Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies

Overview

Journal Molecules

Publisher MDPI

Specialty Biology

Date 2021 Sep 28

PMID 34577051

Citations 7

Authors

Lukasz T Olenginski

Kehinde M Taiwo

Regan M LeBlanc

Theodore K Dayie

Affiliations

Soon will be listed here.

Abstract

RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and limitations of various methods used to obtain isotope-labeled RNA building blocks and how they are used to prepare isotope-labeled RNA for NMR structure and dynamics studies.

Citing Articles

Gram-scale enzymatic synthesis of 2'-deoxyribonucleoside analogues using nucleoside transglycosylase-2.

Salihovic A, Ascham A, Taladriz-Sender A, Bryson S, Withers J, McKean I Chem Sci. 2024; .

PMID: 39234214 PMC: 11368039. DOI: 10.1039/d4sc04938a.

Mapping endocrine networks by stable isotope tracing.

Andrew R, Stimson R Curr Opin Endocr Metab Res. 2024; 26:100381.

PMID: 39185272 PMC: 11344083. DOI: 10.1016/j.coemr.2022.100381.

RNA structure determination: From 2D to 3D.

Deng J, Fang X, Huang L, Li S, Xu L, Ye K Fundam Res. 2024; 3(5):727-737.

PMID: 38933295 PMC: 11197651. DOI: 10.1016/j.fmre.2023.06.001.

Extending the toolbox for RNA biology with SegModTeX: a polymerase-driven method for site-specific and segmental labeling of RNA.

Haslecker R, Pham V, Glanzer D, Kreutz C, Kwaku Dayie T, DSouza V Nat Commun. 2023; 14(1):8422.

PMID: 38110450 PMC: 10728113. DOI: 10.1038/s41467-023-44254-3.

Syntheses of Specifically N-Labeled Adenosine and Guanosine.

Jones R, Gaffney B Curr Protoc. 2022; 2(12):e612.

PMID: 36533886 PMC: 10107765. DOI: 10.1002/cpz1.612.

References

LeBlanc R, Longhini A, Le Grice S, Johnson B, Dayie T . Combining asymmetric 13C-labeling and isotopic filter/edit NOESY: a novel strategy for rapid and logical RNA resonance assignment. Nucleic Acids Res. 2017; 45(16):e146. PMC: 5766159. DOI: 10.1093/nar/gkx591. View

Liu Y, Holmstrom E, Zhang J, Yu P, Wang J, Dyba M . Synthesis and applications of RNAs with position-selective labelling and mosaic composition. Nature. 2015; 522(7556):368-72. PMC: 4800989. DOI: 10.1038/nature14352. View

Lu K, Miyazaki Y, Summers M . Isotope labeling strategies for NMR studies of RNA. J Biomol NMR. 2009; 46(1):113-25. PMC: 2797625. DOI: 10.1007/s10858-009-9375-2. View

Keyhani S, Goldau T, Blumler A, Heckel A, Schwalbe H . Chemo-Enzymatic Synthesis of Position-Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy. Angew Chem Int Ed Engl. 2018; 57(37):12017-12021. DOI: 10.1002/anie.201807125. View

Shallop A, Gaffney B, Jones R . Use of both direct and indirect 13C tags for probing nitrogen interactions in hairpin ribozyme models by 15N NMR. Nucleosides Nucleotides Nucleic Acids. 2004; 23(1-2):273-80. DOI: 10.1081/ncn-120027834. View

Krupp G . RNA synthesis: strategies for the use of bacteriophage RNA polymerases. Gene. 1988; 72(1-2):75-89. DOI: 10.1016/0378-1119(88)90129-1. View

Lunn F, MacDonnell J, Bearne S . Structural requirements for the activation of Escherichia coli CTP synthase by the allosteric effector GTP are stringent, but requirements for inhibition are lax. J Biol Chem. 2007; 283(4):2010-20. DOI: 10.1074/jbc.M707803200. View

Gardiner K, Marsh T, Pace N, Altman S . The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell. 1983; 35(3 Pt 2):849-57. DOI: 10.1016/0092-8674(83)90117-4. View

Weickhmann A, Keller H, Duchardt-Ferner E, Strebitzer E, Juen M, Kremser J . NMR resonance assignments for the SAM/SAH-binding riboswitch RNA bound to S-adenosylhomocysteine. Biomol NMR Assign. 2018; 12(2):329-334. DOI: 10.1007/s12104-018-9834-3. View

10.

Shiba Y, Masuda H, Watanabe N, Ego T, Takagaki K, Ishiyama K . Chemical synthesis of a very long oligoribonucleotide with 2-cyanoethoxymethyl (CEM) as the 2'-O-protecting group: structural identification and biological activity of a synthetic 110mer precursor-microRNA candidate. Nucleic Acids Res. 2007; 35(10):3287-96. PMC: 1904286. DOI: 10.1093/nar/gkm202. View

11.

SantaLucia Jr J, Shen L, Cai Z, Lewis H, Tinoco Jr I . Synthesis and NMR of RNA with selective isotopic enrichment in the bases. Nucleic Acids Res. 1995; 23(23):4913-21. PMC: 307483. DOI: 10.1093/nar/23.23.4913. View

12.

Nelissen F, van Gammeren A, Tessari M, Girard F, Heus H, Wijmenga S . Multiple segmental and selective isotope labeling of large RNA for NMR structural studies. Nucleic Acids Res. 2008; 36(14):e89. PMC: 2504312. DOI: 10.1093/nar/gkn397. View

13.

Seffernick J, Lindert S . Hybrid methods for combined experimental and computational determination of protein structure. J Chem Phys. 2020; 153(24):240901. PMC: 7773420. DOI: 10.1063/5.0026025. View

14.

Arthur P, Alvarado L, Dayie T . Expression, purification and analysis of the activity of enzymes from the pentose phosphate pathway. Protein Expr Purif. 2010; 76(2):229-37. PMC: 4125576. DOI: 10.1016/j.pep.2010.11.008. View

15.

LeBlanc R, Longhini A, Tugarinov V, Dayie T . NMR probing of invisible excited states using selectively labeled RNAs. J Biomol NMR. 2018; 71(3):165-172. DOI: 10.1007/s10858-018-0184-3. View

16.

Coleman T, Wang G, Huang F . Superior 5' homogeneity of RNA from ATP-initiated transcription under the T7 phi 2.5 promoter. Nucleic Acids Res. 2004; 32(1):e14. PMC: 373309. DOI: 10.1093/nar/gnh007. View

17.

Barnwal R, Yang F, Varani G . Applications of NMR to structure determination of RNAs large and small. Arch Biochem Biophys. 2017; 628:42-56. PMC: 5555312. DOI: 10.1016/j.abb.2017.06.003. View

18.

Keane S, Heng X, Lu K, Kharytonchyk S, Ramakrishnan V, Carter G . RNA structure. Structure of the HIV-1 RNA packaging signal. Science. 2015; 348(6237):917-21. PMC: 4492308. DOI: 10.1126/science.aaa9266. View

19.

Gaffney B, Jones R . Regioselective 2'-silylation of purine ribonucleosides for phosphoramidite RNA synthesis. Curr Protoc Nucleic Acid Chem. 2008; Chapter 2:Unit 2.8. DOI: 10.1002/0471142700.nc0208s06. View

20.

Krieg P, Melton D . In vitro RNA synthesis with SP6 RNA polymerase. Methods Enzymol. 1987; 155:397-415. DOI: 10.1016/0076-6879(87)55027-3. View