Structure and dynamics of nucleic acids

Topics in Current Chemistry

Volumn 321, Issue , 2012, Pages 159-198

  Krstić, Ivan ^a   Endeward, Burkhard ^a   Margraf, Dominik ^a   Marko, Andriy ^a   Prisner, Thomas F ^a  

^a GOETHE UNIVERSITY   (Germany)

Author keywords

CW EPR spectroscopy; Dynamics; ENDOR; ESEEM; Hyperfine spectroscopy; In cell EPR; Nucleic acids; PELDOR; RNA ligand interactions; RNA protein interactions; Structure

Indexed keywords

NUCLEIC ACID;

ARTICLE; CHEMISTRY; CONFORMATION; ELECTRON SPIN RESONANCE; SPIN LABELING;

ELECTRON SPIN RESONANCE SPECTROSCOPY; NUCLEIC ACID CONFORMATION; NUCLEIC ACIDS; SPIN LABELS;

EID: 84859757968     PISSN: 03401022     EISSN: None     Source Type: Book Series    
DOI: 10.1007/128_2011_300     Document Type: Article

References (121)

1. Fürtig B, Richter C, Wöhnert J, Schwalbe H (2003) NMR spectroscopy of RNA. Chembiochem 4(10):936-962. doi:10.1002/cbic.200300700 (Pubitemid 37267582)
2. Varani G, Aboul-ela F, Allain FHT (1996) NMR investigation of RNA structure. Prog Nucl Magn Reson Spectr 29(1-2):51-127 (Pubitemid 126381972)
3. Klostermeier D, Millar DP (2001) RNA conformation and folding studied with fluorescence resonance energy transfer. Methods 23(3):240-254 (Pubitemid 32848424)
4. Roy R, Hohng S, Ha T (2008) A practical guide to single-molecule FRET. Nat Methods 5 (6):507-516. doi:10.1038/nmeth.1208 (Pubitemid 351761757)
5. Wachowius F, Höbartner C (2010) Chemical RNA modifications for studies of RNA structure and dynamics. Chembiochem 11(4):469-480. doi:10.1002/cbic.200900697
6. Klare JP, Steinhoff HJ (2009) Spin labeling EPR. Photosynth Res 102(2-3):377-390
7. Schiemann O, Piton N, Plackmeyer J, Bode BE, Prisner TF, Engels JW (2007) Spin labeling of oligonucleotides with the nitroxide TPA and use of PELDOR, a pulse EPR method, to measure intramolecular distances. Nat Protoc 2(4):904-923. doi:10.1038/nprot.2007.97 (Pubitemid 46758809)
8. Sowa GZ, Qin PZ (2008) Site-directed spin labeling studies on nucleic acid structure and dynamics. Prog Nucleic Acid Res Mol Biol 82:147-197. doi:10.1016/S0079-6603(08)00005-6
9. Berliner LJ (1998) Spin labeling: the next millenium. Biological magnetic resonance. Plenum Press, New York
10. Caron M, Dugas H (1976) Specific spin-labeling of transfer ribonucleic-acid molecules. Nucleic Acids Res 3(1):19-34
11. Sprinzl M, Kramer E, Stehlik D (1974) Structure of phenylalanine transfer-RNA from yeast-spin-label studies. Eur J Biochem 49(3):595-605
12. Sprinzl M, Scheit KH, Cramer F (1973) Preparation in-vitro of a 2-thiocytidine-containing yeast transfer-RNA Phe-A73-C74-S2c75-A76 and its interaction with para-hydroxymercuribenzoate. Eur J Biochem 34(2):306-310
13. Hara H, Horiuchi T, Saneyosh M, Nishimur S (1970) 4-Thiouridine-specific spin-labeling of E. coli transfer RNA. Biochem Biophys Res Commun 38(2):305
14. Mcintosh AR, Caron M, Dugas H (1973) Specific spin labeling of anticodon of Escherichiacoli transfer-RNA Glu. Biochem Biophys Res Commun 55(4):1356-1363
15. Qin PZ, Hideg K, Feigon J, Hubbell WL (2003) Monitoring RNA base structure and dynamics using site-directed spin labeling. Biochemistry-US 42(22):6772-6783. doi:10.1021/bi027222p (Pubitemid 36666118)
16. 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(42):10992-10993 (Pubitemid 28507453)
17. Spaltenstein A, Robinson BH, Hopkins PB (1989) Sequence-dependent and structure-dependent DNA-base dynamics-synthesis, structure, and dynamics of site and sequence specifically spin-labeled DNA. Biochemistry-US 28(24):9484-9495 (Pubitemid 20000727)
