Nucleic Acids Research, 1992, Vol. 20, No. 4 819-824
© 1992
Articles |
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
Department of Chemistry and Laboratory of Chemical Biodynamics, University of California Berkeley, CA 94720, USA
*To whom correspondence should be addressed
Received November 4, 1991. Revised January 21, 1992. Accepted January 21, 1992.
We determined the melting temperatures (Tm) and thermodynamic parameters of 15 RNA and 19 DNA hairpins at 1 M NaCI, 0.01 M sodium phosphate, 0.1 mM EDTA, at pH 7. All these hairpins have loops of four bases, the most common loop size in 16S and 23S ribosomal RNAs. The RNA hairpins varied in loop sequence, loop-closing base pair (A.U, C G, or G.C), base sequence of the stem, and stem size (four or five base pairs). The DNA hairpins varied in loop sequence, loop-closing base pair (C-G, or G-C), and base sequence of the four base-pair stem. Thermodynamic properties of a hairpin may be represented by nearest-neighbor interactions of the stem plus contributions from the loop. Thus, we obtained thermodynamic parameters for the formation of RNA and DNA tetraloops. For the tetraloops we studied, a free energy of loop formation (at 37°C) of about +3 kcal/mol is most common for either RNA or DNA. There are extra stable loops with 
G°37 near +1 kcal/mol, but the sequences are not necessarily the same for RNA and DNA. The closing base pair is also important; changing from C-G to G-C lowered the stability of several tetraloops in both RNA and DNA. These values will be useful in predicting RNA and DNA secondary structures.
+Present address: Geraldine Brush Cancer Research Institute, Medical Research Institute of San Francisco, 2330 Clay Street, San Francisco, CA 94115, USA
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  W. Rypniewski, D. A. Adamiak, J. Milecki, and R. W. Adamiak Noncanonical G(syn)-G(anti) base pairs stabilized by sulphate anions in two X-ray structures of the (GUGGUCUGAUGAGGCC) RNA duplex RNA, September 1, 2008; 14(9): 1845 - 1851. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
K. R. Julien, M. Sumita, P.-H. Chen, I. A. Laird-Offringa, and C. G. Hoogstraten Conformationally restricted nucleotides as a probe of structure-function relationships in RNA RNA, August 1, 2008; 14(8): 1632 - 1643. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 E. Kierzek, R. Kierzek, W. N. Moss, S. M. Christensen, T. H. Eickbush, and D. H. Turner Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function Nucleic Acids Res., April 1, 2008; 36(6): 1770 - 1782. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Kannan and M. Zacharias Folding of a DNA Hairpin Loop Structure in Explicit Solvent Using Replica-Exchange Molecular Dynamics Simulations Biophys. J., November 1, 2007; 93(9): 3218 - 3228. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
E. J. Belfield, R. K. Hughes, N. Tsesmetzis, M. J. Naldrett, and R. Casey The gateway pDEST17 expression vector encodes a -1 ribosomal frameshifting sequence Nucleic Acids Res., February 28, 2007; 35(4): 1322 - 1332. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. N. Singh, R. N. Singh, and E. J. Androphy Modulating role of RNA structure in alternative splicing of a critical exon in the spinal muscular atrophy genes Nucleic Acids Res., January 28, 2007; 35(2): 371 - 389. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Z. J. Lu, D. H. Turner, and D. H. Mathews A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation Nucleic Acids Res., October 18, 2006; 34(17): 4912 - 4924. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. M. Garrey, R. Voelker, and J. A. Berglund An Extended RNA Binding Site for the Yeast Branch Point-binding Protein and the Role of Its Zinc Knuckle Domains in RNA Binding J. Biol. Chem., September 15, 2006; 281(37): 27443 - 27453. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. T. Woodside, W. M. Behnke-Parks, K. Larizadeh, K. Travers, D. Herschlag, and S. M. Block Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins PNAS, April 18, 2006; 103(16): 6190 - 6195. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Hsiao, S. Mohan, E. Hershkovitz, A. Tannenbaum, and L. D. Williams Single nucleotide RNA choreography Nucleic Acids Res., March 10, 2006; 34(5): 1481 - 1491. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. CAO and S.-J. CHEN Predicting RNA folding thermodynamics with a reduced chain representation model RNA, December 1, 2005; 11(12): 1884 - 1897. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. L. Kuznetsova, M. A. Zenkova, H. J. Gross, and V. V. Vlassov Enhanced RNA cleavage within bulge-loops by an artificial ribonuclease Nucleic Acids Res., February 24, 2005; 33(4): 1201 - 1212. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Kampmann Obstacle Bypass in Protein Motion along DNA by Two-dimensional Rather than One-dimensional Sliding J. Biol. Chem., September 10, 2004; 279(37): 38715 - 38720. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
D. H. Mathews, M. D. Disney, J. L. Childs, S. J. Schroeder, M. Zuker, and D. H. Turner Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure PNAS, May 11, 2004; 101(19): 7287 - 7292. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Sarzynska, L. Nilsson, and T. Kulinski Effects of Base Substitutions in an RNA Hairpin from Molecular Dynamics and Free Energy Simulations Biophys. J., December 1, 2003; 85(6): 3445 - 3459. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
O. Schrader, T. Baumstark, and D. Riesner A Mini-RNA containing the tetraloop, wobble-pair and loop E motifs of the central conserved region of potato spindle tuber viroid is processed into a minicircle Nucleic Acids Res., February 1, 2003; 31(3): 988 - 998. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
V. Baumruk, C. Gouyette, T. Huynh-Dinh, J.-S. Sun, and M. Ghomi Comparison between CUUG and UUCG tetraloops: thermodynamic stability and structural features analyzed by UV absorption and vibrational spectroscopy Nucleic Acids Res., October 1, 2001; 29(19): 4089 - 4096. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Astatke, N. D. F. Grindley, and C. M. Joyce Deoxynucleoside Triphosphate and Pyrophosphate Binding Sites in the Catalytically Competent Ternary Complex for the Polymerase Reaction Catalyzed by DNA Polymerase I (Klenow Fragment) J. Biol. Chem., January 27, 1995; 270(4): 1945 - 1954. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
Y. Xu, O. Potapova, A. E. Leschziner, N. D. F. Grindley, and C. M. Joyce Contacts between the 5' Nuclease of DNA Polymerase I and Its DNA Substrate J. Biol. Chem., August 3, 2001; 276(32): 30167 - 30177. [Abstract] [Full Text] [PDF]
|
|