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Isotope Labeling and Segmental Labeling of Larger RNAs for NMR Structural Studies

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Book cover Isotope labeling in Biomolecular NMR

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 992))

Abstract

NMR spectroscopy has become substantial in the elucidation of RNA structures and their complexes with other nucleic acids, proteins or small molecules. Almost half of the RNA structures deposited in the Protein Data Bank were determined by NMR spectroscopy, whereas NMR accounts for only 11% for proteins. Recent improvements in isotope labeling of RNA have strongly contributed to the high impact of NMR in RNA structure determination. In this book chapter, we review the advances in isotope labeling of RNA focusing on larger RNAs. We start by discussing several ways for the production and purification of large quantities of pure isotope labeled RNA. We continue by reviewing different strategies for selective deuteration of nucleotides. Finally, we present a comparison of several approaches for segmental isotope labeling of RNA. Selective deuteration of nucleotides in combination with segmental isotope labeling is paving the path for studying RNAs of ever increasing size.

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References

  1. Sharp PA (2009) The centrality of RNA. Cell 136:577–580

    Article  PubMed  CAS  Google Scholar 

  2. Mattick JS (2011) The central role of RNA in human development and cognition. FEBS Lett 585:1600–1616

    Article  PubMed  CAS  Google Scholar 

  3. Varani G, Aboulela F, Allain FHT (1996) NMR investigation of RNA structure. Prog Nucl Magn Reson Spectrosc 29:51–127

    Article  CAS  Google Scholar 

  4. Wijmenga SS, van Buuren BNM (1998) The use of NMR methods for conformational studies of nucleic acids. Prog Nucl Magn Reson Spectrosc 32:287–387

    Article  CAS  Google Scholar 

  5. Dominguez C, Schubert M, Duss O, Ravindranathan S, Allain FHT (2011) Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy. Prog Nucl Magn Reson Spectrosc 58:1–61

    Article  PubMed  CAS  Google Scholar 

  6. Lukavsky PJ, Puglisi JD (2005) Structure determination of large biological RNAs. Methods Enzymol 394:399–416

    Article  PubMed  CAS  Google Scholar 

  7. Tzakos AG, Grace CRR, Lukavsky PJ, Riek R (2006) NMR techniques for very large proteins and RNAs in solution. Annu Rev Biophys Biomol Struct 35:319–342

    Article  PubMed  CAS  Google Scholar 

  8. Zuo XB, Wang JB, Foster TR, Schwieters CD, Tiede DM, Butcher SE, Wang YX (2008) Global molecular structure and interfaces: refining an RNA: RNA complex structure using solution X-ray scattering data. J Am Chem Soc 130:3292–3293

    Article  PubMed  CAS  Google Scholar 

  9. Hudson BP, Martinez-Yamout MA, Dyson HJ, Wright PE (2004) Recognition of the mRNA AU-rich element by the zinc finger domain of TIS11d. Nat Struct Mol Biol 11:257–264

    Article  PubMed  CAS  Google Scholar 

  10. Perez-Canadillas JM (2006) Grabbing the message: structural basis of mRNA 3′UTR recognition by Hrp1. EMBO J 25:3167–3178

    Article  PubMed  CAS  Google Scholar 

  11. Ohtsuki T, Vinayak R, Watanabe Y, Kita K, Kawai G, Watanabe K (1996) Automated chemical synthesis of biologically active tRNA having a sequence corresponding to Ascaris suum mitochondrial tRNA(Met) toward NMR measurements. J Biochem 120:1070–1073

    Article  PubMed  CAS  Google Scholar 

  12. Scaringe SA, Wincott FE, Caruthers MH (1998) Novel RNA synthesis method using 5′-O-silyl-2′-O-orthoester protecting groups. J Am Chem Soc 120:11820–11821

    Article  CAS  Google Scholar 

  13. Pitsch S, Weiss PA (2002) Chemical synthesis of RNA sequences with 2′-O-[(triisopropylsilyl)oxy]methyl-protected ribonucleoside phosphoramidites. Curr Protoc Nucleic Acid Chem Chapter 3:Unit 3.8

    Google Scholar 

  14. Ramos A, Varani G (1998) A new method to detect long-range protein-RNA contacts: NMR detection of electron-proton relaxation induced by nitroxide spin-labeled RNA. J Am Chem Soc 120:10992–10993

