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Chemo-enzymatic synthesis of [2-13C, 7-15 N]-ATP for facile NMR analysis of RNA

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Abstract

We report the efficient chemo-enzymatic synthesis of an [2-13C, 7-15N]-adenosine 5′-triphosphate building block for incorporation into RNA via T7 RNA polymerase-based in vitro transcription. Such atom-specific labeling alleviates spectral crowding and simplifies the analysis of large RNAs by solution NMR spectroscopy. Applications to probe adenosine C2 and N7 sites in a large 61 nucleotide viral RNA with two- and three-dimensional NMR experiments are demonstrated.

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References

  1. Fürtig B, Richter C, Wöhnert J, Schwalbe H (2003) ChemBioChem 4:936

    Article  PubMed  CAS  Google Scholar 

  2. Marušič M, Schlagnitweit J, Petzold K (2019) ChemBioChem 20:2685

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  3. Dethoff EA, Chugh J, Mustoe AM, Al-Hashimi HM (2012) Nature 482:322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Ganser LR, Kelly ML, Herschlag D, Al-Hashimi HM (2019) Nat Rev Mol Cell Biol 20:474

    Article  CAS  PubMed  Google Scholar 

  5. Keyhani S, Goldau T, Blümler A, Heckel A, Schwalbe H (2018) Angew Chem Int Ed 57:12017

    Article  CAS  Google Scholar 

  6. Scott LG, Hennig M (2016) Methods Enzymol 566:59

    Article  CAS  PubMed  Google Scholar 

  7. Dayie KT (2008) Int J Mol Sci 9:1214

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Becette O, Olenginski LT, Dayie TK (2019) Molecules 24:3476

    Article  CAS  PubMed Central  Google Scholar 

  9. Asadi-Atoi P, Barraud P, Tisne C, Kellner S (2019) Biol Chem 400:847

    Article  CAS  PubMed  Google Scholar 

  10. Le MT, Brown RE, Simon AE, Dayie TK (2015) Methods Enzymol 565:495

    Article  CAS  PubMed  Google Scholar 

  11. Alvarado LJ, Longhini AP, Leblanc RM, Chen B, Kreutz C, Dayie TK (2014) Methods Enzymol 549:133

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Lu K, Miyazaki Y, Summers MF (2010) J Biomol NMR 46:113

    Article  CAS  PubMed  Google Scholar 

  13. Liu Y, Holmstrom E, Zhang J, Yu P, Wang J, Dyba MA, Chen D, Ying J, Lockett S, Nesbitt DJ, Ferré-D’Amaré AR, Sousa R, Stagno JR, Wang YX (2015) Nature 522:368

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Batey RT, Inada M, Kujawinski E, Puglisi JD, Williamson JR (1992) Nucleic Acids Res 20:4515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Wyatt JR, Chastain M, Puglisi JD (1991) Biotechniques 11:764

    CAS  PubMed  Google Scholar 

  16. Nikonowicz EP, Sirr A, Legault P, Jucker FM, Baer LM, Pardi A (1992) Nucleic Acids Res 20:4507

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Milligan JF, Uhlenbeck OC (1989) Methods Enzymol 180:51

    Article  CAS  PubMed  Google Scholar 

  18. Thakur CS, Dayie TK (2012) J Biomol NMR 52:65

    Article  CAS  PubMed  Google Scholar 

  19. Thakur CS, Sama JN, Jackson ME, Chen B, Dayie TK (2010) J Biomol NMR 48:179

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Johnson JE, Julien KR, Hoogstraten CG (2006) J Biomol NMR 35:261

    Article  CAS  PubMed  Google Scholar 

  21. Hoffman DW, Holland JA (1995) Nucleic Acids Res 23:3361

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Schultheisz HL, Szymczyna BR, Scott LG, Williamson JR (2008) ACS Chem Biol 3:499

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Schultheisz HL, Szymczyna BR, Scott LG, Williamson JR (2011) J Am Chem Soc 133:297

    Article  CAS  PubMed  Google Scholar 

  24. Tolbert TJ, Williamson JR (1996) J Am Chem Soc 118:7929

    Article  CAS  Google Scholar 

  25. Leblanc RM, Longhini AP, Le Grice SFJ, Johnson BA, Dayie TK (2017) Nucleic Acids Res 45:146

    Article  CAS  Google Scholar 

  26. Nam H, Becette O, Leblanc RM, Oh D, Case DA, Dayie TK (2020) J Biomol NMR 74:321

    Article  CAS  PubMed  Google Scholar 

  27. Longhini AP, Leblanc RM, Becette O, Salguero C, Wunderlich CH, Johnson BA, Dsouza VM, Kreutz C, Dayie TK (2015) Nucleic Acids Res 44:52

