Probing RNA folding by hydroxyl radical footprinting

Methods in Molecular Biology

Volumn 1086, Issue , 2014, Pages 119-142

  Costa, Maria ^a   Monachello, Dario ^a  

^a CENTRE DE GÉNÉTIQUE MOLÉCULAIRE   (France)

Author keywords

Fe(II) EDTA; Group II intron; Hydroxyl radical footprinting; Intron exon binding; Ribozyme; RNA folding; RNA tertiary structure; Structural probing of RNA

Indexed keywords

HYDROXYL RADICAL;

ACCURACY; ARTICLE; CONFORMATIONAL TRANSITION; DNA SEQUENCE; LIGAND BINDING; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN FOOTPRINTING; RNA CONFORMATION; RNA DEGRADATION; RNA FOLDING; RNA PROBE; RNA SEQUENCE;

DENATURING GRADIENT GEL ELECTROPHORESIS; DNA PRIMERS; EDETIC ACID; FERROUS COMPOUNDS; HYDROXYL RADICAL; NUCLEIC ACID CONFORMATION; RNA; RNA FOLDING; TRANSCRIPTION, GENETIC;

EID: 84934435713     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-667-2_7     Document Type: Article

References (38)

1. Atkins JF, Gesteland RF, Cech TR (eds) (2011) RNA Worlds: from life's origins to diversity in gene regulation. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
2. Ehresmann C, Baudin F, Mougel M et al (1987) Probing the structure of RNAs in solution. Nucleic Acids Res 15:9109-9128
3. Brunel C, Romby P (2000) Probing RNA structure and RNA-ligand complexes with chemical probes. Methods Enzymol 318:3-21
4. Soukup GA, Breaker RR (1999) Relationship between internucleotide linkage geometry and the stability of RNA. RNA 5:1308-1325
5. Nahvi A, Sudarsan N, Ebert MS et al (2002) Genetic control by a metabolite binding mRNA. Chem Biol 9:1043
6. Winkler W, Nahvi A, Breaker RR (2002) Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419:952-956
7. Merino EJ, Wilkinson KA, Coughlan JL et al (2005) RNA structure analysis at single nucleotide resolution by selective 2?-hydroxyl acylation and primer extension (SHAPE). J Am Chem Soc 127:4223-4231
8. Wilkinson KA, Merino EJ, Weeks KM (2006) Selective 2?-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc 1:1610-1616
9. Costa M, Christian EL, Michel F (1998) Differential chemical probing of a group II self-splicing intron identifi es bases involved in tertiary interactions and supports an alternative secondary structure model of domain V. RNA 4:1055-1068
10. Fedorova O, Waldsich C, Pyle AM (2007) Group II intron folding under nearphysiological conditions: collapsing to the near-native state. J Mol Biol 366:1099-1114
11. Weinberg Z, Regulski EE, Hammond MC et al (2008) The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. RNA 14:822-828
12. Low JT, Weeks KM (2010) SHAPE-directed RNA secondary structure prediction. Methods 52:150-158
13. Celander DW, Cech TR (1991) Visualizing the higher order folding of a catalytic RNA molecule. Science 251:401-407
14. Laggerbauer B, Murphy FL, Cech TR (1994) Two major tertiary folding transitions of the Tetrahymena catalytic RNA. EMBO J 13: 2669-2676
15. Brenowitz M, Chance MR, Dhavan G et al (2002) Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting". Curr Opin Struct Biol 12:648-653
16. Loizos N (2004) Mapping protein-ligand interactions by hydroxyl-radical protein footprinting. Methods Mol Biol 261:199-210
17. Buxton GV, Greenstock CL, Helman WP et al (1988) Critical review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals in aqueous solution. J Phys Chem Ref Data 17:513
18. Balasubramanian B, Pogozelski WK, Tullius TD (1998) 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
19. Celander DW, Cech TR (1990) Iron(II)-ethylenediaminetetraacetic acid catalyzed cleavage of RNA and DNA oligonucleotides: similar reactivity toward single-and double-stranded forms. Biochemistry 29:1355-1361
20. Latham JA, Cech TR (1989) Defi ning the inside and outside of a catalytic RNA molecule. Science 245:276-282
21. Powers T, Noller HF (1995) A temperaturedependent conformational rearrangement in the ribosomal protein S4.16 S rRNA complex. J Biol Chem 270:1238-1242
22. Powers T, Noller HF (1995) Hydroxyl radical footprinting of ribosomal proteins on 16S rRNA. RNA 1:194-209
23. Costa M, Michel F, Westhof E (2000) A threedimensional perspective on exon binding by a group II self-splicing intron. EMBO J 19: 5007-5018
24. Dann CE 3rd, Wakeman CA, Sieling CL et al (2007) Structure and mechanism of a metalsensing regulatory RNA. Cell 130:878-892
25. Sclavi B, Woodson S, Sullivan M et al (1997) Time-resolved synchrotron X-ray "footprinting", a new approach to the study of nucleic acid structure and function: application to protein-DNA interactions and RNA folding. J Mol Biol 266:144-159
26. Hayes JJ, Kam L, Tullius TD (1990) Footprinting protein-DNA complexes with gamma-rays. Methods Enzymol 186:545-549
27. King PA, Jamison E, Strahs D et al (1993) 'Footprinting' proteins on DNA with peroxonitrous acid. Nucleic Acids Res 21:2473-2478
28. Swisher JF, Su LJ, Brenowitz M et al (2002) Productive folding to the native state by a group II intron ribozyme. J Mol Biol 315: 297-310
29. Fenton HJH (1894) The oxidation of tartaric acid in presence of iron. J Chem Soc 65: 899-910
30. Haber F, Weiss J (1934) The catalytic decomposition of hydrogen peroxide by iron salts. Proc R Soc Lond A 147:332-351
31. Heilek GM, Noller HF (1996) Site-directed hydroxyl radical probing of the rRNA neighborhood of ribosomal protein S5. Science 272:1659-1662
32. Newcomb LF, Noller HF (1999) Directed hydroxyl radical probing of 16S ribosomal RNA in 70S ribosomes from internal positions of the RNA. Biochemistry 38:945-951
33. Shcherbakova I, Mitra S, Beer RH et al (2006) Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins. Nucleic Acids Res 34:e48
34. Toor N, Keating KS, Fedorova O et al (2010) Tertiary architecture of the Oceanobacillus iheyensis group II intron. RNA 16:57-69
35. Das R, Laederach A, Pearlman SM et al (2005) SAFA: semi-automated footprinting analysis software for high-throughput quantifi cation of nucleic acid footprinting experiments. RNA 11:344-354
36. Kao C, Zheng M, Rudisser S (1999) A simple and effi cient method to reduce nontemplated nucleotide addition at the 3 terminus of RNAs transcribed by T7 RNA polymerase. RNA 5: 1268-1272
37. Costa M, Fontaine JM, Loiseaux-de GS et al (1997) A group II self-splicing intron from the brown alga Pylaiella littoralis is active at unusually low magnesium concentrations and forms populations of molecules with a uniform conformation. J Mol Biol 274:353-364
38. Vasa SM, Guex N, Wilkinson KA et al (2008) ShapeFinder: a software system for highthroughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA 14:1979-1990