Three-dimensional RNA structure refinement by hydroxyl radical probing

Nature Methods

Volumn 9, Issue 6, 2012, Pages 603-608

  Ding, Feng ^a,b   Lavender, Christopher A ^c   Weeks, Kevin M ^c   Dokholyan, Nikolay V ^a,b  

^a UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA   (United States)

^c University of North Carolina at Chapel Hill   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROXYL RADICAL; NUCLEOTIDE DERIVATIVE; SOLVENT;

ANALYTIC METHOD; ARTICLE; BASE PAIRING; HYDROXYL RADICAL PROBING; LABORATORY TEST; MEASUREMENT; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MODEL; MOLECULAR PROBE; MOLECULAR SIZE; NONHUMAN; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; RNA SEQUENCE; RNA STRUCTURE; SIMULATION;

BASE PAIRING; BASE SEQUENCE; HYDROXYL RADICAL; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; RNA; RNA, TRANSFER; SOFTWARE;

EID: 84861978778     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.1976     Document Type: Article

References (42)

1. Gesteland, R.F., Cech, T.R. & Atkins, J.F. eds. The RNA World: The Nature of Modern RNA Suggests a Prebiotic RNA World. (Cold Spring Harbor Lab Press, Plainview, NY, 2006).
2. Das, R. & Baker, D. Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl. Acad. Sci. USA 104, 14664-14669 (2007).
3. Ding, F. et al. Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA 14, 1164-1173 (2008).
4. Parisien, M. & Major, F. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452, 51-55 (2008).
5. Cao, S. & Chen, S.J. Physics-based de novo prediction of RNA 3D structures. J. Phys. Chem. B 115, 4216-4226 (2011).
6. Das, R. et al. Structural inference of native and partially folded RNA by high-throughput contact mapping. Proc. Natl. Acad. Sci. USA 105, 4144-4149 (2008).
7. Yu, E.T., Hawkins, A., Eaton, J. & Fabris, D. MS3D structural elucidation of the HIV-1 packaging signal. Proc. Natl. Acad. Sci. USA 105, 12248-12253 (2008).
8. Gherghe, C.M. et al. Native-like RNA tertiary structures using a sequence-encoded cleavage agent and refinement by discrete molecular dynamics. J. Am. Chem. Soc. 131, 2541-2546 (2009).
9. Jonikas, M.A. et al. Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA 15, 189-199 (2009).
10. Lavender, C.A., Ding, F., Dokholyan, N.V. & Weeks, K.M. Robust and generic RNA modeling using inferred constraints: a structure for the hepatitis C virus IRES pseudoknot domain. Biochemistry 49, 4931-4933 (2010).
11. Yang, S., Parisien, M., Major, F. & Roux, B. RNA structure determination using SAXS data. J. Phys. Chem. B 114, 10039-10048 (2010).
12. Michel, F. & Westhof, E. Modelling of the three-dimensional architecture of group I catalytic introns based on comparative sequence analysis. J. Mol. Biol. 216, 585-610 (1990).
13. Gutell, R.R. et al. Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res. 20, 5785-5795 (1992).
14. Deigan, K.E., Li, T.W., Mathews, D.H. & Weeks, K.M. Accurate SHAPE-directed RNA structure determination. Proc. Natl. Acad. Sci. USA 106, 97-102 (2009).
15. Weeks, K.M. Advances in RNA structure analysis by chemical probing. Curr. Opin. Struct. Biol. 20, 295-304 (2010).
16. Hajdin, C.E., Ding, F., Dokholyan, N.V. & Weeks, K.M. On the significance of an RNA tertiary structure prediction. RNA 16, 1340-1349 (2010).
17. Bailor, M.H., Mustoe, A.M., Brooks, C.L. III & Al-Hashimi, H.M. Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. Curr. Opin. Struct. Biol. 21, 296-305 (2011).
18. Tullius, T.D. & Greenbaum, J.A. Mapping nucleic acid structure by hydroxyl radical cleavage. Curr. Opin. Chem. Biol. 9, 127-134 (2005).
