A facile method for attaching nitroxide spin labels at the 5′ terminus of nucleic acids

Nucleic Acids Research

Volumn 35, Issue 10, 2007, Pages

  Grant, Gian Paola G ^a   Qin, Peter Z ^a  

^a UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METHYL GROUP; NITROXIDE; NUCLEIC ACID; PHOSPHOROTHIOIC ACID DERIVATIVE; POLYNUCLEOTIDE 5' HYDROXYL KINASE; TRANSFER RNA; DNA; NITROGEN OXIDE; NUCLEOTIDE; PHENYLALANINE TRANSFER RNA; RNA;

5' UNTRANSLATED REGION; ANALYTIC METHOD; ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME SYNTHESIS; NUCLEIC ACID ANALYSIS; NUCLEIC ACID PROBE; PRIORITY JOURNAL; PROTEIN FOLDING; RNA SYNTHESIS; SPIN LABELING; BIOCHEMISTRY; CHEMISTRY; ELECTRON SPIN RESONANCE; EVALUATION; METABOLISM; METHODOLOGY; SYNTHESIS;

BIOCHEMISTRY; DNA; ELECTRON SPIN RESONANCE SPECTROSCOPY; NITROGEN OXIDES; POLYNUCLEOTIDE 5'-HYDROXYL-KINASE; RNA; RNA, TRANSFER, PHE; SPIN LABELS; THIONUCLEOTIDES;

EID: 34250822871     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm240     Document Type: Article

References (32)

