Local RNA conformational dynamics revealed by 2-aminopurine solvent accessibility

Biochemistry

Volumn 47, Issue 27, 2008, Pages 7043-7052

  Ballin, Jeff D ^a   Prevas, James P ^a   Bharill, Shashank ^b   Gryczynski, Ignacy ^b   Gryczynski, Zygmunt ^b   Wilson, Gerald M ^a  

^a UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH TEXAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMIDES; FLUIDS; FLUORESCENCE; FLUORESCENCE SPECTROSCOPY; LIGHT EMISSION; LUMINESCENCE; PHOTOACOUSTIC EFFECT; QUENCHING; RNA; SOLVENTS;

(I ,J) CONDITIONS; 2 AMINOPURINE (2AP); ACRYLAMIDE (PAM); CONFORMATIONAL DYNAMICS; ENVIRONMENTAL INFLUENCES; FLUORESCENT PROBING; IN-VITRO; MONITOR (CO); NEAREST NEIGHBOR (NN); PHOTOPHYSICS; POPULATION MODELING; QUENCHING PARAMETERS; RNA SECONDARY STRUCTURES; RNA STRUCTURES; RNA SUBSTRATES; SOLVENT ACCESSIBILITY; SOLVENT EXPOSURE; TWO-STATE;

NUCLEIC ACIDS;

2 AMINOPURINE; ACRYLAMIDE; SOLVENT;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; FLUORESCENCE; HIGH TEMPERATURE; MOLECULAR DYNAMICS; PHOTOCHEMISTRY; PRIORITY JOURNAL; RNA CONFORMATION; RNA STRUCTURE; SOLVENT EFFECT; THERMODYNAMICS;

2-AMINOPURINE; ACRYLAMIDE; ALGORITHMS; BASE PAIRING; BASE SEQUENCE; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; RNA; SOLVENTS; TEMPERATURE;

EID: 46849116813     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi800487c     Document Type: Article

References (50)