18. Strube T, Schiemann O, MacMillan F, Prisner T, Engels JW (2001) A new facile method for spin-labeling of oligonucleotides. Nucleosides Nucleotides Nucleic Acids 20 (4-7):1271-1274 (Pubitemid 32821969)
19. Schiemann O, Piton N, Mu YG, Stock G, Engels JW, Prisner TF (2004) A PELDOR-based nanometer distance ruler for oligonucleotides. J Am Chem Soc 126(18):5722-5729. doi:10.1021/ja0393877 (Pubitemid 38621411)
20. Piton N, Schiemann O, Mu YG, Stock G, Prisner T, Engels JW (2005) Synthesis of spinlabeled RNAs for long range distance measurements by PELDOR. Nucleosides Nucleotides Nucleic Acids 24(5-7):771-775 (Pubitemid 41440691)
21. Piton N, Mu YG, Stock G, Prisner TF, Schiemann O, Engels JW (2007) Base-specific spinlabeling of RNA for structure determination. Nucleic Acids Res 35(9):3128-3143. doi:10.1093/nar/gkm169 (Pubitemid 47073650)
22. Spaltenstein A, Robinson BH, Hopkins PB (1988) A rigid and nonperturbing probe for duplex DNA motion. J Am Chem Soc 110(4):1299-1301 (Pubitemid 18058822)
23. Gannett PM, Darian E, Powell J, Johnson EM 2nd, Mundoma C, Greenbaum NL, Ramsey CM, Dalal NS, Budil DE (2002) Probing triplex formation by EPR spectroscopy using a newly synthesized spin label for oligonucleotides. Nucleic Acids Res 30(23):5328-5337 (Pubitemid 36033052)
24. Frolow O, Bode BE, Engels JW (2007) The synthesis of EPR differentiable spinlabels and their coupling to uridine. Nucleosides Nucleotides Nucleic Acids 26(6-7):655-659. doi:10.1080/15257770701490522 (Pubitemid 350239208)
25. Hustedt EJ, Kirchner JJ, Spaltenstein A, Hopkins PB, Robinson BH (1995) Monitoring DNA dynamics using spin-labels with different independent mobilities. Biochemistry-US 34 (13):4369-4375
26. Ding P, Wunnicke D, Steinhoff HJ, Seela F (2010) Site-directed spin-labeling of DNA by the azide-alkyne 'Click' reaction: nanometer distance measurements on 7-deaza-20-deoxyadenosine and 20-deoxyuridine nitroxide conjugates spatially separated or linked to a 'dA-dT' base pair. Chem Eur J 16(48):14385-14396
27. Bobst AM, Kao SC, Toppin RC, Ireland JC, Thomas IE (1984) Dipsticking the major groove of DNA with enzymatically incorporated spin-labeled deoxyuridines by electron-spin resonance spectroscopy. J Mol Biol 173(1):63-74 (Pubitemid 14199549)
28. Bobst AM, Pauly GT, Keyes RS, Bobst EV (1988) Enzymatic sequence-specific spin labeling of a DNA fragment containing the recognition sequence of ecori endonuclease. FEBS Lett 228(1):33-36
29. Okamoto A, Inasaki T, Saito I (2004) Nitroxide-labeled guanine as an ESR spin probe for structural study of DNA. Bioorg Med Chem Lett 14(13):3415-3418. doi:10.1016/j. bmcl.2004.04.076 (Pubitemid 38737138)
30. Sicoli G, Wachowius F, Bennati M, Höbartner C (2010) Probing secondary structures of spinlabeled RNA by pulsed EPR spectroscopy. Angew Chem Int Ed Engl 49(36):6443-6447. doi:10.1002/anie.201000713
31. Miller TR, Alley SC, Reese AW, Solomon MS, Mccallister WV, Mailer C, Robinson BH, Hopkins PB (1995) A probe for sequence-dependent nucleic-acid dynamics. J Am Chem Soc 117(36):9377-9378
32. Okonogi TM, Alley SC, Reese AW, Hopkins PB, Robinson BH (2000) Sequence-dependent dynamics in duplex DNA. Biophys J 78(5):2560-2571 (Pubitemid 30313814)
33. Barhate N, Cekan P, Massey AP, Sigurdsson ST (2007) A nucleoside that contains a rigid nitroxide spin label: a fluorophore in disguise. Angew Chem Int Ed Engl 46(15):2655-2658. doi:10.1002/anie.200603993 (Pubitemid 46973555)