    Article  Google Scholar 

  28. Alvarado LJ, LeBlanc RM, Longhini AP, Keane SC, Jain N, Yildiz ZF, Tolbert BS, D’Souza VM, Summers MF, Kreutz C, Dayie TK (2014) ChemBioChem 15:1573

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Arthur PK, Alvarado LJ, Dayie TK (2011) Protein Expr Purif 76:229

    Article  CAS  PubMed  Google Scholar 

  30. Traube W (1904) Liebig’s Ann Chem 331:64

    Article  CAS  Google Scholar 

  31. Ouwerkerk N, van Boom J, Lugtenburg J, Raap J (2002) Eur J Org Chem 2002:2356

    Article  Google Scholar 

  32. Pagano AR, Lajewski WM, Jones RA (1995) J Am Chem Soc 117:11669

    Article  CAS  Google Scholar 

  33. Sethi SK, Gupta SP, Jenkins EE, Whitehead CW, Townsend LB, McCloskey JA (1982) J Am Chem Soc 104:3349

    Article  CAS  Google Scholar 

  34. Kremser J, Strebitzer E, Plangger R, Juen MA, Nußbaumer F, Glasner H, Breuker K, Kreutz C (2017) ChemComm 53:12938

    CAS  Google Scholar 

  35. SantaLucia J, Shen LX, Cai Z, Lewis H, Tinoco I (1995) Nucleic Acids Res 23:4913

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Battaglia U, Long JE, Searle MS, Moody CJ (2011) Org Biomol Chem 9:2227

    Article  CAS  PubMed  Google Scholar 

  37. Gaffney BL, Rung PP, Jones RA (1990) J Am Chem Soc 112:6748

    Article  CAS  Google Scholar 

  38. Yamazaki T, Muhandiram R, Kay LE (1994) J Am Chem Soc 116:8266

    Article  CAS  Google Scholar 

  39. Flodell S, Petersen M, Girard F, Zdunek J, Kidd-Ljunggren K, Rgen Schleucher J, Wijmenga S (2006) Nucleic Acids Res 34:4449

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Lee WM (1997) N Engl J Med 337:1733

    Article  CAS  PubMed  Google Scholar 

  41. Bendich A, Russell PJ, Fox JJ (1954) J Am Chem Soc 76:6073

    Article  CAS  Google Scholar 

  42. Nardi-Schreiber A, Sapir G, Gamliel A, Kakhlon O, Sosna J, Gomori JM, Meiner V, Lossos A, Katz-Brull R (2017) ChemComm 53:9121

    CAS  Google Scholar 

  43. Wijmenga SS, Van Buuren BNM (1998) Prog Nucl Magn Reson Spectrosc 32:287

    Article  CAS  Google Scholar 

  44. Palmer AG (2004) Chem Rev 104:3623

    Article  CAS  PubMed  Google Scholar 

  45. Hansen AL, Al-Hashimi HM (2007) J Am Chem Soc 129:16072

    Article  CAS  PubMed  Google Scholar 

  46. Dieckmann T, Feigon J (1997) J Biomol NMR 9:259

    Article  CAS  PubMed  Google Scholar 

  47. Hoffman DW (2000) J Biomol NMR 16:165

    Article  CAS  PubMed  Google Scholar 

  48. Hyberts SG, Takeuchi K, Wagner G (2010) J Am Chem Soc 132:2145

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Lakomek NA, Kaufman JD, Stahl SJ, Louis JM, Grishaev A, Wingfield PT, Bax A (2013) Angew Chem Int Ed 52:3911

    Article  CAS  Google Scholar 

  50. Johnson BA, Blevins RA (1994) J Biomol NMR 4:603

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

This research was financially supported by NSF for labeling work (1808705 to T.K.D.). We acknowledge Dr. Serge Beaucage (FDA) for hosting L.T.O. for the synthetic work, Joshua Wilhide (UMBC) for mass spectrometric analysis, and Dr. Jeffery Davis (UMD) for helpful comments.

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  1. Center for Biomolecular Structure and Organization, Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA

    Lukasz T. Olenginski & Theodore K. Dayie

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  1. Lukasz T. Olenginski
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  2. Theodore K. Dayie
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Correspondence to Theodore K. Dayie.

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Olenginski, L.T., Dayie, T.K. Chemo-enzymatic synthesis of [2-13C, 7-15 N]-ATP for facile NMR analysis of RNA. Monatsh Chem 151, 1467–1473 (2020). https://doi.org/10.1007/s00706-020-02667-6

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