1. Hubbell,W.L. and Altenbach,C. (1994) Investigation of structure and dynamics in membrane proteins using site-directed spin labeling. Curr. Opin. Struct. Biol., 4, 566-573.
2. Feix,J.B. and Klug,C.S. (1998) In Berliner,L.J. (ed.), Biological Magnetic Resonance. Plenum Press, New York, NY, Vol. 14, pp. 251-281.
3. Fajer,P.G. (2000) In Meyers,R. (ed.), Encyclopedia of Analytical Chemistry. John Wiley & Sons, Chichester, pp. 5725-5761.
4. Hubbell,W.L., Cafiso,D.S. and Altenbach,C. (2000) Identifying conformational changes with site-directed spin labeling. Nat. Struct. Biol., 7, 735-739.
5. Borbat,P.P., Costa-Filho,A.J., Earle,K.A., Moscicki,J.K. and Freed,J.H. (2001) Electron spin resonance in studies of membranes and proteins. Science, 291, 266-269.
6. Columbus,L. and Hubbell,W.L. (2002) A new spin on protein dynamics. Trends Biochem. Sci., 27, 288-295.
7. Fanucci,G.E. and Cafiso,D.S. (2006) Recent Advances and applications of site-directed spin labeling. Curr. Opin. Struct. Biol., 16, 644-653.
8. Qin,P.Z. and Dieckmann,T. (2004) Application of NMR and EPR methods to the study of RNA. Curr. Opin. Struct. Biol., 14, 350-359.
9. Schiemann,O., Piton,N., Mu,Y., Stock,G., Engels,J.W. and Prisner,T.F. (2004) A PELDOR based nanometer distance ruler for oligonucleotides. J. Am. Chem. Soc., 126, 5722-5729.
10. Cai,Q., Kusnetzow,A.K., Hubbell,W.L., Haworth,I.S., Gacho,G.P., Van Eps,N., Hideg,K., Chambers,E.J. and Qin,P.Z. (2006) Site-directed spin labeling measurements of nanometer distances in nucleic acids using a sequence-independent nitroxide probe. Nucl. Acids Res., 34, 4722-4734.
11. Macosko,J.C., Pio,M.S., Tinoco,I.Jr and Shin,Y.-K. (1999) A novel 5′ displacement spin-labeling technique for electron paramagnetic resonance spectroscopy of RNA. RNA, 5, 1158-1166.
12. Schiemann,O., Weber,A., Edwards,T.E., Prisner,T.F. and Sigurdsson,S.T. (2003) Nanometer distance measurements on RNA using PELDOR. J. Am. Chem. Soc., 125, 3334-3335.
13. Borbat,P.P., Davis,J.H., Butcher,S.E. and Freed,J.H. (2004) Measurement of large distances in biomolecules using double-quantum filtered refocused electron spin-echoes. J. Am. Chem. Soc., 126, 7746-7747.
14. Kim,N., Murali,A. and DeRose,V.J. (2004) A distance ruler for RNA using EPR and site-directed spin labeling. Chem. Biol., 11, 939-948.
15. Qin,P.Z., Butcher,S.E., Feigon,J. and Hubbell,W.L. (2001) Quantitative analysis of the GAAA tetraloop/receptor interaction in solution: A site-directed spin labeling study. Biochemistry, 40, 6929-6936.
16. Edwards,T.E., Okonogi,T.M., Robinson,B.H. and Sigurdsson,S.T. (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, 1527-1528.
17. Kao,S.C. and Bobst,A.M. (1985) Local base dynamics and local structural features in RNA and DNA duplexes. Biochemistry, 24, 5465-5469.
18. Spaltenstein,A., Robinson,B.H. and Hopkins,P.B. (1989) Sequence and structure- dependent DNA base dynamics: Synthesis, structure, and dynamics of site and sequence specifically spin-labeled DNA. Biochemistry, 28, 9484-9495.
19. Gannett,P.M., Darian,E., Powell,J., Johnson,E.M., Mundoma,C., Greenbaum,N.L., Ramsey,C.M., Dalal,N.S. and Budil,D.E. (2002) Probing triplex formation by EPR spectroscopy using a newly synthesized spin label for oligonucleotides. Nucleic Acids Res., 30, 5328-5337.
20. Qin,P.Z., Hideg,K., Feigon,J. and Hubbell,W.L. (2003) Monitoring RNA base structure and dynamics using site-directed spin labeling. Biochemistry, 42, 6772-6783.
21. Qin,P.Z., Feigon,J. and Hubbell,W.L. (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, 1-8.
22. Dugas,H. and Caron,M. (1976) Specific spin-labeling of transfer ribonucleic acid molecules. Nucleic Acids Res., 3, 19-34.
23. Fang,Y., Cai,Q. and Qin,P.Z. (2005) The procapsid binding domain of phi29 packaging RNA has a modular architecture and requires 2′-hydroxyl groups in packaging RNA interaction. Biochemistry, 44, 9348-9358.
24. Qin,P.Z., Jennifer,I. and Oki,A. (2006) A model system for investigating lineshape/structure correlations in RNA site-directed spin labeling. Biochem. Biophys. Res. Commun., 343, 117-124.
25. Knowles,P.F., Marsh,D. and Rattle,H.W.E. (1976) Magnetic Resonance of Biomolecules. John Wiley & Sons Ltd., New York, pp. 168-207.
26. RajBhandary,U.L., Chang,S.H., Stuart,A., Faulkner,R.D., Hoskinson,R.M. and Khorana,H.G. (1967) Studies on Polynucleotides, LXVIII. The Primary Structure of Yeast Phenylalanine Transfer RNA. Proc. Natl. Acad. Sci. 57, 751-758.
27. Klose,R.J. and Bird,A.P. (2006) Genomic DNA methylation: The mark and its mediators. Trends Biochem. Sci., 31, 89-97.
28. Moore,P.B. and Steitz,T.A. (2005) The ribosome revealed. Trends Biochem. Sci., 30, 281-283.
29. Sharp,P.A. (2005) The discovery of split genes and RNA splicing. Trends Biochem. Sci., 30, 279-281.
30. Mattick,J.S. and Makunin,I.V. (2006) Non-coding RNA. Hum. Mol. Genet. 15, R17-R29.
31. Pan,T., Gutell,R.R. and Uhlenbeck,O.C. (1991) Folding of circular permuted tRNAs as specific photoaffinity probes of ribonuclease P RNA structure. Science, 254, 1361-1364.
32. Ramos,A. and 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.