34. Lin KY, Jones RJ, Matteucci M (1995) Tricyclic 20-deoxycytidine analogs-syntheses and incorporation into oligodeoxynucleotides which have enhanced binding to complementary RNA. J Am Chem Soc 117(13):3873-3874
35. Cekan P, Smith AL, Barhate N, Robinson BH, Sigurdsson ST (2008) Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation. Nucleic Acids Res 36 (18):5946-5954. doi:10.1093/nar/gkn562
36. Cekan P, Sigurdsson ST (2008) Single base interrogation by afluorescent nucleotide: each of the four DNA bases identified by fluorescence spectroscopy. Chem Commun (29):3393-3395. doi:10.1039/B801833b (Pubitemid 352009186)
37. Shelke SA, Sigurdsson ST (2010) Noncovalent and site-directed spin labeling of nucleic acids. Angew Chem Int Ed Engl 49(43):7984-7986. doi:10.1002/anie.201002637
38. Nagahara S, Murakami A, Makino K (1992) Spin-labeled oligonucleotides site specifically labeled at the internucleotide linkage-separation of stereoisomeric probes and EPR spectroscopical detection of hybrid formation in solution. Nucleos Nucleot 11(2-4):889-901
39. Grant GP, Boyd N, Herschlag D, Qin PZ (2009) Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin labeling. J Am Chem Soc 131(9):3136-3137. doi:10.1021/ja808217s
40. Qin PZ, Haworth IS, Cai Q, Kusnetzow AK, Grant GPG, Price EA, Sowa GZ, Popova A, Herreros B, He H (2007) Measuring nanometer distances in nucleic acids using a sequenceindependent nitroxide probe. Nat Protoc 2(10):2354-2365. doi:10.1038/nprot.2007.308
41. Qin PZ, Butcher SE, Feigon J, Hubbell WL (2001) Quantitative analysis of the isolated GAAA tetraloop/receptor interaction in solution: a site-directed spin labeling study. Biochemistry-US 40(23):6929-6936 (Pubitemid 32538240)
42. Cai Q, Kusnetzow AK, Hideg K, Price EA, Haworth IS, Qin PZ (2007) Nanometer distance measurements in RNA using site-directed spin labeling. Biophys J 93(6):2110-2117. doi:10.1529/biophysj.107.109439 (Pubitemid 47437593)
43. Cai Q, Kusnetzow AK, Hubbell WL, Haworth IS, Gacho GPC, Van Eps N, Hideg K, Chambers EJ, Qin PZ (2006) Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe. Nucleic Acids Res 34(17):4722-4730. doi:10.1093/nar/gkl546 (Pubitemid 44605618)
44. Flaender M, Sicoli G, Fontecave T, Mathis G, Saint-Pierre C, Boulard Y, Gambarelli S, Gasparutto D (2008) Site-specific insertion of nitroxide-spin labels into DNA probes by click chemistry for structural analyses by ELDOR spectroscopy. Nucleic Acids Symp Ser 52:147-148. doi:10.1093/nass/nrn075
45. Kim NK, Murali A, DeRose VJ (2004) A distance ruler for RNA using EPR and site-directed spin labeling. Chem Biol 11(7):939-948. doi:10.1016/j.chembiol. 2004.04.013 (Pubitemid 38991788)
46. Edwards TE, Sigurdsson ST (2007) Site-specific incorporation of nitroxide spin-labels into 20-positions of nucleic acids. Nat Protoc 2(8):1954-1962. doi:10.1038/nprot.2007.273 (Pubitemid 47308134)
47. Edwards TE, Okonogi TM, Robinson BH, Sigurdsson ST (2001) Site-specific incorporation of nitroxide spin-labels into internal sites of the TAR RNA; structure-dependent dynamics of RNA by EPR spectroscopy. J Am Chem Soc 123(7):1527-1528 (Pubitemid 32167355)
48. Schweiger A, Jeschke G (2001) Principles of pulse electron paramagnetic resonance. Oxford University Press, USA
49. Atherton NM (1993) Principles of electron spin resonance. Ellis Horwood, New York
50. Abragam A (1961) The principles of nuclear magnetism. The international series of monographs on physics. Clarendon, Oxford
