018).
Moruno-Manchon, J. F. et al. Small-molecule G-quadruplex stabilizers reveal a novel pathway of autophagy regulation in neurons. eLife 9, e52283 (2020).
Di Antonio, M. et al. Single-molecule visualization of DNA G-quadruplex formation in live cells. Nat. Chem. 12, 832–837 (2020).
Zafferani, M. & Hargrove, A. E. Small molecule targeting of biologically relevant RNA tertiary and quaternary structures. Cell Chem. Biol. 28, 594–609 (2021).
Tao, Y., Zheng, Y., Zhai, Q. & Wei, D. Recent advances in the development of small molecules targeting RNA G-quadruplexes for drug discovery. Bioorg. Chem. 110, 104804 (2021).
Arthanari, H., Basu, S., Kawano, T. L. & Bolton, P. H. Fluorescent dyes specific for quadruplex DNA. Nucleic Acids Res. 26, 3724–3728 (1998).
Paramasivan, S. & Bolton, P. H. Mix and measure fluorescence screening for selective quadruplex binders. Nucleic Acids Res. 36, e106 (2008).
Ren, J. et al. Label-free detection of nucleic acids by turn-on and turn-off G-quadruplex-mediated fluorescence. Anal. Bioanal. Chem. 399, 2763–2770 (2011).
Xu, S. et al. Thioflavin T as an efficient fluorescence sensor for selective recognition of RNA G-quadruplexes. Sci. Rep. 6, 24793 (2016).
Renaud de la Faverie, A., Guedin, A., Bedrat, A., Yatsunyk, L. A. & Mergny, J. L. Thioflavin T as a fluorescence light-up probe for G4 formation. Nucleic Acids Res. 42, e65 (2014).
Hu, M. H. et al. Specific targeting of telomeric multimeric G-quadruplexes by a new triaryl-substituted imidazole. Nucleic Acids Res. 45, 1606–1618 (2017).
Hu, M. H. et al. Discovery of a new four-leaf clover-like ligand as a potent c-MYC transcription inhibitor specifically targeting the promoter G-quadruplex. J. Med. Chem. 61, 2447–2459 (2018).
Hu, M. H. et al. Development of a smart fluorescent sensor that specifically recognizes the c-MYC G-quadruplex. Anal. Chem. 91, 2480–2487 (2019).
Sun, R. et al. c-Myc G-quadruplex is sensitively and specifically recognized by a fluorescent probe. Talanta 226, 122125 (2021).
Fernando, H. et al. Genome-wide analysis of a G-quadruplex-specific single-chain antibody that regulates gene expression. Nucleic Acids Res. 37, 6716–6722 (2009).
Biffi, G., Tannahill, D., McCafferty, J. & Balasubramanian, S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat. Chem. 5, 182–186 (2013).
Lam, E. Y., Beraldi, D., Tannahill, D. & Balasubramanian, S. G-quadruplex structures are stable and detectable in human genomic DNA. Nat. Commun. 4, 1796 (2013).
Biffi, G., Di Antonio, M., Tannahill, D. & Balasubramanian, S. Visualization and selective chemical targeting of RNA G-quadruplex structures in the cytoplasm of human cells. Nat. Chem. 6, 75–80 (2014).
Henderson, A. et al. Detection of G-quadruplex DNA in mammalian cells. Nucleic Acids Res. 42, 860–869 (2014).
Dang, D. T. & Phan, A. T. Development of fluorescent protein probes specific for parallel DNA and RNA G-quadruplexes. Chembiochem 17, 42–45 (2016).
Ngo, K. H. et al. Cyclization of a G4-specific peptide enhances its stability and G-quadruplex binding affinity. Chem. Commun. 56, 1082–1084 (2020).
Zheng, K. W. et al. Detection of genomic G-quadruplexes in living cells using a small artificial protein. Nucleic Acids Res. 48, 11706–11720 (2020).
Liu, K. C. et al. Affinity-selected bicyclic peptide G-quadruplex ligands mimic a protein-like binding mechanism. J. Am. Chem. Soc. 142, 8367–8373 (2020).