    Article  CAS  Google Scholar 

  15. Wenter P, Reymond L, Auweter SD, Allain FH, Pitsch S (2006) Short, synthetic and selectively 13C-labeled RNA sequences for the NMR structure determination of protein-RNA complexes. Nucleic Acids Res 34:e79

    Article  PubMed  Google Scholar 

  16. Oberstrass FC, Auweter SD, Erat M, Hargous Y, Henning A, Wenter P, Reymond L, Amir-Ahmady B, Pitsch S, Black DL, Allain FH (2005) Structure of PTB bound to RNA: specific binding and implications for splicing regulation. Science 309:2054–2057

    Article  PubMed  CAS  Google Scholar 

  17. Auweter SD, Fasan R, Reymond L, Underwood JG, Black DL, Pitsch S, Allain FH (2006) Molecular basis of RNA recognition by the human alternative splicing factor Fox-1. EMBO J 25:163–173

    Article  PubMed  CAS  Google Scholar 

  18. Oberstrass FC, Lee A, Stefl R, Janis M, Chanfreau G, Allain FH (2006) Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. Nat Struct Mol Biol 13:160–167

    Article  PubMed  CAS  Google Scholar 

  19. Skrisovska L, Bourgeois CF, Stefl R, Grellscheid SN, Kister L, Wenter P, Elliott DJ, Stevenin J, Allain FH (2007) The testis-specific human protein RBMY recognizes RNA through a novel mode of interaction. EMBO Rep 8:372–379

    Article  PubMed  CAS  Google Scholar 

  20. Dominguez C, Fisette JF, Chabot B, Allain FH-T (2010) Structural basis of G-tract recognition and encaging by hnRNP F quasi RRMs. Nat Struct Mol Biol 17:853–861

    Article  PubMed  CAS  Google Scholar 

  21. Hobartner C, Rieder R, Kreutz C, Puffer B, Lang K, Polonskaia A, Serganov A, Micura R (2005) Syntheses of RNAs with up to 100 nucleotides containing site-specific 2′-methylseleno labels for use in X-ray crystallography. J Am Chem Soc 127:12035–12045

    Article  PubMed  Google Scholar 

  22. Rieder R, Lang K, Graber D, Micura R (2007) Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control. Chembiochem 8:896–902

    Article  PubMed  CAS  Google Scholar 

  23. Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC (1987) Oligoribonucleotide synthesis using T7 RNA-polymerase and synthetic DNA templates. Nucleic Acids Res 15:8783–8798

    Article  PubMed  CAS  Google Scholar 

  24. Gurevich VV, Pokrovskaya ID, Obukhova TA, Zozulya SA (1991) Preparative in vitro messenger-RNA synthesis using Sp6 and T7 RNA-polymerases. Anal Biochem 195:207–213

    Article  PubMed  CAS  Google Scholar 

  25. Pokrovskaya ID, Gurevich VV (1994) In-vitro transcription – preparative RNA yields in analytical scale reactions. Anal Biochem 220:420–423

    Article  PubMed  CAS  Google Scholar 

  26. Price SR, Ito N, Oubridge C, Avis JM, Nagai K (1995) Crystallization of RNA-protein complexes.1. Methods for the large-scale preparation of RNA suitable for crystallographic studies. J Mol Biol 249:398–408

    Article  PubMed  CAS  Google Scholar 

  27. Nikonowicz EP, Sirr A, Legault P, Jucker FM, Baer LM, Pardi A (1992) Preparation of C-13 and N-15 labeled RNAs for heteronuclear multidimensional NMR-studies. Nucleic Acids Res 20:4507–4513

    Article  PubMed  CAS  Google Scholar 

  28. Batey RT, Battiste JL, Williamson JR (1995) Preparation of isotopically enriched RNAs for heteronuclear NMR. Methods Enzymol 261:300–322

    Article  PubMed  CAS  Google Scholar 

  29. Scott LG, Tolbert TJ, Williamson JR (2000) Preparation of specifically H-2- and C-13-labeled ribonucleotides. Methods Enzymol 317:18–38

    Article  PubMed  CAS  Google Scholar 

  30. Cromsigt J, Schleucher J, Gustafsson T, Kihlberg J, Wijmenga S (2002) Preparation of partially H-2/C-13-labelled RNA for NMR studies. Stereo-specific deuteration of the H5″ in nucleotides. Nucleic Acids Res 30:1639–1645