51. Freed JH, Fraenkel GK (1963) Theory of linewidths in electron spin resonance spectra. J Chem Phys 39(2):326
52. Kivelson D (1960) Theory of ESR linewidths of free radicals. J Chem Phys 33(4):1094-1106
53. Stoll S, Schweiger A (2006) EasySpin, a comprehensive software package for spectral simulation and analysis in EPR. J Magn Reson 178(1):42-55. doi:10.1016/j.jmr.2005.08.013 (Pubitemid 41774010)
54. Schneider DJ, Freed JH (1989) Calculating slow motional magnetic resonance spectra: a user's guide. In: Berliner LJ, Reuben J (eds) Spin labeling: theory and applications. Biological magnetic resonance. Plenum Press, New York
55. Mims WB, Nassau K, Mcgee JD (1961) Spectral diffusion in electron resonance lines. Phys Rev 1(6):2059-2069
56. Rowan LG, Hahn EL, Mims WB (1965) Electron-spin-echo envelope modulation. Phys Rev 137(1A):61-71
57. Mims WB (1972) Electron spin echoes. In: Geschwind S (ed) Electron paramagnetic resonance. Plenum Press, New York
58. Hofer P, Grupp A, Nebenfuhr H, Mehring M (1986) Hyperfine sublevel correlation (HYSCORE) spectroscopy-a 2D electron-spin-resonance investigation of the squaric acid radical. Chem Phys Lett 132(3):279-282
59. Ichikawa T, Kevan L, Bowman MK, Dikanov SA, Tsvetkov YD (1979) Ratio analysis of electron spin echo modulation envelopes in disordered matrixes and application to the structure of solvated electrons in 2-methyltetrahydrofuran glass. J Chem Phys 71 (3):1167-1174
60. Flanagan HL, Singel DJ (1987) Analysis of 14N ESEEM patterns of randomly oriented solids. J Chem Phys 87(10):5606-5616
61. Jeschke G, Rakhmatullin R, Schweiger A (1998) Sensitivity enhancement by matched microwave pulses in one-and two-dimensional electron spin echo envelope modulation spectroscopy. J Magn Reson 131(2):261-271 (Pubitemid 128450565)
62. Feher G (1956) Observation of nuclear magnetic resonances via the electron spin resonance line. Phys Rev 103(3):834-834
63. Davies ER (1974) A new pulse endor technique. Phys Lett A 47(1):1-2
64. Mims WB (1965) Pulsed electron nuclear double resonance (E.N.DO.R.) experiments. Proc Roy Soc (London) 283(Ser. A;1395):452-457
65. Epel B, Manikandan P, Kroneck PMH, Goldfarb D (2001) High-field ENDOR and the sign of the hyperfine coupling. Appl Magn Reson 21(3-4):287-297 (Pubitemid 33571725)
66. Cook RJ, Whiffen DH (1964) Relative signs of hyperfine coupling constants by a double ENDOR experiment. Proc Phys Soc Lond 84(6):845-845
67. Bode BE, Margraf D, Plackmeyer J, Durner G, Prisner TF, Schiemann O (2007) Counting the monomers in nanometer-sized oligomers by pulsed electron-electron double resonance. J Am Chem Soc 129(21):6736-6745. doi:10.1021/ja065787t (Pubitemid 46847515)
68. Marko A, Margraf D, Yu H, Mu Y, Stock G, Prisner T (2009) Molecular orientation studies by pulsed electron-electron double resonance experiments. J Chem Phys 130(6):064102. doi:10.1063/1.3073040
69. Margraf D, Cekan P, Prisner TF, Sigurdsson ST, Schiemann O (2009) Ferro-and antiferromagnetic exchange coupling constants in PELDOR spectra. Phys Chem Chem Phys 11 (31):6708-6714. doi:10.1039/b905524j
70. Marko A, Margraf D, Cekan P, Sigurdsson ST, Schiemann O, Prisner TF (2010) Analytical method to determine the orientation of rigid spin labels in DNA. Phys Rev E 81(2)
71. Margraf D, Bode BE, Marko A, Schiemann O, Prisner TF (2007) Conformational flexibility of nitroxide biradicals determined by X-band PELDOR experiments. Mol Phys 105 (15-16):2153-2160 (Pubitemid 351426631)