19. Cate, J.H. et al. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273, 1678-1685 (1996).
20. Pastor, N., Weinstein, H., Jamison, E. & Brenowitz, M. A detailed interpretation of OH radical footprints in a TBP-DNA complex reveals the role of dynamics in the mechanism of sequence-specific binding. J. Mol. Biol. 304, 55-68 (2000).
21. Bergman, N.H. et al. The three-dimensional architecture of the class I ligase ribozyme. RNA 10, 176-184 (2004).
22. Rangan, P., Masquida, B., Westhof, E. & Woodson, S.A. Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme. Proc. Natl. Acad. Sci. USA 100, 1574-1579 (2003).
23. Dokholyan, N.V., Buldyrev, S.V., Stanley, H.E. & Shakhnovich, E.I. Discrete molecular dynamics studies of the folding of a protein-like model. Fold. Des. 3, 577-587 (1998).
24. Dann, C.E. III et al. Structure and mechanism of a metal-sensing regulatory RNA. Cell 130, 878-892 (2007).
25. Balasubramanian, B., Pogozelski, W.K. & Tullius, T.D. DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone. Proc. Natl. Acad. Sci. USA 95, 9738-9743 (1998).
26. Berman, H.M. et al. The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000).
27. Westhof, E., Dumas, P. & Moras, D. Restrained refinement of 2 crystalline forms of yeast aspartic-acid and phenylalanine transfer-RNA crystals. Acta Crystallogr. A 44, 112-123 (1988).
28. Serganov, A. et al. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441, 1167-1171 (2006).
29. Krasilnikov, A.S., Yang, X., Pan, T. & Mondragon, A. Crystal structure of the specificity domain of ribonuclease P. Nature 421, 760-764 (2003).
30. Adams, P.L. et al. Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45-50 (2004).
31. Cochrane, J.C., Lipchock, S.V., Smith, K.D. & Strobel, S.A. Structural and chemical basis for glucosamine 6-phosphate binding and activation of the glmS ribozyme. Biochemistry 48, 3239-3246 (2009).
32. Serganov, A., Huang, L. & Patel, D.J. Structural insights into amino acid binding and gene control by a lysine riboswitch. Nature 455, 1263-1267 (2008).
33. Kazantsev, A.V., Krivenko, A.A. & Pace, N.R. Mapping metal-binding sites in the catalytic domain of bacterial RNase P RNA. RNA 15, 266-276 (2009).
34. Toor, N. et al. Tertiary architecture of the Oceanobacillus iheyensis group II intron. RNA 16, 57-69 (2010).
35. Milligan, J.F., Groebe, D.R., Witherell, G.W. & Uhlenbeck, O.C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res. 15, 8783-8798 (1987).
36. Merino, E.J., Wilkinson, K.A., Coughlan, J.L. & Weeks, K.M. RNA structure analysis at single nucleotide resolution by Selective 2′-Hydroxyl Acylation and Primer Extension (SHAPE). J. Am. Chem. Soc. 127, 4223-4231 (2005).
37. Duncan, C.D.S. & Weeks, K.M. The Mrs1 splicing factor binds the bI3 group I intron at each of two tetraloop-receptor motifs. PLoS One 5, e8983 (2010).
38. Murphy, F.L. & Cech, T.R. An independently folding domain of RNA tertiary structure within the Tetrahymena ribozyme. Biochemistry 32, 5291-5300 (1993).
39. Latham, J.A. & Cech, T.R. Defining the inside and outside of a catalytic RNA molecule. Science 245, 276-282 (1989).
40. Klein, D.J., Been, M.D. & Ferre-D'Amare, A.R. Essential role of an active-site guanine in glmS ribozyme catalysis. J. Am. Chem. Soc. 129, 14858-14859 (2007).
41. McGinnis, J.L., Duncan, C.D. & Weeks, K.M. High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assembly. Methods Enzymol. 468, 67-89 (2009).
42. Vasa, S.M. et al. ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA 14, 1979-1990 (2008).