    Article  PubMed  CAS  Google Scholar 

  31. Lu K, Miyazaki Y, Summers MF (2010) Isotope labeling strategies for NMR studies of RNA. J Biomol NMR 46:113–125

    Article  PubMed  Google Scholar 

  32. Price RP, Oubridge C, Varani G, Nagai K (1998) Preparation of RNA: protein complexes for X-ray cristallography and NMR. In: Smith CWJ (ed) RNA-protein interactions: a practical approach. Oxford University Press, Oxford, pp 37–74

    Google Scholar 

  33. Gallo S, Furler M, Sigel RKO (2005) In vitro transcription and purification of RNAs of different size. Chimia 59:812–816

    Article  CAS  Google Scholar 

  34. Pleiss JA, Derrick ML, Uhlenbeck OC (1998) T7 RNA polymerase produces 5′ end heterogeneity during in vitro transcription from certain templates. RNA 4:1313–1317

    Article  PubMed  CAS  Google Scholar 

  35. Dayie KT (2008) Key labeling technologies to tackle sizeable problems in RNA structural biology. Int J Mol Sci 9:1214–1240

    Article  PubMed  CAS  Google Scholar 

  36. Ferre-D’Amare AR, Doudna JA (1996) Use of cis- and trans-ribozymes to remove 5′ and 3′ heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res 24:977–978

    Article  PubMed  Google Scholar 

  37. Duss O, Maris C, von Schroetter C, Allain FHT (2010) A fast, efficient and sequence-independent method for flexible multiple segmental isotope labeling of RNA using ribozyme and RNase H cleavage. Nucleic Acids Res 38:e188

    Article  PubMed  Google Scholar 

  38. Schurer H, Lang K, Schuster J, Morl M (2002) A universal method to produce in vitro transcripts with homogeneous 3′ ends. Nucleic Acids Res 30:e56

    Article  PubMed  Google Scholar 

  39. Walker SC, Avis JM, Conn GL (2003) General plasmids for producing RNA in vitro transcripts with homogeneous ends. Nucleic Acids Res 31:e82

    Article  PubMed  Google Scholar 

  40. Guo HC, Collins RA (1995) Efficient trans-cleavage of a stem-loop RNA substrate by a ribozyme derived from neurospora VS RNA. EMBO J 14:368–376

    PubMed  CAS  Google Scholar 

  41. Shields TP, Mollova E, Marie LS, Hansen MR, Pardi A (1999) High-performance liquid chromatography purification of homogenous-length RNA produced by trans cleavage with a hammerhead ribozyme. RNA 5:1259–1267

    Article  PubMed  CAS  Google Scholar 

  42. Santoro SW, Joyce GF (1997) A general purpose RNA-cleaving DNA enzyme. Proc Natl Acad Sci USA 94:4262–4266

    Article  PubMed  CAS  Google Scholar 

  43. Santoro SW, Joyce GF (1998) Mechanism and utility of an RNA-cleaving DNA enzyme. Biochemistry 37:13330–13342

    Article  PubMed  CAS  Google Scholar 

  44. Pyle AM, Chu VT, Jankowsky E, Boudvillain M (2000) Using DNAzymes to cut, process, and map RNA molecules for structural studies or modification. Methods Enzymol 317:140–146

    Article  PubMed  CAS  Google Scholar 

  45. Inoue H, Hayase Y, Iwai S, Ohtsuka E (1987) Sequence-dependent hydrolysis of RNA using modified oligonucleotide splints and RNase H. FEBS Lett 215:327–330

    Article  PubMed  CAS  Google Scholar 

  46. Lapham J, Crothers DM (1996) RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation. RNA 2:289–296

    PubMed  CAS  Google Scholar 

  47. Kao C, Zheng M, Rudisser S (1999) A simple and efficient method to reduce nontemplated nucleotide addition at the 3′ terminus of RNAs transcribed by T7 RNA polymerase. RNA 5:1268–1272