72. Zhang XJ, Cekan P, Sigurdsson ST, Qin PZ (2009) Studying RNA using site-directed spinlabeling and continuous-wave electron paramagnetic resonance spectroscopy. Method Enzymol 469:303-328. doi:10.1016/S0076-6879(09)69015-7
73. Krstić I, Frolow O, Sezer D, Endeward B, Weigand JE, Suess B, Engels JW, Prisner TF (2010) PELDOR spectroscopy reveals preorganization of the neomycin-responsive riboswitch tertiary structure. J Am Chem Soc 132(5):1454-1455. doi:10.1021/ja9077914
74. Moore PB (1999) Structural motifs in RNA. Annu Rev Biochem 68:287-300. doi:10.1146/annurev.biochem.68.1.287 (Pubitemid 29449194)
75. Duchardt-Ferner E, Weigand JE, Ohlenschlager O, Schtnidtke SR, Suess B, Wohnert J (2010) Highly modular structure and ligand binding by conformational capture in a minimalistic riboswitch. Angew Chem Int Ed Engl 49(35):6216-6219
76. Edwards TE, Robinson BH, Sigurdsson ST (2005) Identification of amino acids that promote specific and rigid TAR RNA-Tat protein complex formation. Chem Biol 12(3):329-337. doi:10.1016/j.chembiol.2005.01.012 (Pubitemid 40406280)
77. Edwards TE, Sigurdsson ST (2003) EPR spectroscopic analysis of TAR RNA-metal ion interactions. Biochem Biophys Res Commun 303(2):721-725 (Pubitemid 36349228)
78. Edwards TE, Sigurdsson ST (2002) Electron paramagnetic resonance dynamic signatures of TAR RNA-small molecule complexes provide insight into RNA structure and recognition. Biochemistry-US 41(50):14843-14847 (Pubitemid 35470662)
79. Edwards TE, Okonogi TM, Sigurdsson ST (2002) Investigation of RNA-protein and RNAmetal ion interactions by electron paramagnetic resonance spectroscopy. The HIV TAR-Tat motif. Chem Biol 9(6):699-706 (Pubitemid 34653064)
80. Ippolito JA, Steitz TA (1998) A 1.3-A resolution crystal structure of the HIV-1 transactivation response region RNA stem reveals a metal ion-dependent bulge conformation. Proc Natl Acad Sci USA 95(17):9819-9824
81. Qin PZ, Feigon J, Hubbell WL (2005) Site-directed spin labeling studies reveal solution conformational changes in a GAAA tetraloop receptor upon Mg2+-dependent docking of a GAAA tetraloop. J Mol Biol 351(1):1-8. doi:10.1016/j.jmb.2005.06.007 (Pubitemid 40967050)
82. Feig AL (2000) The use of manganese as a probe for elucidating the role of magnesium ions in ribozymes. Met Ions Biol Syst 37:157-182
83. Pley HW, Flaherty KM, Mckay DB (1994) 3-Dimensional structure of a hammerhead ribozyme. Nature 372(6501):68-74
84. Scott WG, Murray JB, Arnold JRP, Stoddard BL, Klug A (1996) Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 274(5295):2065-2069 (Pubitemid 27020698)
85. Horton TE, Clardy DR, DeRose VJ (1998) Electron paramagnetic resonance spectroscopic measurement of Mn2+ binding affinities to the hammerhead ribozyme and correlation with cleavage activity. Biochemistry-US 37(51):18094-18101 (Pubitemid 29023966)
86. Schiemann O, Fritscher J, Kisseleva N, Sigurdsson ST, Prisner TF (2003) Structural investigation of a high-affinity MnII binding site in the hammerhead ribozyme by EPR spectroscopy and DFT calculations. Effects of neomycin B on metal-ion binding. Chembiochem 4 (10):1057-1065. doi:10.1002/cbic.200300653 (Pubitemid 37267595)
87. Kisseleva N, Khvorova A, Westhof E, Schiemann O (2005) Binding of manganese(II) to a tertiary stabilized hammerhead ribozyme as studied by electron paramagnetic resionance spectroscopy. RNA 11(1):1-6 (Pubitemid 40041567)
88. Kim NK, Murali A, DeRose VJ (2005) Separate metal requirements for loop interactions and catalysis in the extended hammerhead ribozyme. J Am Chem Soc 127(41):14134-14135. doi:10.1021/ja0541027 (Pubitemid 41457549)
