Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1976 Sep;3(9):2233–2241. doi: 10.1093/nar/3.9.2233

The kinetics of binding of U-U-C-A to a dodecanucleotide anticodon fragment from yeast tRNA-Phe.

K Yoon, D H Turner, I Tinoco Jr, F Haar, F Cramer
PMCID: PMC343079  PMID: 787934

Abstract

The kinetics of U-U-C-A binding to the dodecanucleotide (A-Cm-U-Gm-A-A-Y-A-psi-m5C-U-Gp) isolated from the anticodon region of yeast tRNA-Phe are similar to the kinetics of binding of U-U-C-A to intact tRNA-Phe. A large enhancement in binding constant over that predicted for U-U-C-A-U-G-A-A is observed for both the complexes of dodecanucleotide and tRNA-Phe with U-U-C-A. This strongly suggests that both the anticodon loop in tRNA-Phe and the dodecanucleotide can form four base pairs with U-U-C-A. Furthermore, the enhanced stability cannot be attributed to a special conformation of the anticodon loop, but instead the anticodon loop is probably flexible. A likely explanation for the increased binding is the effect of non-base-paired ends. This increased thermodynamic stability comes from a larger entropy gain rather than a larger enthalpy decrease.

Full text

PDF
2236

Images in this article

2236Image
on p.2236

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Beardsley K., Tao T., Cantor C. R. Studies on the conformation of the anticodon loop of phenylalanine transfer ribonucleic acid. Effect of environment on the fluorescence of the Y base. Biochemistry. 1970 Sep 1;9(18):3524–3532. doi: 10.1021/bi00820a005. [DOI] [PubMed] [Google Scholar]
  2. Borer P. N., Dengler B., Tinoco I., Jr, Uhlenbeck O. C. Stability of ribonucleic acid double-stranded helices. J Mol Biol. 1974 Jul 15;86(4):843–853. doi: 10.1016/0022-2836(74)90357-x. [DOI] [PubMed] [Google Scholar]
  3. Drake A. F., Mason S. F., Trim A. R. Optical studies of the base-stacking properties of 2'-O-methylated dinucleoside monophosphates. J Mol Biol. 1974 Jul 15;86(4):727–739. doi: 10.1016/0022-2836(74)90349-0. [DOI] [PubMed] [Google Scholar]
  4. Eisinger J. Complex formation between transfer RNA'S with complementary anticodons. Biochem Biophys Res Commun. 1971 May 21;43(4):854–861. doi: 10.1016/0006-291x(71)90695-4. [DOI] [PubMed] [Google Scholar]
  5. Eisinger J., Feuer B., Yamane T. Codon-anticodon binding in tRNAphe. Nat New Biol. 1971 May 26;231(21):126–128. doi: 10.1038/newbio231126a0. [DOI] [PubMed] [Google Scholar]
  6. Eisinger J., Gross N. The anticodon-anticodon complex. J Mol Biol. 1974 Sep 5;88(1):165–174. doi: 10.1016/0022-2836(74)90302-7. [DOI] [PubMed] [Google Scholar]
  7. Eisinger J., Spahr P. F. Binding of complementary pentanucleotides to the anticodon loop of transfer RNA. J Mol Biol. 1973 Jan;73(1):131–137. doi: 10.1016/0022-2836(73)90165-4. [DOI] [PubMed] [Google Scholar]
  8. Grosjean H., Söll D. G., Crothers D. M. Studies of the complex between transfer RNAs with complementary anticodons. I. Origins of enhanced affinity between complementary triplets. J Mol Biol. 1976 May 25;103(3):499–519. doi: 10.1016/0022-2836(76)90214-x. [DOI] [PubMed] [Google Scholar]
  9. Jaskunas S. R., Cantor C. R., Tinoco I., Jr Association of complementary oligoribonucleotides in aqueous solution. Biochemistry. 1968 Sep;7(9):3164–3178. doi: 10.1021/bi00849a020. [DOI] [PubMed] [Google Scholar]
  10. Ladner J. E., Jack A., Robertus J. D., Brown R. S., Rhodes D., Clark B. F., Klug A. Atomic co-ordinates for yeast phenylalanine tRNA. Nucleic Acids Res. 1975 Sep;2(9):1629–1637. doi: 10.1093/nar/2.9.1629. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Maelicke A., von der Haar F., Cramer F. Spectroscopic properties of oligonucleotides excised from the anticodon region of phenylalanine tRNA from yeast. Biopolymers. 1973;12(1):27–43. doi: 10.1002/bip.1973.360120104. [DOI] [PubMed] [Google Scholar]
  12. Martin F. H., Uhlenbeck O. C., Doty P. Self-complementary oligoribonucleotides: adenylic acid-uridylic acid block copolymers. J Mol Biol. 1971 Apr 28;57(2):201–215. doi: 10.1016/0022-2836(71)90341-x. [DOI] [PubMed] [Google Scholar]
  13. Ohashi Ziro, Harada Fumio, Nishimura Susumu. Primary sequence of glutamic acid tRNA II from Escherichia coli. FEBS Lett. 1972 Feb 1;20(2):239–241. doi: 10.1016/0014-5793(72)80804-4. [DOI] [PubMed] [Google Scholar]
  14. Pongs O., Reinwald E. Function of Y in codon-anticodon interaction of tRNA Phe . Biochem Biophys Res Commun. 1973 Jan 23;50(2):357–363. doi: 10.1016/0006-291x(73)90848-6. [DOI] [PubMed] [Google Scholar]
  15. Pörchke D. The nature of stacking interations in polynucleotides. Molecular states in Oligo- and polyribocytidylic acids by relaxation analysis. Biochemistry. 1976 Apr 6;15(7):1495–1499. doi: 10.1021/bi00652a021. [DOI] [PubMed] [Google Scholar]
  16. Quigley G. J., Seeman N. C., Wang A. H., Suddath F. L., Rich A. Yeast phenylalanine transfer RNA: atomic coordinates and torsion angles. Nucleic Acids Res. 1975 Dec;2(12):2329–2341. doi: 10.1093/nar/2.12.2329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Singh H., Hillier B. Oligonucleotide studies: optical rotatory dispersion of normal and 2'-O-methylated diribonucleoside monophosphates. Biopolymers. 1971;10(12):2445–2457. doi: 10.1002/bip.360101208. [DOI] [PubMed] [Google Scholar]
  18. Yoon K., Turner D. H., Tinoco I., Jr The kinetics of codon-anticodon interaction in yeast phenylalanine transfer RNA. J Mol Biol. 1975 Dec 25;99(4):507–518. doi: 10.1016/s0022-2836(75)80169-0. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES