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A fast selenium derivatization strategy for crystallization and phasing of RNA structures.

Olieric V, Rieder U, Lang K, Serganov A, Schulze-Briese C, Micura R, Dumas P, Ennifar E
RNA 15 707-15 (2009)
Related entries: 3dvz, 3dw4, 3dw6, 3dw7

Cited: 31 times
EuropePMC logo PMID: 19228585

Abstract

Site-specific 2'-methylseleno RNA labeling is a promising tool for tackling the phase problem in RNA crystallography. We have developed an efficient strategy for crystallization and structure determination of RNA and RNA/protein complexes based on preliminary crystallization screening of 2'-OCH(3)-modified RNA sequences, prior to the replacement of 2'-OCH(3) groups with their 2'-SeCH(3) counterparts. The method exploits the similar crystallization properties of 2'-OCH(3)- and 2'-SeCH(3)-modified RNAs and has been successfully validated for two test cases. In addition, our data show that 2'-SeCH(3)-modified RNA have an increased resistance to X-ray radiolysis in comparison with commonly used 5-halogen-modified RNA, which permits collection of experimental electron density maps of remarkable quality.

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Reviews citing this publication (5)

  1. Chemical RNA modifications for studies of RNA structure and dynamics. Wachowius F, Höbartner C. Chembiochem 11 469-480 (2010)
  2. Nucleic acid X-ray crystallography via direct selenium derivatization. Lin L, Sheng J, Huang Z. Chem Soc Rev 40 4591-4602 (2011)
  3. Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies. Sheng J, Huang Z. Chem Biodivers 7 753-785 (2010)
  4. New molecular engineering approaches for crystallographic studies of large RNAs. Zhang J, Ferré-D'Amaré AR. Curr Opin Struct Biol 26 9-15 (2014)
  5. Specific labeling: An effective tool to explore the RNA world. Liu Y, Sousa R, Wang YX. Bioessays 38 192-200 (2016)

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  1. 2'-Azido RNA, a versatile tool for chemical biology: synthesis, X-ray structure, siRNA applications, click labeling. Fauster K, Hartl M, Santner T, Aigner M, Kreutz C, Bister K, Ennifar E, Micura R. ACS Chem Biol 7 581-589 (2012)
  2. Computer Folding of RNA Tetraloops: Identification of Key Force Field Deficiencies. Kührová P, Best RB, Bottaro S, Bussi G, Šponer J, Otyepka M, Banáš P. J Chem Theory Comput 12 4534-4548 (2016)
  3. LOOP IIId of the HCV IRES is essential for the structural rearrangement of the 40S-HCV IRES complex. Angulo J, Ulryck N, Deforges J, Chamond N, Lopez-Lastra M, Masquida B, Sargueil B. Nucleic Acids Res 44 1309-1325 (2016)
  4. Molecular mechanism of preQ1 riboswitch action: a molecular dynamics study. Banáš P, Sklenovský P, Wedekind JE, Šponer J, Otyepka M. J Phys Chem B 116 12721-12734 (2012)
  5. Surprising base pairing and structural properties of 2'-trifluoromethylthio-modified ribonucleic acids. Košutić M, Jud L, Da Veiga C, Frener M, Fauster K, Kreutz C, Ennifar E, Micura R. J Am Chem Soc 136 6656-6663 (2014)
  6. Understanding the Sequence Preference of Recurrent RNA Building Blocks using Quantum Chemistry: The Intrastrand RNA Dinucleotide Platform. Mládek A, Sponer JE, Kulhánek P, Lu XJ, Olson WK, Sponer J. J Chem Theory Comput 8 335-347 (2012)
  7. Applications of PLOR in labeling large RNAs at specific sites. Liu Y, Yu P, Dyba M, Sousa R, Stagno JR, Wang YX. Methods 103 4-10 (2016)
  8. Role of a ribosomal RNA phosphate oxygen during the EF-G-triggered GTP hydrolysis. Koch M, Flür S, Kreutz C, Ennifar E, Micura R, Polacek N. Proc Natl Acad Sci U S A 112 E2561-8 (2015)
  9. Base pairs and pseudo pairs observed in RNA-ligand complexes. Kondo J, Westhof E. J Mol Recognit 23 241-252 (2010)
  10. Facile synthesis of nucleoside 5'-(α-P-seleno)-triphosphates and phosphoroselenoate RNA transcription. Lin L, Caton-Williams J, Kaur M, Patino AM, Sheng J, Punetha J, Huang Z. RNA 17 1932-1938 (2011)
  11. Screening mutant libraries of T7 RNA polymerase for candidates with increased acceptance of 2'-modified nucleotides. Siegmund V, Santner T, Micura R, Marx A. Chem Commun (Camb) 48 9870-9872 (2012)
  12. Structural insights into synthetic ligands targeting A-A pairs in disease-related CAG RNA repeats. Mukherjee S, Błaszczyk L, Rypniewski W, Falschlunger C, Micura R, Murata A, Dohno C, Nakatani K, Kiliszek A. Nucleic Acids Res 47 10906-10913 (2019)
  13. Heavy-atom labeling of RNA by PLOR for de novo crystallographic phasing. Stagno JR, Yu P, Dyba MA, Wang YX, Liu Y. PLoS One 14 e0215555 (2019)
  14. 2'-O-Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy. Himmelstoß M, Erharter K, Renard E, Ennifar E, Kreutz C, Micura R. Chem Sci 11 11322-11330 (2020)
  15. Impact of 3-deazapurine nucleobases on RNA properties. Bereiter R, Himmelstoß M, Renard E, Mairhofer E, Egger M, Breuker K, Kreutz C, Ennifar E, Micura R. Nucleic Acids Res 49 4281-4293 (2021)
  16. 1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis. Bereiter R, Renard E, Breuker K, Kreutz C, Ennifar E, Micura R. J Am Chem Soc 144 10344-10352 (2022)
  17. Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA. Mair S, Erharter K, Renard E, Brillet K, Brunner M, Lusser A, Kreutz C, Ennifar E, Micura R. Nucleic Acids Res 50 6038-6051 (2022)
  18. Advances in chaperone-assisted RNA crystallography using synthetic antibodies. Banna HA, Das NK, Ojha M, Koirala D. BBA Adv 4 100101 (2023)
  19. Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy. Li M, Teng B, Lu W, Zhang JZ. J Mol Model 26 31 (2020)
  20. Cryo neutron crystallography demonstrates influence of RNA 2'-OH orientation on conformation, sugar pucker and water structure. Harp JM, Lybrand TP, Pallan PS, Coates L, Sullivan B, Egli M. Nucleic Acids Res 50 7721-7738 (2022)
  21. Occurrence and stability of anion-π interactions between phosphate and nucleobases in functional RNA molecules. Chawla M, Kalra K, Cao Z, Cavallo L, Oliva R. Nucleic Acids Res 50 11455-11469 (2022)
  22. On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective. Piña MLN, Bauzá A. Int J Mol Sci 24 13035 (2023)
  23. Robust synthesis of 2'-azido modified RNA from 2'-amino precursors by diazotransfer reaction. Moreno S, Ramos Pittol JM, Hartl M, Micura R. Org Biomol Chem 20 7845-7850 (2022)
  24. Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations. Mlýnský V, Kührová P, Stadlbauer P, Krepl M, Otyepka M, Banáš P, Šponer J. J Chem Theory Comput 19 8423-8433 (2023)


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