89. Kisseleva N, Kraut S, Jaschke A, Schiemann O (2007) Characterizing multiple metal ion binding sites within a ribozyme by cadmium-induced EPR silencing. HFSP J 1(2):127-136
90. Zhang X, Lee SW, Zhao L, Xia T, Qin PZ (2010) Conformational distributions at the N-peptide/boxB RNA interface studied using site-directed spin labeling. RNA 16 (12):2474-2483. doi:10.1261/rna.2360610
91. Xi X, Sun Y, Karim CB, Grigoryants VM, Scholes CP (2008) HIV-1 nucleocapsid protein NCp7 and its RNA stem loop 3 partner: rotational dynamics of spin-labeled RNA stem loop 3. Biochemistry-US 47(38):10099-10110. doi:10.1021/bi800602e
92. Spaltenstein A, Robinson BH, Hopkins PB (1989) DNA structural data from a dynamics probe-the dynamic signatures of single-stranded, hairpin-looped, and duplex forms of DNA are distinguishable. J Am Chem Soc 111(6):2303-2305
93. Cekan P, Sigurdsson ST (2009) Identification of single-base mismatches in duplex DNA by EPR spectroscopy. J Am Chem Soc 131(50):18054-18056. doi:10.1021/ja905623k
94. Jakobsen U, Shelke SA, Vogel S, Sigurdsson ST (2010) Site-directed spin-labeling of nucleic acids by click chemistry: detection of abasic sites in duplex DNA by EPR spectroscopy. J Am Chem Soc 132(30):10424-10428. doi:10.1021/ja102797k
95. Okonogi TM, Reese AW, Alley SC, Hopkins PB, Robinson BH (1999) Flexibility of duplex DNA on the submicrosecond timescale. Biophys J 77(6):3256-3276. doi:10.1016/S0006-3495(99)77157-2
96. Popova AM, Kalai T, Hideg K, Qin PZ (2009) Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes. Biochemistry-US 48 (36):8540-8550. doi:10.1021/bi900860w
97. Keyes RS, Bobst AM (1995) Detection of internal and overall dynamics of a 2-atom-tethered spin-labeled DNA. Biochemistry-US 34(28):9265-9276
98. Smith AL, Cekan P, Brewood GP, Okonogi TM, Alemayehu S, Hustedt EJ, Benight AS, Sigurdsson ST, Robinson BH (2009) Conformational equilibria of bulged sites in duplex DNA studied by EPR spectroscopy. J Phys Chem B 113(9):2664-2675
99. Okonogi TM, Alley SC, Harwood EA, Hopkins PB, Robinson BH (2002) Phosphate backbone neutralization increases duplex DNA flexibility: a model for protein binding. Proc Natl Acad Sci USA 99(7):4156-4160 (Pubitemid 34285958)
100. Columbus L, Hubbell WL (2004) Mapping backbone dynamics in solution with site-directed spin labeling: GCN4-58 bZip free and bound to DNA. Biochemistry-US 43(23):7273-7287 (Pubitemid 38745748)
101. Steinhoff HJ, Suess B (2003) Molecular mechanisms of gene regulation studied by sitedirected spin labeling. Methods 29(2):188-195 (Pubitemid 36269205)
102. Morrissey SR, Horton TE, Grant CV, Hoogstraten CG, Britt RD, DeRose VJ (1999) Mn2+-nitrogen interactions in RNA probed by electron spin-echo envelope modulation spectroscopy: application to the hammerhead ribozyme. J Am Chem Soc 121(39):9215-9218
103. Vogt M, Lahiri S, Hoogstraten CG, Britt RD, DeRose VJ (2006) Coordination environment of a site-bound metal ion in the hammerhead ribozyme determined by N-15 and H-2 ESEEM spectroscopy. J Am Chem Soc 128(51):16764-16770. doi:10.1021/Ja057035p (Pubitemid 46043125)
104. Morrissey SR, Horton TE, DeRose VJ (2000) Mn2+ sites in the hammerhead ribozyme investigated by EPR and continuous-wave Q-band ENDOR spectroscopies. J Am Chem Soc 122(14):3473-3481 (Pubitemid 30211121)
105. Schiemann O, Carmieli R, Goldfarb D (2007) W-band P-31-ENDOR on the high-affinity Mn2+ binding site in the minimal and tertiary stabilized hammerhead ribozymes. Appl Magn Reson 31(3-4):543-552
