References
- Montange RK, Batey RT. Riboswitches: emerging themes in RNA structure and function. Annu Rev Biophys. 2008;37:117–133.
- Watters KE, Abbott TR, Lucks JB. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq. Nucleic Acids Res. 2016;44:e12.
- Piao M, Sun L, Zhang QC. RNA regulations and functions decoded by transcriptome-wide RNA structure probing. Genomics Proteomics Bioinformatics. 2017;15:267–278.
- Asadi-Atoi P, Barraud P, Tisne C, et al. Benefits of stable isotope labeling in RNA analysis. Biol Chem. 2019;400:847–865.
- Marchanka A, Kreutz C, Carlomagno T. Isotope labeling for studying RNA by solid-state NMR spectroscopy. J Biomol NMR. 2018;71:151–164.
- Scott LG, Hennig M. 19F-site-specific-labeled nucleotides for nucleic acid structural analysis by NMR. Methods Enzymol. 2016;566:59–87.
- LeBlanc RM, Longhini AP, Le Grice SFJ, et al. Combining asymmetric 13C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment. Nucleic Acids Res. 2017;45:e146.
- Stagno JR, Yu P, Dyba MA, et al. Heavy-atom labeling of RNA by PLOR for de novo crystallographic phasing. PLoS One. 2019;14:e0215555.
- Sheng J, Huang Z. Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies. Chem Biodivers. 2010;7:753–785.
- Golden BL, Gooding AR, Podell ER, et al. X-ray crystallography of large RNAs: heavy-atom derivatives by RNA engineering. RNA. 1996;2:1295–1305.
- van der Feltz C, Hoskins AA. Methodologies for studying the spliceosome’s RNA dynamics with single-molecule FRET. Methods. 2017;125:45–54.
- Boerneke MA, Hermann T. Conformational flexibility of viral RNA switches studied by FRET. Methods. 2015;91:35–39.
- Walter NG. Probing RNA structural dynamics and function by fluorescence resonance energy transfer (FRET). Curr Protoc Nucleic Acid Chem. 2003. Chapter 11:Unit11.10:1–23.
- Selvam C, Mutisya D, Prakash S, et al. Therapeutic potential of chemically modified siRNA: recent trends. Chem Biol Drug Des. 2017;90:665–678.
- Ku SH, Jo SD, Lee YK, et al. Chemical and structural modifications of RNAi therapeutics. Adv Drug Deliv Rev. 2016;104:16–28.
- Becette O, Olenginski LT, Dayie TK. Solid-phase chemical synthesis of stable isotope-labeled RNA to aid structure and dynamics studies by NMR spectroscopy. Molecules. 2019;24:e3476.
- Paredes E, Evans M, Das SR. RNA labeling, conjugation and ligation. Methods. 2011;54:251–259.
- Milligan JF, Groebe DR, Witherell GW, et al. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 1987;15:8783–8798.
- Milligan JF, Uhlenbeck OC. Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol. 1989;180:51–62.
- Liu Y, Holmstrom E, Yu P, et al. Incorporation of isotopic, fluorescent, and heavy-atom-modified nucleotides into RNAs by position-selective labeling of RNA. Nat Protoc. 2018;13:987–1005.
- Liu Y, Holmstrom E, Zhang J, et al. Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature. 2015;522:368–372.
- Tang GQ, Roy R, Bandwar RP, et al. Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase. Proc Natl Acad Sci USA. 2009;106:22175–22180.
- Steitz TA. The structural changes of T7 RNA polymerase from transcription initiation to elongation. Curr Opin Struct Biol. 2009;19:683–690.
- Cheetham GM, Steitz TA. Structure of a transcribing T7 RNA polymerase initiation complex. Science. 1999;286:2305–2309.
- Brieba LG, Sousa R. T7 promoter release mediated by DNA scrunching. Embo J. 2001;20:6826–6835.
- Mandal M, Breaker RR. Gene regulation by riboswitches. Nat Rev Mol Cell Biol. 2004;5:451–463.
- McCown PJ, Corbino KA, Stav S, et al. Riboswitch diversity and distribution. RNA. 2017;23:995–1011.
- Zhu B, Hernandez A, Tan M, et al. Synthesis of 2ʹ-Fluoro RNA by Syn5 RNA polymerase. Nucleic Acids Res. 2015;43:e94.