Overview of Chemical Methods to Probe RNA Structure with Radionucleotides.
RNA
RNA cleavage
RNA conjugation
radionucleotides
reverse transcription
structure probing
Journal
Current protocols
ISSN: 2691-1299
Titre abrégé: Curr Protoc
Pays: United States
ID NLM: 101773894
Informations de publication
Date de publication:
May 2023
May 2023
Historique:
medline:
19
5
2023
pubmed:
17
5
2023
entrez:
17
5
2023
Statut:
ppublish
Résumé
Structural features of RNA play an important role in its capability to perform various functions in biological systems. To probe structural features, chemical probes are used to conjugate or cleave RNA at solvent-accessible sites, differentiating between flexible and constrained regions. These conjugates or cleaved products are then detected using reverse transcription (RT), where enzymatic RNA-dependent DNA primer extension is abruptly halted at the conjugation site or cleavage site. Here, we provide an overview of methods to probe RNA structure in vitro using radioactively labeled DNA primers, which provide a highly sensitive method to visualize RT stop sites with gel electrophoresis. © 2023 Wiley Periodicals LLC.
Substances chimiques
RNA
63231-63-0
DNA
9007-49-2
DNA Primers
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e781Informations de copyright
© 2023 Wiley Periodicals LLC.
Références
Adilakshmi, T., Lease, R. A., & Woodson, S. A. (2006). Hydroxyl radical footprinting in vivo: Mapping macromolecular structures with synchrotron radiation. Nucleic Acids Research, 34(8), e64. https://doi.org/10.1093/nar/gkl291
Bailey, J. N., Klement, J. F., & McAllister, W. T. (1983). Relationship between promoter structure and template specificities exhibited by the bacteriophage T3 and T7 RNA polymerases. Proceedings of the National Academy of Sciences, 80(10), 2814-2818. https://doi.org/10.1073/pnas.80.10.2814
Beckert, B., & Masquida, B. (2011). Synthesis of RNA by in vitro transcription. In H. Nielsen (Ed.), RNA: Methods and protocols (pp. 29-41). Humana Press. https://doi.org/10.1007/978-1-59745-248-9_3
Bevilacqua, P. C., & Assmann, S. M. (2018). Technique development for probing RNA structure in vivo and genome-wide. Cold Spring Harbor Perspectives in Biology, 10(10), a032250. https://doi.org/10.1101/cshperspect.a032250
Brown, J. E., Klement, J. F., & McAllister, W. T. (1986). Sequences of three promoters for the bacteriophage SP6 RNA polymerase. Nucleic Acids Research, 14(8), 3521-3526. https://doi.org/10.1093/nar/14.8.3521
Busan, S., Weidmann, C. A., Sengupta, A., & Weeks, K. M. (2019). Guidelines for SHAPE reagent choice and detection strategy for RNA structure probing studies. Biochemistry, 58(23), 2655-2664. https://doi.org/10.1021/acs.biochem.8b01218
Chan, D., Feng, C., Zhen, Y., Flynn, R. A., & Spitale, R. C. (2017). Comparative analysis reveals furoyl in vivo selective hydroxyl acylation analyzed by primer extension reagents form stable ribosyl ester adducts. Biochemistry, 56(13), 1811-1814. https://doi.org/10.1021/acs.biochem.7b00128
Das, R., Laederach, A., Pearlman, S. M., Herschlag, D., & Altman, R. B. (2005). SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA, 11(3), 344-354. https://doi.org/10.1261/rna.7214405
Eun, H.-M. (1996). 5-Phosphatases and polynucleotide kinase. In H.-M. Eun (Ed.), Enzymology primer for recombinant DNA technology (pp. 307-344). Academic Press. https://doi.org/10.1016/B978-012243740-3/50008-9
Evans, M. R., & Read, C. A. (1992). 32p 33p and 35S: Selecting a label for nucleic acid analysis. Nature, 358(6386), Article 6386. https://doi.org/10.1038/358520a0