Minard, A. et al. A short peptide that preferentially binds c-MYC G-quadruplex DNA. Chem. Commun. 56, 8940–8943 (2020).
Chen, J. et al. Selective discrimination and classification of G-quadruplex structures with a host–guest sensing array. Nat. Chem. 13, 488–495 (2021).
Chen, S. B. et al. Visualization of NRAS RNA G-quadruplex structures in cells with an engineered fluorogenic hybridization probe. J. Am. Chem. Soc. 138, 10382–10385 (2016).
Tan, D. J. Y., Das, P., Winnerdy, F. R., Lim, K. W. & Phan, A. T. Guanine anchoring: a strategy for specific targeting of a G-quadruplex using short PNA, LNA and DNA molecules. Chem. Commun. 56, 5897–5900 (2020).
He, Y. D. et al. Selective targeting of guanine-vacancy-bearing G-quadruplexes by G-quartet complementation and stabilization with a guanine–peptide conjugate. J. Am. Chem. Soc. 142, 11394–11403 (2020).
Cadoni, E., De Paepe, L., Manicardi, A. & Madder, A. Beyond small molecules: targeting G-quadruplex structures with oligonucleotides and their analogues. Nucleic Acids Res. 49, 6638–6659 (2021).
Jiang, W. et al. Mirror-image polymerase chain reaction. Cell Discov. 3, 17037 (2017).
Ling, J. J. et al. Mirror-image 5S ribonucleoprotein complexes. Angew. Chem. Int. Ed. 59, 3724–3731 (2020).
Wang, M. et al. Mirror-image gene transcription and reverse transcription. Chem 5, 848–857 (2019).
Sczepanski, J. T. & Joyce, G. F. A cross-chiral RNA polymerase ribozyme. Nature 515, 440–442 (2014).
Sefah, K., Shangguan, D., Xiong, X., O’Donoghue, M. B. & Tan, W. Development of DNA aptamers using Cell-SELEX. Nat. Protoc. 5, 1169–1185 (2010).
Kwok, C. K. & Balasubramanian, S. Targeted detection of G-Quadruplexes in Cellular RNAs. Angew. Chem. Int. Ed. 54, 6751–6754 (2015).
Kwok, C. K., Marsico, G., Sahakyan, A. B., Chambers, V. S. & Balasubramanian, S. rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome. Nat. Methods 13, 841–844 (2016).
Kikin, O., D’Antonio, L. & Bagga, P. S. QGRS Mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res. 34, W676–W682 (2006).
Garant, J. M., Perreault, J. P. & Scott, M. S. Motif independent identification of potential RNA G-quadruplexes by G4RNA screener. Bioinformatics 33, 3532–3537 (2017).
Brazda, V. et al. G4Hunter web application: a web server for G-quadruplex prediction. Bioinformatics 35, 3493–3495 (2019).
Yeung, P. Y. et al. Systematic evaluation and optimization of the experimental steps in RNA G-quadruplex structure sequencing. Sci. Rep. 9, 8091 (2019).
Kwok, C. K., Sahakyan, A. B. & Balasubramanian, S. Structural analysis using SHALiPE to reveal RNA G-quadruplex formation in human precursor microRNA. Angew. Chem. Int. Ed. 55, 8958–8961 (2016).
Kwok, C. K., Ding, Y., Tang, Y., Assmann, S. M. & Bevilacqua, P. C. Determination of in vivo RNA structure in low-abundance transcripts. Nat. Commun. 4, 2971 (2013).
Lyu, K., Chen, S. B., Chan, C. Y., Tan, J. H. & Kwok, C. K. Structural analysis and cellular visualization of APP RNA G-quadruplex. Chem. Sci. 10, 11095–11102 (2019).
Chan, K. L. et al. Structural analysis reveals the formation and role of RNA G-quadruplex structures in human mature microRNAs. Chem. Commun. 54, 10878–10881 (2018).
Chan, C. Y., Umar, M. I. & Kwok, C. K. Spectroscopic analysis reveals the effect of a single nucleotide bulge on G-quadruplex structures. Chem. Commun. 55, 2616–2619 (2019).

Development of RNA G-quadruplex (rG4)-targetingl-RNA aptamers by rG4-SELEX

Supplementary information

Reporting Summary

推荐阅读