Deoxyribozyme-mediated ligation for incorporating EPR spin labels and reporter groups into rna

Methods in Enzymology

Volumn 549, Issue C, 2014, Pages 85-104

  Wawrzyniak Turek, Katarzyna ^a,b   Höbartner, Claudia ^a,b  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

Author keywords

Convertible nucleosides; EPR spectroscopy; Nitroxyls; RNA ligation; Solid phase synthesis; Spin labels

Indexed keywords

9DB1 PROTEIN; DEOXYRIBOZYME; UNCLASSIFIED DRUG; NUCLEOSIDE; RIBOSWITCH; RNA; SPIN LABELING;

ARTICLE; CYCLOADDITION; ELECTRON SPIN RESONANCE; HIGH TEMPERATURE; IN VITRO STUDY; INCUBATION TIME; PRIORITY JOURNAL; REPORTER GENE; RIBOSWITCH; RNA SEQUENCE; RNA TRANSCRIPTION; SOLID PHASE SYNTHESIS; SPIN LABELING; SUBSTITUTION REACTION; TRANSESTERIFICATION; CHEMISTRY; METABOLISM; NUCLEOTIDE SEQUENCE; PROCEDURES; SYNTHESIS;

BASE SEQUENCE; DNA, CATALYTIC; ELECTRON SPIN RESONANCE SPECTROSCOPY; NUCLEOSIDES; RIBOSWITCH; RNA; SOLID-PHASE SYNTHESIS TECHNIQUES; SPIN LABELS;

EID: 84925441581     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-801122-5.00004-0     Document Type: Chapter

References (44)