Feng, C., Chan, D., Joseph, J., Muuronen, M., Coldren, W. H., Dai, N., Corrêa, I. R., Furche, F., Hadad, C. M., & Spitale, R. C. (2018). Light-activated chemical probing of nucleobase solvent accessibility inside cells. Nature Chemical Biology, 14(3), Article 3. https://doi.org/10.1038/nchembio.2548
Forconi, M., & Herschlag, D. (2009). Chapter 5-Metal ion-based RNA cleavage as a structural probe. In Methods in enzymology (Vol. 468, pp. 91-106). Academic Press. https://doi.org/10.1016/S0076-6879(09)68005-8
Grant, G. P. G., & Qin, P. Z. (2007). A facile method for attaching nitroxide spin labels at the 5′ terminus of nucleic acids†. Nucleic Acids Research, 35(10), e77. https://doi.org/10.1093/nar/gkm240
Huang, Q., & Fu, W.-L. (2005). Comparative analysis of the DNA staining efficiencies of different fluorescent dyes in preparative agarose gel electrophoresis. Clinical Chemistry and Laboratory Medicine (CCLM), 43(8), 841-842. https://doi.org/10.1515/CCLM.2005.141
Inoue, T., & Cech, T. R. (1985). Secondary structure of the circular form of the Tetrahymena rRNA intervening sequence: A technique for RNA structure analysis using chemical probes and reverse transcriptase. Proceedings of the National Academy of Sciences, 82(3), 648-652. https://doi.org/10.1073/pnas.82.3.648
Kwok, C. K., Tang, Y., Assmann, S. M., & Bevilacqua, P. C. (2015). The RNA structurome: Transcriptome-wide structure probing with next-generation sequencing. Trends in Biochemical Sciences, 40(4), 221-232. https://doi.org/10.1016/j.tibs.2015.02.005
Latham, J. A., & Cech, T. R. (1989). Defining the inside and outside of a catalytic RNA molecule. Science, 245(4915), 276-282. https://doi.org/10.1126/science.2501870
Lempereur, L., Nicoloso, M., Riehl, N., Ehresmann, C., Ehresmann, B., & Bachellerie, J.-P. (1985). Conformation of yeast 18S rRNA. Direct chemical probing of the 5′ domain in ribosomal subunits and in deproteinized RNA by reverse transcriptase mapping of dimethyl sulfate-accessible sites. Nucleic Acids Research, 13(23), 8339-8357. https://doi.org/10.1093/nar/13.23.8339
Mailler, E., Paillart, J.-C., Marquet, R., Smyth, R. P., & Vivet-Boudou, V. (2019). The evolution of RNA structural probing methods: From gels to next-generation sequencing. WIREs RNA, 10(2), e1518. https://doi.org/10.1002/wrna.1518
Metz, D. H., & Brown, G. L. (1969). Investigation of nucleic acid secondary structure by means of chemical modification with a carbodiimide reagent. II. Reaction between N-cyclohexyl-N’-β-(4-methylmorpholinium)ethylcarbodiimide and transfer ribonucleic acid. Biochemistry, 8(6), 2329-2342. https://doi.org/10.1021/bi00834a013
Mitchell, D., Assmann, S. M., & Bevilacqua, P. C. (2019). Probing RNA structure in vivo. Current Opinion in Structural Biology, 59, 151-158. https://doi.org/10.1016/j.sbi.2019.07.008
Mitchell, D., Ritchey, L. E., Park, H., Babitzke, P., Assmann, S. M., & Bevilacqua, P. C. (2018). Glyoxals as in vivo RNA structural probes of guanine base-pairing. RNA, 24(1), 114-124. https://doi.org/10.1261/rna.064014.117
Moazed, D., Stern, S., & Noller, H. F. (1986). Rapid chemical probing of conformation in 16 S ribosomal RNA and 30 S ribosomal subunits using primer extension. Journal of Molecular Biology, 187(3), 399-416. https://doi.org/10.1016/0022-2836(86)90441-9
Mortimer, S. A., Kidwell, M. A., & Doudna, J. A. (2014). Insights into RNA structure and function from genome-wide studies. Nature Reviews Genetics, 15(7), Article 7. https://doi.org/10.1038/nrg3681
Murphy, F. L., & Cech, T. R. (1994). GAAA tetraloop and conserved bulge stabilize tertiary structure of a group I intron domain. Journal of Molecular Biology, 236(1), 49-63. https://doi.org/10.1006/jmbi.1994.1117
Olmsted, J., & Kearns, D. R. (1977). Mechanism of ethidium bromide fluorescence enhancement on binding to nucleic acids. Biochemistry, 16(16), 3647-3654. https://doi.org/10.1021/bi00635a022