106. DeRose VJ (2009) Characterization of nucleic acid-metal Ion binding by spectroscopic techniques. In: Hud NV (ed) Nucleic acid-metal ion interactions. The Royal Society of Chemistry, London
107. Santangelo MG, Antoni PM, Spingler B, Jeschke G (2010) Can copper(II) mediate Hoogsteen base-pairing in a left-handed DNA duplex? A pulse EPR study. Chemphyschem 11(3):599-606. doi:10.1002/cphc.200900672
108. Milov AD, Ponomarev AB, Tsvetkov YD (1984) Electron electron double-resonance in electron-spin echo-model biradical systems and the sensitized photolysis of decalin. Chem Phys Lett 110(1):67-72
109. Schiemann O, Prisner TF (2007) Long-range distance determinations in biomacromolecules by EPR spectroscopy. Q Rev Biophys 40(1):1-53. doi:10.1017/S003358350700460X (Pubitemid 47343581)
110. Jeschke G, Polyhach Y (2007) Distance measurements on spin-labelled biomacromolecules by pulsed electron paramagnetic resonance. Phys Chem Chem Phys 9(16):1895-1910. doi:10.1039/b614920k
111. Schiemann O, Weber A, Edwards TE, Prisner TF, Sigurdsson ST (2003) Nanometer distance measurements on RNA using PELDOR. J Am Chem Soc 125(12):3434-3435. doi:10.1021/ja0274610 (Pubitemid 36512410)
112. Ward R, Keeble DJ, El-Mkami H, Norman DG (2007) Distance determination in heterogeneous DNA model systems by pulsed EPR. Chembiochem 8(16):1957-1964. doi:10.1002/cbic.200700245
113. Schiemann O, Cekan P, Margraf D, Prisner TF, Sigurdsson ST (2009) Relative orientation of rigid nitroxides by PELDOR: beyond distance measurements in nucleic acids. Angew Chem Int Ed Engl 48(18):3292-3295. doi:10.1002/anie. 200805152
114. Marko A, Denysenkov VP, Margraf D, Cekan P, Schiemann O, Sigurdsson ST, Prisner TF (2011) Conformational flexibility of DNA. J Am Chem Soc. doi:10.1021/ja201244u
115. Sicoli G, Mathis G, Delalande O, Boulard Y, Gasparutto D, Gambarelli S (2008) Double electron-electron resonance (DEER): a convenient method to probe DNA conformational changes. Angew Chem Int Ed Engl 47(4):735-737. doi:10.1002/anie.200704133
116. Sicoli G, Mathis G, Aci-Sèche S, Saint-Pierre C, Boulard Y, Gasparutto D, Gambarelli S (2009) Lesion-induced DNA weak structural changes detected by pulsed EPR spectroscopy combined with site-directed spin labelling. Nucleic Acids Res 37(10):3165-3176. doi:10.1093/nar/gkp165
117. Weigand JE, Sanchez M, Gunnesch EB, Zeiher S, Schroeder R, Suess B (2008) Screening for engineered neomycin riboswitches that control translation initiation. RNA 14(1):89-97. doi:10.1261/rna.772408
118. Singh V, Azarkh M, Exner TE, Hartig JS, Drescher M (2009) Human telomeric quadruplex conformations studied by pulsed EPR. Angew Chem Int Ed Engl 48(51):9728-9730. doi:10.1002/anie.200902146
119. Kim NK, Bowman MK, DeRose VJ (2010) Precise mapping of RNA tertiary structure via nanometer distance measurements with double electron-electron resonance spectroscopy. J Am Chem Soc 132(26):8882-8884. doi:10.1021/Ja101317g
120. Wunnicke D, Strohbach D, Weigand JE, Appel B, Feresin E, Suess B, Müller S, Steinhoff HJ (2010) Ligand-induced conformational capture of a synthetic tetracycline riboswitch revealed by pulse EPR. RNA. doi:10.1261/rna.2222811
121. Krstić I, Hänsel R, Romainczyk O, Engels JW, Dötsch V, Prisner TF (2011) Long-range distance measurements on nucleic acids in cells by pulsed EPR spectroscopy. Angew Chem Int Ed Engl 50(22):5070-5074. doi:10.1002/anie.201100886