Sequence-dependent conformational differences of small RNAs revealed by native gel electrophoresis

Analytical Biochemistry

Volumn 273, Issue 2, 1999, Pages 284-290

  Beuning, Penny J ^a   Tessmer, Michael R ^a   Baumann, Christoph G ^a   Kallick, Deborah A ^a   Musier Forsyth, Karin ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

Author keywords

Laser light scattering; Magnesium; Native gel electrophoresis; NMR; RNA

Indexed keywords

LIGHT SCATTERING; MAGNESIUM; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; RNA;

AGGREGATION STATE; BASE STACKING EFFECTS; CONFORMATIONAL DIFFERENCES; LASER LIGHT SCATTERING; NATIVE GEL ELECTROPHORESIS; POLYACRYLAMIDE GEL ELECTROPHORESIS; RNA CONFORMATION; SEQUENCE-DEPENDENT;

ELECTROPHORESIS;

BASE; HYDROXYL GROUP; MAGNESIUM ION; RNA;

AMINO ACID SEQUENCE; ARTICLE; CONFORMATION; LIGHT SCATTERING; MOLECULAR DYNAMICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL;

EID: 0033543603     PISSN: 00032697     EISSN: None     Source Type: Journal    
DOI: 10.1006/abio.1999.4223     Document Type: Article

References (27)

1. Bassi G. S., Murchie A. I. H., Lilley D. M. J. The ion-induced folding of the hammerhead ribozyme: Core sequence changes that perturb folding into the active conformation. RNA. 2:1996;756-768.
2. Maniatis T., Fritsch E. F., Sambrook J. Molecular Cloning: A Laboratory Manual. 1982;Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
3. Scaringe S. A., Francklyn C., Usman N. Chemical synthesis of biologically active oligoribonucleotides using β-cyanoethyl protected ribonucleoside phosphoramidites. Nucleic Acids Res. 18:1990;5433-5441.
4. Sproat B., Colonna F., Mullah B., Tsou D., Andrus A., Hampel A., Vinayak R. An efficient method for the isolation and purification of oligoribonucleotides. Nucleosides Nucleotides. 14:1995;255-273.
5. Pro. Biochemistry. 33:1994;12708-12714.
6. Northrop T. G., Nutter R. L., Sinsheimer R. L. Refractive increment of thymus nucleic acid. J. Am. Chem. Soc. 75:1953;5134-5135.
7. Varani G., Cheong C., Tinoco I. Jr. Structure of an unusually stable RNA hairpin. Biochemistry. 30:1991;3280-3289.
8. Limmer S., Hofmann H.-P., Ott G., Sprinzl M. The 3′-terminal end (NCCA) of tRNA determines the structure and stability of the aminoacyl acceptor stem. Proc. Natl. Acad. Sci. USA. 90:1993;6199-6202.
9. Allain F. H.-T., Varani G. Structure of the P1 helix from group I self-splicing introns. J. Mol. Biol. 250:1995;330-353.
10. Ala. FEBS Lett. 385:1996;15-20.
11. Liu H., Kessler J., Peterson R., Musier-Forsyth K. Evidence for class-specific discrimination of a semiconserved base pair by tRNA synthetases. Biochemistry. 34:1995;9795-9800.
12. Shi J.-P., Martinis S. A., Schimmel P. RNA tetraloops as minimalist substrates for aminoacylation. Biochemistry. 31:1992;4931-4936.
13. Ott G., Arnold L., Limmer S. Proton NMR studies of manganese ion binding to tRNA-derived acceptor stem duplexes. Nucleic Acids Res. 21:1993;5859-5864.
14. Leontis N. B., Ghosh P., Moore P. B. Effect of magnesium ion on the structure of the 5S RNA from Escherichia coli. An imino proton magentic resonance study of helix I, IV, and V regions of the molecule. Biochemistry. 25:1986;7386-7392.
15. Wyatt J. R., Puglisi J. D., Tinoco I. Jr. RNA pseudoknots: Stability and loop requirements. J. Mol. Biol. 214:1990;455-470.
16. 2+ and a conformational transition at the anticodon stem-loop of yeast phenylalanine tRNA. Biochemistry. 32:1993;10249-10253.
17. Cate J. H., Doudna J. A. Metal-binding sites in the major groove of a large ribozyme domain. Structure. 4:1996;1221-1229.
18. Rastogi T., Beattie T. L., Olive J. E., Collins R. A. A long-range pseudoknot is required for activity of the Neurospora VS ribozyme. EMBO J. 15:1996;2820-2825.
19. Scott W. G., Murray J. B., Arnold J. R. P., Stoddard B. L., Klug A. Capturing the structure of a catalytic RNA intermediate: The hammerhead ribozyme. Science. 274:1996;2065-2069.
20. Chen C., Guo P. Magnesium-induced conformational change of packaging RNA for procapsid recognition and binding during phage φ29 DNA encapsidation. J. Virol. 71:1997;495-500.
21. Kirchner R., Vogtherr M., Limmer S., Sprinzl M. Secondary structure dimorphism and interconversion between hairpin and duplex forms of oligoribonucleotides. Antisense Nucleic Acid Drug Dev. 8:1998;507-516.
22. Leulliot N., Baumruk V., Abdelkafi M., Turpin P.-Y., Namane A., Gouyette C., Huynh-Dunh T., Ghomi M. Unusual nucleotide conformations in GNRA and UNCG type tetraloop hairpins: Evidence from Raman markers assignments. Nucleic Acids Res. 27:1999;1398-1404.
23. Freier S. M., Alkema D., Sinclair A., Neilson T., Turner D. H. Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. Biochemistry. 24:1985;4533-4539.
24. Turner D. H., Sugimoto N., Freier S. M. RNA structure prediction. Ann. Rev. Biophys. Biophys. Chem. 17:1988;167-192.
25. Gregorian R. S. Jr., Crothers D. M. Determinants of RNA hairpin loop-loop complex stability. J. Mol. Biol. 248:1995;968-984.
26. Sugimoto N., Kierzek R., Turner D. H. Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry. 26:1987;4554-4558.
27. Ala: Role of the G3:U70 base pair in synthetase recognition. Nucleic Acids Res. 25:1997;2083-2090.