1. Ward, D. C., Reich, E., and Stryer, L. (1969) Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside, and their derivatives. J. Biol. Chem. 244, 1228-1237.
2. Rist, M. J., and Marino, J. P. (2002) Fluorescent nucleotide base analogs as probes of nucleic acid structure, dynamics and interactions. Curr. Org. Chem. 6, 775-793.
3. Millar, D. P. (1996) Fluorescence studies of DNA and RNA structure and dynamics. Curr. Opin. Struct. Biol. 6, 322-326.
4. Ballin, J. D., Bharill, S., Fialcowitz-White, E. J., Gryczynski, I., Gryczynski, Z., and Wilson, G. M. (2007) Site-specific variations in RNA folding thermodynamics visualized by 2-aminopurine fluorescence. Biochemistry 46, 13948-13960.
5. Lee, B. J., Barch, M., Castner, E. W., Volker, J., and Breslauer, K. J. (2007) Structure and Dynamics in DNA Looped Domains: CAG Triplet Repeat Sequence Dynamics Probed by 2-Aminopurine Fluorescence. Biochemistry 46, 10756-10766.
6. Davis, S. P., Matsumura, M., Williams, A., and Nordlund, T. M. (2003) Position dependence of 2-aminopurine spectra in adenosine pentadeoxynucleotides. J. Fluoresc. 13, 249-259.
7. Jean, J. M., and Krueger, B. P. (2006) Structural fluctuations and excitation transfer between adenine and 2-aminopurine in single-stranded deoxytrinucleotides. J. Phys. Chem. B 110, 2899-2909.
8. O'Neill, M. A., and Barton, J. K. (2004) DNA-mediated charge transport requires conformational motion of the DNA bases: Elimination of charge transport in rigid glasses at 77 K. J. Am. Chem. Soc. 126, 13234-13235.
9. Rai, P., Cole, T. D., Thompson, E., Millar, D. P., and Linn, S. (2003) Steady-state and time-resolved fluorescence studies indicate an unusual conformation of 2-aminopurine within ATAT and TATA duplex DNA sequences. Nucleic Acids Res. 31, 2323-2332.
10. Somsen, O. J. G., Hoek, V. A., and Amerongen, V. H. (2005) Fluorescence quenching of 2-aminopurine in dinucleotides. Chem. Phys. Lett. 402, 61-65.
11. Xu, D. G., and Nordlund, T. M. (2000) Sequence dependence of energy transfer in DNA oligonucleotides. Biophys. J. 78, 1042-1058.
12. Rachofsky, E. L., Osman, R., and Ross, J. B. A. (2001) Probing structure and dynamics of DNA with 2-aminopurine: Effects of local environment on fluorescence. Biochemistry 40, 946-956.
13. Hardman, S. J. O., and Thompson, K. C. (2006) Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids. Biochemistry 45, 9145-9155.
14. Lakowicz, J. R. (1999) Principles of Fluorescence Spectroscopy, Kluwer Academic/Plenum, New York.
15. van den Bremer, E. T. J., Keeble, A. H., Visser, A. J. W. G., van Hoek, A., Kleanthous, C., Heck, A. J. R., and Jiskoot, W. (2004) Ligand-induced changes in the conformational dynamics of a bacterial cytotoxic endonuclease. Biochemistry 43, 4347-4355.
16. Thuduppathy, G. R., Craig, J. W., Kholodenko, V., Schon, A., and Hill, R. B. (2006) Evidence that membrane insertion of the cytosolic domain of Bcl-xL is governed by an electrostatic mechanism. J. Mol. Biol. 359, 1045-1058.
17. Padrick, S. B., and Miranker, A. D. (2001) Islet amyloid polypeptide: Identification of long-range contacts and local order on the fibrillogenesis pathway. J. Mol. Biol. 308, 783-794.
18. Kumar, A., Tyagi, N. K., Goyal, P., Pandey, D., Siess, W., and Kinne, R. K. H. (2007) Sodium-independent low-affinity D-glucose transport by human sodium/D-glucose cotransporter 1: Critical role of tryptophan 561. Biochemistry 46, 2758-2766.
19. Gao, H., Wang, Y. N., Fan, Y. G., and Ma, J. B. (2006) Interactions of some modified mono- and bis-β-cyclodextrins with bovine serum albumin. Bioorg. Med. Chem. 14, 131-137.
20. Provitera, P., Bouamr, F., Murray, D., Carter, C., and Scarlata, S. (2000) Binding of equine infectious anemia virus matrix protein to membrane bilayers involves multiple interactions. J. Mol. Biol. 296, 887-898.
21. Gorbenko, G. P., Ioffe, V. M., and Kinnunen, P. K. J. (2007) Binding of lysozyme to phospholipid bilayers: Evidence for protein aggregation upon membrane association. Biophys. J. 93, 140-153.
22. Nandi, P. K., Bera, A., and Sizaret, P. Y. (2006) Osmolyte trimethylamine N-oxide converts recombinant α-helical prion protein to its soluble β-structured form at high temperature. J. Mol. Biol. 362, 810-820.
23. Brewer, B. Y., Ballin, J. D., Fialcowitz-White, E. J., Blackshear, P. J., and Wilson, G. M. (2006) Substrate dependence of conformational changes in the RNA-binding domain of tristetraprolin assessed by fluorescence spectroscopy of tryptophan mutants. Biochemistry 45, 13807-13817.