    Article  PubMed  CAS  Google Scholar 

  48. Ponchon L, Dardel F (2007) Recombinant RNA technology: the tRNA scaffold. Nat Methods 4:571–576

    Article  PubMed  CAS  Google Scholar 

  49. Ponchon L, Beauvais G, Nonin-Lecomte S, Dardel F (2009) A generic protocol for the expression and purification of recombinant RNA in Escherichia coliusing a tRNA scaffold. Nat Protoc 4:947–959

    Article  PubMed  CAS  Google Scholar 

  50. Kim I, Mckenna SA, Puglisi EV, Puglisi JD (2007) Rapid purification of RNAs using fast performance liquid chromatography (FPLC). RNA 13:289–294

    Article  PubMed  CAS  Google Scholar 

  51. Lukavsky PJ, Puglisi JD (2004) Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides. RNA 10:889–893

    Article  PubMed  CAS  Google Scholar 

  52. Anderson AC, Scaringe SA, Earp BE, Frederick CA (1996) HPLC purification of RNA for crystallography and NMR. RNA 2:110–117

    PubMed  CAS  Google Scholar 

  53. Easton LE, Shibata Y, Lukavsky PJ (2010) Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography. RNA 16:647–653

    Article  PubMed  CAS  Google Scholar 

  54. Cathala G, Brunel C (1990) Use of n-butanol for efficient recovery of minute amounts of small RNA fragments and branched nucleotides from dilute solutions. Nucleic Acids Res 18:201

    Article  PubMed  CAS  Google Scholar 

  55. McKenna SA, Kim I, Puglisi EV, Lindhout DA, Aitken CE, Marshall RA, Puglisi JD (2007) Purification and characterization of transcribed RNAs using gel filtration chromatography. Nat Protoc 2:3270–3277

    Article  PubMed  CAS  Google Scholar 

  56. Murray JB, Collier AK, Arnold JRP (1994) A general purification procedure for chemically synthesized oligoribonucleotides. Anal Biochem 218:177–184

    Article  PubMed  CAS  Google Scholar 

  57. Cheong HK, Hwang E, Lee C, Choi BS, Cheong C (2004) Rapid preparation of RNA samples for NMR spectroscopy and X-ray crystallography. Nucleic Acids Res 32:e84

    Article  PubMed  Google Scholar 

  58. Kieft JS, Batey RT (2004) A general method for rapid and nondenaturing purification of RNAs. RNA 10:988–995

    Article  PubMed  CAS  Google Scholar 

  59. Batey RT, Kieft JS (2007) Improved native affinity purification of RNA. RNA 13:1384–1389

    Article  PubMed  CAS  Google Scholar 

  60. Walker SC, Scott FH, Srisawat C, Engelke DR (2008) RNA affinity tags for the rapid purification and investigation of RNAs and RNA-protein complexes. Methods Mol Biol 488:23–40

    Article  PubMed  CAS  Google Scholar 

  61. Allain FH, Varani G (1997) How accurately and precisely can RNA structure be determined by NMR? J Mol Biol 267:338–351

    Article  PubMed  CAS  Google Scholar 

  62. Tugarinov V, Muhandiram R, Ayed A, Kay LE (2002) Four-dimensional NMR spectroscopy of a 723-residue protein: chemical shift assignments and secondary structure of malate synthase g. J Am Chem Soc 124:10025–10035

    Article  PubMed  CAS  Google Scholar 

  63. Marino JP, Diener JL, Moore PB, Griesinger C (1997) Multiple-quantum coherence dramatically enhances the sensitivity of CH and CH2 correlations in uniformly C-13-labeled RNA. J Am Chem Soc 119:7361–7366

    Article  CAS  Google Scholar 

  64. Lukavsky PJ, Puglisi JD (2001) RNAPack: an integrated NMR approach to RNA structure determination. Methods 25:316–332

    Article  PubMed  CAS  Google Scholar 

  65. Tolbert TJ, Williamson JR (1997) Preparation of specifically deuterated and C-13-labeled RNA for NMR studies using enzymatic synthesis. J Am Chem Soc 119:12100–12108

    Article  CAS  Google Scholar 

  66. Davis JH, Tonelli M, Scott LG, Jaeger L, Williamson JR, Butcher SE (2006) RNA helical packing in solution: NMR structure of a 30 kDa GAAA tetraloop-receptor complex (vol 351, pg 371, 2005). J Mol Biol 360:742

