Imino proton exchange and base-pair kinetics in the AMP-RNA aptamer complex

Journal of Molecular Biology

Volumn 268, Issue 2, 1997, Pages 359-374

  Nonin, Sylvie ^a   Jiang, Feng ^a   Patel, Dinshaw J ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

AMP RNA aptamer complex; Base pair dissociation constants; Imino proton exchange; Mismatch pair opening; Sugar 2' OH groups

Indexed keywords

ADENOSINE PHOSPHATE; IMINO ACID; PROTON; RNA;

ARTICLE; BASE PAIRING; DISSOCIATION CONSTANT; HYDROGEN BOND; ION EXCHANGE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEIC ACID STRUCTURE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

EID: 0031547976     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.0986     Document Type: Article

References (34)

1. Allain F. H.-T., Varani G. Structure of the P1 helix from group I self-splicing introns. J. Mol. Biol. 250:1995;333-353.
2. Dieckmann T., Suzuki E., Nakamura G. K., Feigon J. Solution structure of an ATP-binding RNA aptamer reveals a novel fold. RNA. 2:1996;628-640.
3. Folta-Stogniew E., Russu I. M. Base-catalysis of imino proton exchange in DNA: Effects of catalyst upon DNA structure and dynamics. Biochemistry. 35:1996;8439-8449.
4. Forsèn S., Hoffman R. A. Study of moderately rapid chemical exchange reaction by means of nuclear magnetic double resonance. J. Chem. Phys. 39:1963;2892-2901.
5. Fritzsche H., Kan L. S., Ts'o P. O. P. NMR study of the exchange behaviour of the NH-N of a ribonucleic acid miniduplex. Biochemistry. 22:1983;277-280.
6. Gehring K., Leroy J. L., Guéron M. A tetrameric DNA structure with protonated cytosine-cytosine base-pairs. Nature. 363:1993;561-565.
7. Guéron M., Leroy J. L. Studies of base-pair kinetics by NMR measurement of proton exchange. Methods in enzymology. 1995;Academic Press, San Diego.
8. Guéron M., Kochoyan M., Leroy J. L. A single mode of DNA base-pair opening drives imino proton exchange. Nature. 328:1987;89-92.
9. Guéron M., Charretier E., Hagerhorst J., Kochoyan M., Leroy J. L., Moraillon A. Application of imino proton exchange to nucleic acid kinetics and structure. Sarma R. H., Sarma M. H. Structure and Methods, Proceedings of the Sixth Conversation in Biomolecular Stereodynamics. 1989;Adenine Press, NY.
10. Jiang F., Kumar R. A., Jones R. A., Patel D. J. Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex. Nature. 382:1996a;183-186.
11. Jiang F., Fiala R., Live D., Kumar R. A., Patel D. J. RNA folding topology and intermolecular contacts in the AMP-RNA aptamer complex. Biochemistry. 35:1996b;13250-13256.
12. Jiang F., Patel D. J., Zhang X., Zhao H., Jones R. A. Specific labeling approaches to guanine and adenine imino and amino proton assignments in the AMP-RNA aptamer complex. J. Biomol. NMR. 9:1997;55-62.
13. Kochoyan M., Leroy J. L., Guéron M. Proton exchange and base-pair lifetimes in a deoxy-duplex containing a purine-pyrimidine step, and in the duplex of inverse sequence. J. Mol. Biol. 196:1987;599-608.
14. Kochoyan M., Leroy J. L., Guéron M. Processes of base-pair opening and proton exchange in Z-DNA. Biochemistry. 29:1990;4799-4805.
15. Leontis N. B., Moore P. B. Imino proton exchange in the 5 S RNA of E. coli and its complex with the protein L25 at 490 Mhz. Biochemistry. 25:1986;5736-5744.
16. Leroy J. L., Bolo N., Figueroa N., Plateau P., Guéron M. Internal motions of transfer RNA: A study of exchanging protons by magnetic resonance. J. Biomol. Struct. Dynam. 2:1985a;915-939.
17. Leroy J. L., Broseta D., Guéron M. Proton exchange and base-pair kinetics of poly(rA).poly(rU) and poly(rI).poly(rC). J. Mol. Biol. 184:1985b;165-178.
18. Leroy J. L., Charretier E., Kochoyan M., Guéron M. Evidence from base-pair kinetics for two adenine tract structures in solution: their relation to DNA curvature. Biochemistry. 27:1988a;8894-8898.
19. Leroy J. L., Kochoyan M., Huynh-Dinh T., Guéron M. Characterization of base-pair opening in deoxy-duplexes, using catalyzed exchange of the imino proton. J. Mol. Biol. 200:1988b;223-238.
20. Leroy J. L., Gao X., Guéron M., Patel D. J. Proton exchange and internal motions in two chromomycin dimer-DNA oligomer complexes. Biochemistry. 30:1991;5653-5661.
21. Leroy J. L., Gao X., Misra V., Guéron M., Patel D. J. Proton exchange in DNA-luzopeptin and DNA-echinomycin bisintercalation complexes: Rates and processes of base-pair opening. Biochemistry. 31:1992;1407-1414.
22. Leroy J. L., Gehring A., Kettani A., Guéron M. Acid multimers of oligo-deoxy-cytidine strands: Stoichiometry, base-pair characterization and proton exchange properties. Biochemistry. 32:1993;6019-6031.
23. Maltseva T. V., Yamakage S.-I., Chattoppadhyaya J. Direct estimation of base-pair exchange kinetics in oligo-DNA by a combination of NOESY and ROESY experiments. Nucl. Acids Res. 21:1993;4288-4295.
24. Maltseva T. V., Zarytova V. F., Chattoppadhyaya J. Base-pair exchange kinetics of the imino and amino protons of the 3′-phenazinium tethered DNA-RNA duplex, r(5′-GAUUGAA-3′):d(5′-TCAATC-3′-Pzn), and their comparison with those of B -DNA. J. Biochem. Biophys. Methods. 30:1995;163-177.
25. Moe J. G., Folta Stogniew E., Russu I. M. Energetics of base-pair opening in a DNA dodecamer containing an A3T3 tract. Nucl. Acids Res. 23:1995;1984-1989.
26. Moe J. G., Russu I. M. Proton exchange and base-pair opening in d(CGCGAATTCGCG) and related dodecamers. Nucl. Acids Res. 18:1990;821-827.
27. Morris G. A., Freeman R. Selective excitation techniques in Fourier transform NMR. J. Magn. Res. 29:1978;433-462.
28. Nonin, S. 1995, Elucidation des phénomènes d'échange des protons imino de l'ADN: cas des bases modifiées, des paires terminales, et de la catalyse acide des paires G·C, Thèse de doctorat de l'Université Pierre et Marie Curie, Paris VI.
29. 4tetramer. J. Mol. Biol. 261:1996;399-414.
30. Nonin S., Leroy J. L., Guéron M. Terminal base-pairs of oligo-deoxynucleotides: imino proton exchange and fraying. Biochemistry. 34:1995;10652-10659.
31. Nonin S., Leroy J. L., Guéron M. Acid-induced exchange of the imino proton in G·C base-pair. Nucl. Acids Res. 24:1996;586-595.
32. Plateau P., Guéron M. Exchangeable proton without base line distortion using a new strong pulse sequence. J. Am. Chem. Soc. 104:1982;7310-7311.
33. Sassanfar M., Szostak J. W. An RNA motif that binds ATP. Nature. 364:1993;550-553.
34. Ts'o P. O. P. Basic Principles of Nucleic Acid Chemistry. 1974;Academic Press, New York and London.