24. Yi-Brunozzi, H. Y., Stephens, O. M., and Beal, P. A. (2001) Conformational changes that occur during an RNA-editing adenosine deamination reaction. J. Biol. Chem. 276, 37827-37833.
25. Deb, S., Bandyopadhyay, S., and Roy, S. (2000) DNA sequence dependent and independent conformational changes in multipartite operator recognition by λ-repressor. Biochemistry 39, 3377-3383.
26. 7GTP and mRNA analogues. J. Biol. Chem. 270, 29904-29909.
27. Li, J., Correia, J. J., Wang, L., Trent, J. O., and Chaires, J. B. (2005) Not so crystal clear: The structure of the human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic Acids Res. 33, 4649-4659.
28. Stivers, J. T. (1998) 2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: Metal-ion and base sequence effects. Nucleic Acids Res. 26, 3837-3844.
29. Tleugabulova, D., and Reha-Krantz, L. J. (2007) Probing DNA polymerase-DNA interactions: Examining the template strand in exonuclease complexes using 2-aminopurine fluorescence and acrylamide quenching. Biochemistry 46, 6559-6569.
30. Malta, E., Moolenaar, G. F., and Goosen, N. (2006) Base flipping in nucleotide excision repair. J. Biol. Chem. 281, 2184-2194.
31. Walter, N. G., Harris, D. A., Pereira, M. J. B., and Rueda, D. (2001) In the fluorescent spotlight: Global and local conformational changes of small catalytic RNAs. Biopolymers 61, 224-242.
32. Sakamoto, T., Mahara, A., Yamagata, K., Iwase, R., Yamaoka, T., and Murakami, A. (2005) Evaluation of dynamic features of Escherichia coli 16S ribosomal RNA in homogeneous physiological solution. Biophys. J. 89, 4122-4128.
33. Chao, P. W., and Chow, C. S. (2007) Monitoring aminoglycoside-induced conformational changes in 16S rRNA through acrylamide quenching. Bioorg. Med. Chem. 15, 3825-3831.
34. Balbo, P. B., Toth, J., and Bohm, A. (2007) X-ray crystallographic and steady state fluorescence characterization of the protein dynamics of yeast polyadenylate polymerase. J. Mol. Biol. 366, 1401-1415.
35. Hermann, T., and Patel, D. J. (2000) RNA bulges as architectural and recognition motifs. Structure 8, R47-R54.
36. Borer, P. N., Lin, Y., Wang, S., Roggenbuck, M. W., Gott, J. M., Uhlenbeck, O. C., and Pelczer, I. (1995) Proton NMR and structural features of a 24-nucleotide RNA hairpin. Biochemistry 34, 6488-6503.
37. Ennifar, E., and Dumas, P. (2006) Polymorphism of bulged-out residues in HIV-1 RNA DIS kissing complex and structure comparison with solution studies. J. Mol. Biol. 356, 771-782.
38. Berglund, J. A., Rosbash, M., and Schultz, S. C. (2001) Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines. RNA 7, 682-691.
39. Jaeger, J. A., and Tinoco, I. (1993) An NMR study of the HIV-1 TAR element hairpin. Biochemistry 32, 12522-12530.
40. Colvin, R. A., White, S. W., Garcia-Blanco, M. A., and Hoffman, D. W. (1993) Structural features of an RNA containing the CUGGGA loop of the human immunodeficiency virus type 1 transactivation response element. Biochemistry 32, 1105-1112.
41. Klinck, R., Sprules, T., and Gehring; K. (1997) Structural characterization of three RNA hexanucleotide loops from the internal ribosome entry site of polioviruses. Nucleic Acids Res. 25, 2129-2137.
42. Wilson, G. M., Sun, Y., Lu, H., and Brewer, G. (1999) Assembly of AUF1 oligomers on U-rich RNA targets by sequential dimer association. J. Biol. Chem. 274, 33374-33381.
43. Myers, R. H. (1990) Criteria for choice of best model. In Classical and Modern Regression with Applications, 2nd ed., pp 164-208, PWS-KENT Publishing Co., Boston.
44. Madan, B., and Sharp, K. A. (2001) Hydration heat capacity of nucleic acid constituents determined from the Random Network Model. Biophys. J. 81, 1881-1887.
45. Poland, D., Vournakis, J. N., and Scheraga, H. A. (1966) Cooperative interactions in single-strand oligomers of adenylic acid. Biopolymers 4, 223-235.
46. Bloomfield, V. A., Crothers, D. M., and Tinoco, I., Jr. (2000) Nucleic Acids: Structure, Properties and Functions, University Science, Sausalito, CA.
47. Dornberger, U., Hillisch, A., Gollmick, F. A., Fritzsche, H., and Diekmann, S. (1999) Solution structure of a five-adenine bulge loop within a DNA duplex. Biochemistry 38, 12860-12868.
48. Smoluchowski, M. V. (1917) Versuch einer mathematischen theorie der koagulationskinetik kolloider lösungen. Z. Phys. Chem. 92, 129-168.
49. Eftink, M. R., and Chiron, C. A. (1976) Fluorescence quenching of indole and model micelle systems. J. Phys. Chem. 80, 486-493.
50. Kawahara, K., and Tanford, C. (1966) Viscosity and density of aqueous solutions of urea and guanidine hydrochloride. J. Biol. Chem. 241, 3228-3232.