    Article  CAS  Google Scholar 

  67. Varani G, Tinoco I (1991) RNA structure and NMR-spectroscopy. Q Rev Biophys 24:479–532

    Article  PubMed  CAS  Google Scholar 

  68. Nikonowicz EP (2001) Preparation and use of H-2-labeled RNA oligonucleotides in nuclear magnetic resonance studies. Nucl Magn Reson Biol Macromol Pt A 338:320–341

    Article  CAS  Google Scholar 

  69. Bullock SL, Ringel I, Ish-Horowicz D, Lukavsky PJ (2010) A′-form RNA helices are required for cytoplasmic mRNA transport in Drosophila. Nat Struct Mol Biol 17:703–709

    Article  PubMed  CAS  Google Scholar 

  70. D’Souza V, Dey A, Habib D, Summers MF (2004) NMR structure of the 101-nucleotide core encapsidation signal of the Moloney murine leukemia virus. J Mol Biol 337:427–442

    Article  PubMed  Google Scholar 

  71. D’Souza V, Summers MF (2004) Structural basis for packaging the dimeric genome of Moloney murine leukaemia virus. Nature 431:586–590

    Article  PubMed  Google Scholar 

  72. Miyazaki Y, Irobalieva RN, Tolbert BS, Smalls-Mantey A, Iyalla K, Loeliger K, D’Souza V, Khant H, Schmid MF, Garcia EL, Telesnitsky A, Chiu W, Summers MF (2010) Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography. J Mol Biol 404:751–772

    Article  PubMed  CAS  Google Scholar 

  73. Kim I, Lukavsky PJ, Puglisi JD (2002) NMR study of 100 kDa HCV IRES RNA using segmental isotope labeling. J Am Chem Soc 124:9338–9339

    Article  PubMed  CAS  Google Scholar 

  74. Lukavsky PJ, Kim I, Otto GA, Puglisi JD (2003) Structure of HCV IRES domain II determined by NMR. Nat Struct Biol 10:1033–1038

    Article  PubMed  CAS  Google Scholar 

  75. Lu K, Heng X, Garyu L, Monti S, Garcia EL, Kharytonchyk S, Dorjsuren B, Kulandaivel G, Jones S, Hiremath A, Divakaruni SS, LaCotti C, Barton S, Tummillo D, Hosic A, Edme K, Albrecht S, Telesnitsky A, Summers MF (2011) NMR detection of structures in the HIV-1 5′-leader RNA that regulate genome packaging. Science 334:242–245

    Article  PubMed  CAS  Google Scholar 

  76. Serganov A, Keiper S, Malinina L, Tereshko V, Skripkin E, Hobartner C, Polonskaia A, Phan AT, Wombacher R, Micura R, Dauter Z, Jaschke A, Patel DJ (2005) Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation. Nat Struct Mol Biol 12:218–224

    Article  PubMed  CAS  Google Scholar 

  77. Akiyama BM, Stone MD (2009) Assembly of complex RNAs by splinted ligation. Methods Enzymol 469:27–46

    Article  PubMed  CAS  Google Scholar 

  78. Moore MJ, Query CC (2000) Joining of RNAs by splinted ligation. Methods Enzymol 317:109–123

    Article  PubMed  CAS  Google Scholar 

  79. Frilander MJ, Turunen JJ (2005) RNA ligation using T4 DNA ligase. In: Hartmann RK, Bindereif A, Schön A, Westhof E (eds) Handbook of RNA biochemistry. WILEY-VCH Verlag GmBH & Co, Weinheim, pp 36–52

    Chapter  Google Scholar 

  80. Persson T, Willkomm DK, Hartmann RK (2005) T4 RNA ligase. In: Hartmann RK, Bindereif A, Schön A, Westhof E (eds) Handbook of RNA biochemistry. WILEY-VCH Verlag GmBH & Co, Weinheim, pp 53–74

    Chapter  Google Scholar 

  81. Purtha WE, Coppins RL, Smalley MK, Silverman SK (2005) General deoxyribozyme-catalyzed synthesis of native 3′-5′ RNA linkages. J Am Chem Soc 127:13124–13125

    Article  PubMed  CAS  Google Scholar 

  82. Lang K, Micura R (2008) The preparation of site-specifically modified riboswitch domains as an example for enzymatic ligation of chemically synthesized RNA fragments. Nat Protoc 3:1457–1466