1. Y.L. Ahmed, and R. Ficner RNA synthesis and purification for structural studies RNA Biology 11 2014 427 432
2. C.R. Allerson, S.L. Chen, and G.L. Verdine a chemical method for site-specific modification of RNA: The convertible nucleoside approach Journal of the American Chemical Society 119 1997 7423 7433
3. M. Azarkh, V. Singh, O. Okle, I.T. Seemann, D.R. Dietrich, and J.S. Hartig Site-directed spin-labeling of nucleotides and the use of in-cell EPR to determine long-range distances in a biologically relevant environment Nature Protocols 8 2013 131 147
4. N. Barhate, P. Cekan, A.P. Massey, and S.T. Sigurdsson A nucleoside that contains a rigid nitroxide spin label: A fluorophore in disguise Angewandte Chemie, International Edition 46 2007 2655 2658
5. D.A. Baum, and S.K. Silverman Deoxyribozyme-catalyzed labeling of RNA Angewandte Chemie, International Edition 46 2007 3502 3504
6. B.M. Brandsen, T.E. Velez, A. Sachdeva, N.A. Ibrahim, and S.K. Silverman DNA-catalyzed lysine side chain modification Angewandte Chemie, International Edition 53 2014 9045 9050
7. K. Burgess, and D. Cook Syntheses of nucleoside triphosphates Chemical Reviews 100 2000 2047 2060
8. L. Büttner, F. Javadi-Zarnaghi, and C. Höbartner Site-specific labeling of RNA at internal ribose hydroxyl groups: Terbium-assisted deoxyribozymes at work Journal of the American Chemical Society 136 2014 8131 8137
9. L. Büttner, J. Seikowski, K. Wawrzyniak, A. Ochmann, and C. Höbartner Synthesis of spin-labeled riboswitch RNAs using convertible nucleosides and DNA-catalyzed RNA ligation Bioorganic and Medicinal Chemistry 21 2013 6171 6180
10. T. Carlomagno Present and future of NMR for RNA-protein complexes: A perspective of integrated structural biology Journal of Magnetic Resonance 241 2014 126 136
11. T.M. Coleman, G. Wang, and F. Huang Superior 5′ homogeneity of RNA from ATP-initiated transcription under the T7 phi 2.5 promoter Nucleic Acids Research 32 2004 e14
12. P. Ding, D. Wunnicke, H.J. Steinhoff, and F. Seela Site-directed spin-labeling of DNA by the azide-alkyne 'click' reaction: Nanometer distance measurements on 7-deaza-2′-deoxyadenosine and 2′-deoxyuridine nitroxide conjugates spatially separated or linked to a 'dA-dT' base pair Chemistry 16 2010 14385 14396
13. T.E. Edwards, and S.T. Sigurdsson Site-specific incorporation of nitroxide spin-labels into 2′-positions of nucleic acids Nature Protocols 2 2007 1954 1962
14. J.M. Esquiaqui, E.M. Sherman, S.A. Ionescu, J.D. Ye, and G.E. Fanucci Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling Biochemistry 53 2014 3526 3528
15. M.J. Frilander, and J.J. Turunen RNA ligation using T4 DNA ligase R.K. Hartmann, A. Bindereif, A. Schön, E. Westhof, Handbook of RNA biochemistry 2008 Wiley-VCH Verlag GmbH Weinheim, Germany 36 52
16. R. Hänsel, L.M. Luh, I. Corbeski, L. Trantirek, and V. Dötsch In-cell NMR and EPR spectroscopy of biomacromolecules Angewandte Chemie, International Edition 53 2014 10300 10314
17. B. Heppell, S. Blouin, A.M. Dussault, J. Mulhbacher, E. Ennifar, and J.C. Penedo Molecular insights into the ligand-controlled organization of the SAM-I riboswitch Nature Chemical Biology 7 2011 384 392
18. C. Höbartner, G. Sicoli, F. Wachowius, D.B. Gophane, and S.T. Sigurdsson Synthesis and characterization of RNA containing a rigid and non-perturbing cytidine-derived spin label Journal of Organic Chemistry 77 2012 7749 7754
19. C. Höbartner, and S.K. Silverman Recent advances in DNA catalysis Biopolymers 87 2007 279 292
20. U. Jakobsen, S.A. Shelke, S. Vogel, and S.T. Sigurdsson Site-directed spin-labeling of nucleic acids by click chemistry: Detection of a basic sites in duplex DNA by EPR spectroscopy Journal of the American Chemical Society 132 2010 10424 10428
21. I. Krstic, B. Endeward, D. Margraf, A. Marko, and T.F. Prisner Structure and dynamics of nucleic acids Topics in Current Chemistry 321 2012 159 198
22. K. Lang, and R. Micura The preparation of site-specifically modified riboswitch domains as an example for enzymatic ligation of chemically synthesized RNA fragments Nature Protocols 3 2008 1457 1466
23. C.S. Lee, T.P. Mui, and S.K. Silverman Improved deoxyribozymes for synthesis of covalently branched DNA and RNA Nucleic Acids Research 39 2011 269 279
24. J.F. Milligan, D.R. Groebe, G.W. Witherell, and O.C. Uhlenbeck Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates Nucleic Acids Research 15 1987 8783 8798
25. T. Persson, D.K. Willkomm, and R.K. Hartmann T4 RNA ligase 2005 Wiley-VCH Weinheim, Germany 53 74
26. N. Piton, Y. Mu, G. Stock, T.F. Prisner, O. Schiemann, and J.W. Engels Base-specific spin-labeling of RNA for structure determination Nucleic Acids Research 35 2007 3128 3143
27. W.E. Purtha, R.L. Coppins, M.K. Smalley, and S.K. Silverman General deoxyribozyme-catalyzed synthesis of native 3′-5′ RNA linkages Journal of the American Chemical Society 127 2005 13124 13125
28. G.W. Reginsson, and O. Schiemann Pulsed electron-electron double resonance: Beyond nanometre distance measurements on biomacromolecules The Biochemical Journal 434 2011 353 363
29. G.W. Reginsson, and O. Schiemann Studying biomolecular complexes with pulsed electron-electron double resonance spectroscopy Biochemical Society Transactions 39 2011 128 139
30. O. Schiemann, N. Piton, J. Plackmeyer, B.E. Bode, T.F. Prisner, and J.W. Engels Spin labeling of oligonucleotides with the nitroxide TPA and use of PELDOR, a pulse EPR method, to measure intramolecular distances Nature Protocols 2 2007 904 923
31. K. Schlosser, and Y. Li Biologically inspired synthetic enzymes made from DNA Chemistry and Biology 16 2009 311 322
32. S.A. Shelke, G.B. Sandholt, and S.T. Sigurdsson Nitroxide-labeled pyrimidines for non-covalent spin-labeling of abasic sites in DNA and RNA duplexes Organic and Biomolecular Chemistry 12 2014 7366 7774
33. S.A. Shelke, and S.T. Sigurdsson Noncovalent and site-directed spin labeling of nucleic acids Angewandte Chemie, International Edition 49 2010 7984 7986
34. S.A. Shelke, and S.T. Sigurdsson Site-directed spin labelling of nucleic acids European Journal of Organic Chemistry 2012 2012 2291 2301
35. G. Sicoli, G. Mathis, O. Delalande, Y. Boulard, D. Gasparutto, and S. Gambarelli Double electron-electron resonance (DEER): A convenient method to probe DNA conformational changes Angewandte Chemie, International Edition 47 2008 735 737
36. G. Sicoli, F. Wachowius, M. Bennati, and C. Höbartner Probing secondary structures of spin-labeled RNA by pulsed EPR spectroscopy Angewandte Chemie, International Edition 49 2010 6443 6447
37. S.K. Silverman Deoxyribozymes: Selection design and serendipity in the development of DNA catalysts Accounts of Chemical Research 42 2009 1521 1531
38. S.K. Silverman, and D.A. Baum Use of deoxyribozymes in RNA research Methods in Enzymology 469 2009 95 117
39. P. St-Pierre, K. McCluskey, E. Shaw, J.C. Penedo, and D.A. Lafontaine Fluorescence tools to investigate riboswitch structural dynamics Biochimica et Biophysica Acta 1839 2014 1005 1019
40. I. Tkach, S. Pornsuwan, C. Höbartner, F. Wachowius, S.T. Sigurdsson, and T.Y. Baranova Orientation selection in distance measurements between nitroxide spin labels at 94 GHz EPR with variable dual frequency irradiation Physical Chemistry Chemical Physics 15 2013 3433 3437
41. S. Viollet, R.T. Fuchs, D.B. Munafo, F. Zhuang, and G.B. Robb T4 RNA ligase 2 truncated active site mutants: Improved tools for RNA analysis BMC Biotechnology 11 2011 72
42. F. Wachowius, and C. Höbartner Probing essential nucleobase functional groups in aptamers and deoxyribozymes by nucleotide analogue interference mapping of DNA Journal of the American Chemical Society 133 2011 14888 14891
43. F. Wachowius, F. Javadi-Zarnaghi, and C. Höbartner Combinatorial mutation interference analysis reveals functional nucleotides required for DNA catalysis Angewandte Chemie, International Edition 49 2010 8504 8508
44. I. Zlatev, T. Lavergne, F. Debart, J.J. Vasseur, M. Manoharan, and F. Morvan Efficient solid-phase chemical synthesis of 5′-triphosphates of DNA, RNA, and their analogues Organic Letters 12 2010 2190 2193