Peattie, D. A., & Gilbert, W. (1980). Chemical probes for higher-order structure in RNA. Proceedings of the National Academy of Sciences, 77(8), 4679-4682. https://doi.org/10.1073/pnas.77.8.4679
Peng, Y., Soper, T. J., & Woodson, S. A. (2012). RNase footprinting of protein binding sites on an mRNA target of small RNAs. In K. C. Keiler (Ed.), Bacterial regulatory RNA: Methods and protocols (pp. 213-224). Humana Press. https://doi.org/10.1007/978-1-61779-949-5_13
Rio, D. C. (2014). 5′-End labeling of RNA with [γ-32P]ATP and T4 polynucleotide kinase. Cold Spring Harbor Protocols, 2014(4), pdb.prot080739. https://doi.org/10.1101/pdb.prot080739
Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9(7), Article 7. https://doi.org/10.1038/nmeth.2089
Shelness, G. S., & Williams, D. L. (1985). Secondary structure analysis of apolipoprotein II mRNA using enzymatic probes and reverse transcriptase. Evaluation of primer extension for high resolution structure mapping of mRNA. Journal of Biological Chemistry, 260(14), 8637-8646. https://doi.org/10.1016/S0021-9258(17)39519-4
Solayman, M., Litfin, T., Singh, J., Paliwal, K., Zhou, Y., & Zhan, J. (2022). Probing RNA structures and functions by solvent accessibility: An overview from experimental and computational perspectives. Briefings in Bioinformatics, 23(3), bbac112. https://doi.org/10.1093/bib/bbac112
Spitale, R. C., & Incarnato, D. (2023). Probing the dynamic RNA structurome and its functions. Nature reviews. Genetics, 24(3), 178-196. https://doi.org/10.1038/s41576-022-00546-w
Strobel, E. J., Yu, A. M., & Lucks, J. B. (2018). High-throughput determination of RNA structures. Nature reviews. Genetics, 19(10), 615-634. https://doi.org/10.1038/s41576-018-0034-x
Tabor, S. (1987). Phosphatases and kinases. Current Protocols in Molecular Biology, 00(1), 3.10.1-3.10.5. https://doi.org/10.1002/0471142727.mb0310s00
Tijerina, P., Mohr, S., & Russell, R. (2007). DMS footprinting of structured RNAs and RNA-protein complexes. Nature Protocols, 2(10), 2608-2623. https://doi.org/10.1038/nprot.2007.380
Tullius, T. D., & Dombroski, B. A. (1986). Hydroxyl radical “footprinting”: High-resolution information about DNA-protein contacts and application to lambda repressor and Cro protein. Proceedings of the National Academy of Sciences, 83(15), 5469-5473. https://doi.org/10.1073/pnas.83.15.5469
Vlassov, V. V., Giege, R., & Ebel, J. P. (1980). The tertiary structure of yeast tRNAPhe in solution studied by phosphodiester bond modification with ethylnitrosourea. Febs Letters, 120(1), 12-16. https://doi.org/10.1016/0014-5793(80)81034-9
Walker, S. E., & Lorsch, J. (2013). Chapter twenty-Reverse transcriptase dideoxy sequencing of RNA. In J. Lorsch (Ed.), Methods in enzymology (Vol. 530, pp. 347-359). Academic Press. https://doi.org/10.1016/B978-0-12-420037-1.00020-8
Wang, P. Y., Sexton, A. N., Culligan, W. J., & Simon, M. D. (2019). Carbodiimide reagents for the chemical probing of RNA structure in cells. RNA, 25(1), 135-146. https://doi.org/10.1261/rna.067561.118
Xu, Z., & Culver, G. M. (2009). Chapter 8-chemical probing of RNA and RNA/protein complexes. In Methods in enzymology (Vol. 468, pp. 147-165). Academic Press. https://doi.org/10.1016/S0076-6879(09)68008-3
Ying, B.-W., Fourmy, D., & Yoshizawa, S. (2007). Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA. RNA, 13(11), 2042-2050. https://doi.org/10.1261/rna.637907
Ziehler, W. A., & Engelke, D. R. (2000). Probing RNA Structure with Chemical Reagents and Enzymes. Current Protocols in Nucleic Acid Chemistry, 00(1), 6.1.1-6.1.21. https://doi.org/10.1002/0471142700.nc0601s00