    Article  PubMed  CAS  Google Scholar 

  83. Stark MR, Pleiss JA, Deras M, Scaringe SA, Rader SD (2006) An RNA ligase-mediated method for the efficient creation of large, synthetic RNAs. RNA 12:2014–2019

    Article  PubMed  CAS  Google Scholar 

  84. Ohtsuki T, Kawai G, Watanabe Y, Kita K, Nishikawa K, Watanabe K (1996) Preparation of biologically active Ascaris suum mitochondrial tRNAMet with a TV-replacement loop by ligation of chemically synthesized RNA fragments. Nucleic Acids Res 24:662–667

    Article  PubMed  CAS  Google Scholar 

  85. Ohtsuki T, Kawai G, Watanabe K (1998) Stable isotope-edited NMR analysis of Ascaris suum mitochondrial tRNAMet having a TV-replacement loop. J Biochem 124:28–34

    Article  PubMed  CAS  Google Scholar 

  86. Xu J, Lapham J, Crothers DM (1996) Determining RNA solution structure by segmental isotopic labeling and NMR: application to Caenorhabditis elegans spliced leader RNA 1. Proc Natl Acad Sci USA 93:44–48

    Article  PubMed  CAS  Google Scholar 

  87. Tzakos AG, Easton LE, Lukavsky PJ (2006) Complementary segmental labeling of large RNAs: economic preparation and simplified NMR spectra for measurement of more RDCs. J Am Chem Soc 128:13344–13345

    Article  PubMed  CAS  Google Scholar 

  88. Tzakos AG, Easton LE, Lukavsky PJ (2007) Preparation of large RNA oligonucleotides with complementary isotope-labeled segments for NMR structural studies. Nat Protoc 2:2139–2147

    Article  PubMed  CAS  Google Scholar 

  89. Nelissen FH, van Gammeren AJ, Tessari M, Girard FC, Heus HA, Wijmenga SS (2008) Multiple segmental and selective isotope labeling of large RNA for NMR structural studies. Nucleic Acids Res 36:e89

    Article  PubMed  Google Scholar 

  90. Kawahara I, Haruta K, Ashihara Y, Yamanaka D, Kuriyama M, Toki N, Kondo Y, Teruya K, Ishikawa J, Furuta H, Ikawa Y, Kojima C, Tanaka Y (2012) Site-specific isotope labeling of long RNA for structural and mechanistic studies. Nucleic Acids Res 40:e7

    Article  PubMed  CAS  Google Scholar 

  91. Schubert M, Lapouge K, Duss O, Oberstrass FC, Jelesarov I, Haas D, Allain FH (2007) Molecular basis of messenger RNA recognition by the specific bacterial repressing clamp RsmA/CsrA. Nat Struct Mol Biol 14:807–813

    Article  PubMed  CAS  Google Scholar 

  92. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415

    Article  PubMed  CAS  Google Scholar 

  93. Hayase Y, Inoue H, Ohtsuka E (1990) Secondary structure in formylmethionine tRNA influences the site-directed cleavage of ribonuclease H using chimeric 2′-O-methyl oligodeoxyribonucleotides. Biochemistry 29:8793–8797

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

We thank Christophe Maris for setting up the HPLC and Christine von Schroetter for the production of isotopically labeled NTPs. This work was supported by the SNF-NCCR Iso-lab, the SNF grant Nr. 3100A0-118118 (to F.A.) and the grant from HFSP [RGP0024/2008] (to P.J.L.).

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  1. Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology Zürich, ETH Hönggerberg, CH-8093, Zürich, Switzerland

    Olivier Duss, Peter J. Lukavsky & Frédéric H.-T. Allain

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  1. Olivier Duss
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  2. Peter J. Lukavsky
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  3. Frédéric H.-T. Allain
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Correspondence to Peter J. Lukavsky or Frédéric H.-T. Allain .

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  1. , NMR Research Centre, Indian Institute of Science, Bangalore, India

    Hanudatta S. Atreya

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Duss, O., Lukavsky, P.J., Allain, F.HT. (2012). Isotope Labeling and Segmental Labeling of Larger RNAs for NMR Structural Studies. In: Atreya, H. (eds) Isotope labeling in Biomolecular NMR. Advances in Experimental Medicine and Biology, vol 992. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-4954-2_7

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