P K a shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning

Biochemistry

Volumn 52, Issue 42, 2013, Pages 7470-7476

  Wilcox, Jennifer L ^a,b   Bevilacqua, Philip C ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b SAINT FRANCIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHLORINE COMPOUNDS; MAGNESIUM COMPOUNDS; POTASSIUM COMPOUNDS; PROTONATION;

ACID-BASE CATALYSIS; BIOLOGICAL PROCESS; DOUBLE-STRANDED RNA; DOUBLE-STRANDED RNA (DSRNA); DRIVING FORCES; GENERAL MODEL; NEAREST NEIGHBORS; STRUCTURAL ENVIRONMENT;

RNA;

DOUBLE STRANDED RNA; MAGNESIUM ION; RIBOZYME; ADENINE; MAGNESIUM;

ARTICLE; BASE PAIRING; CATALYSIS; CONCENTRATION RESPONSE; CONFORMATIONAL TRANSITION; PH; PHOSPHORUS NUCLEAR MAGNETIC RESONANCE; PKA; PRIORITY JOURNAL; PROTON TRANSPORT; RIBOSOMAL FRAMESHIFTING; RNA EDITING; RNA PROCESSING; RNA SEQUENCE; RNA STRUCTURE; TEMPERATURE SENSITIVITY; CHEMISTRY; CONFORMATION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; THERMODYNAMICS;

ADENINE; BASE PAIRING; HYDROGEN-ION CONCENTRATION; MAGNESIUM; MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID CONFORMATION; RNA, DOUBLE-STRANDED; THERMODYNAMICS;

EID: 84886800210     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi400768q     Document Type: Article

References (31)

1. Saenger, W. (1984) Principles of nucleic acid structure, Springer-Verlag, New York.
2. a shift at the active site of a lead-dependent ribozyme J. Am. Chem. Soc. 119, 6621-6628
3. Bevilacqua, P. C., Brown, T. S., Nakano, S., and Yajima, R. (2004) Catalytic roles for proton transfer and protonation in ribozymes Biopolymers 73, 90-109
4. Wilcox, J. L., Ahluwalia, A. K., and Bevilacqua, P. C. (2011) Charged nucleobases and their potential for RNA catalysis Acc. Chem. Res. 44, 1270-1279
5. Su, L., Chen, L., Egli, M., Berger, J. M., and Rich, A. (1999) Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot Nat. Struct. Biol. 6, 285-292
6. Nakano, S., Chadalavada, D. M., and Bevilacqua, P. C. (2000) General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme Science 287, 1493-1497
7. a near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography J. Am. Chem. Soc. 129, 13335-13342
8. Nakano, S. and Bevilacqua, P. C. (2007) Mechanistic characterization of the HDV genomic ribozyme: A mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons Biochemistry 46, 3001-3012
9. Nixon, P. L., Cornish, P. V., Suram, S. V., and Giedroc, D. P. (2002) Thermodynamic analysis of conserved loop-stem interactions in P1-P2 frameshifting RNA pseudoknots from plant luteoviridae Biochemistry 41, 10665-10674
10. a's J. Am. Chem. Soc. 135, 7390-7393
11. a shifting in an A(+)·C wobble: Effects of helix position, temperature, and ionic strength Biochemistry 49, 3225-3236
12. Lau, N. C., Lim, L. P., Weinstein, E. G., and Bartel, D. P. (2001) An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans Science 294, 858-862
13. Lagos-Quintana, M., Rauhut, R., Lendeckel, W., and Tuschl, T. (2001) Identification of novel genes coding for small expressed RNAs Science 294, 853-858
14. Lee, R. C. and Ambros, V. (2001) An extensive class of small RNAs in Caenorhabditis elegans Science 294, 862-864
15. Goodman, R. A., Macbeth, M. R., and Beal, P. A. (2012) ADAR proteins: Structure and catalytic mechanism Curr. Top. Microbiol. Immunol. 353, 1-33
16. Kuttan, A. and Bass, B. L. (2012) Mechanistic insights into editing-site specificity of ADARs Proc. Natl. Acad. Sci. U. S. A. 109, E3295-3304
17. Xia, T., SantaLucia, J., Jr., Burkard, M. E., Kierzek, R., Schroeder, S. J., Jiao, X., Cox, C., and Turner, D. H. (1998) Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs Biochemistry 37, 14719-14735
18. Mathewc, D. H., Sabina, J., Zuker, M., and Turner, D. H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure J. Mol. Biol. 288, 911-940
19. a shifting RNA 11, 157-172
20. a of neutrality in dsDNA J. Am. Chem. Soc. 126, 10200-10201
21. Siegfried, N. A. and Bevilacqua, P. C. (2009) Thinking inside the box: Designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding Methods Enzymol 455, 365-393
22. Allawi, H. T. and SantaLucia, J., Jr. (1998) Nearest-neighbor thermodynamics of internal A·C mismatches in DNA: Sequence dependence and ph effects Biochemistry 37, 9435-9444
23. Allain, F. H. and Varani, G. (1995) Structure of the P1 helix from group I self-splicing introns J. Mol. Biol. 250, 333-353
24. Varani, G., Cheong, C., and Tinoco, I., Jr. (1991) Structure of an unusually stable RNA hairpin Biochemistry 30, 3280-3289
25. Proctor, D. J., Kierzek, E., Kierzek, R., and Bevilacqua, P. C. (2003) Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine J. Am. Chem. Soc. 125, 2390-2391
26. London, R. E. (1991) Methods for measurement of intracellular magnesium: NMR and fluorescence Annu. Rev. Physiol. 53, 241-258
27. Grubbs, R. D. (2002) Intracellular magnesium and magnesium buffering Biometals 15, 251-259
28. Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K., and Watson, J. D. (1994) Molecular biology of the cell, 3 rd ed., Garland Science, New York.
29. Feig, A. L. and Uhlenbeck, O. C. (1999) The role of metal ions in RNA biochemistry, in The RNA world, Cold Spring Harbor Press, New York.
30. Wong, S. K., Sato, S., and Lazinski, D. W. (2001) Substrate recognition by ADAR1 and ADAR2 RNA 7, 846-858
31. Giedroc, D. P., Theimer, C. A., and Nixon, P. L. (2000) Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting J. Mol. Biol. 298, 167-185