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2001 | 48 | 2 |

Tytuł artykułu

Elements of thermodynamics in RNA evolution

Warianty tytułu

Języki publikacji

EN

Abstrakty

EN
The pa per pres ents some as pects cor re lat ing ther mal sta bil ity of RNA fold ing and the oc cur rence of struc tural mo tifs in nat u ral ri bo nu cleic ac ids. Par tic u larly, the ther- mody namic sta bil ity of 2 -5' and 3'-5' linked RNA and the contribution of unpaired ter mi nal nu cleo tides (dan gling ends) in sec ond ary (2D) and ter tiary (3D) struc tures of RNA are dis cussed. Both ex am ples sug gest that dur ing evo lu tion na ture se lected se­quences and struc tures of RNA which are the most ther mally sta ble and ef fi cient for their bi o log i cal func tion.

Słowa kluczowe

Wydawca

-

Rocznik

Tom

48

Numer

2

Opis fizyczny

p.485-493,fig.

Twórcy

autor
  • Polish Academy of Sciences, Z.Noskowskiego 12-14, 60-704 Poznan, Poland
autor
autor

Bibliografia

  • 1.Gesteland, R.F. & Atkins, J.F. (1993) The RNA world. Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
  • 2.Matysiak, M., Wrzesinski, J. & Ciesiolka, J. (1999) Sequentional folding of the genomic ribozyme of the hepatitis delta virus: Structural analysis of RNA transcription intermediates. J. Mol. Biol. 291, 283-294.
  • 3.Jaeger, J.A., Turner, D.H. & Zucker, M. (1989) Improved prediction of secondary structure for RNA. Proc. Natl. Acad. Sci. U.S.A. 86, 7706-7710.
  • 4.Baglioni, C., Minks, M.A. & Maroney, P.A. (1978) Interferon action may be mediated by activation of a nuclease by pppA2'p5'A2' p5'A. Nature 273, 684-687.
  • 5.Orgel, L.E. (1987) Evolution of the genetic apparatus: A review. Cold Spring Harbor Symp. Quant. Biol. 52, 123-133.
  • 6.Breslow, R., Anslyn, E. & Huang, D.-L. (1991) Ribonuclease mimics. Tetrahedron 47, 2365- 2376.
  • 7.Usher, D.A. (1972) RNA double helix and the evolution of the 3',5' linkage. Nat. New Biology 235, 207-208.
  • 8.Usher, D.A. & McHale, A.H. (1976) Hydrolytic stability of helical RNA: A selective advantage for the natural 3',5'-bond. Proc. Natl. Acad. Sci. U.S.A. 73, 1149-1153.
  • 9.Kierzek, R., He, L. & Turner, D.H. (1992) Association of 2'-5' oligoribonucleotides. Nucleic Acids Res. 20, 1685-1690.
  • 10.Xia, T., SantaLucia, J., Burkard, M.E., Kierzek, R., Schroeder, S.J., Cox, C. & Turner, D.H. (1998) Parameters for expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pair. Biochemistry 37, 14719-14735.
  • 11.Kierzek, R., Burkard, M.E. & Turner, D.H. (1999) The thermodynamics of single mismatches in RNA duplexes. Biochemistry 38, 14214-14223.
  • 12.Tunis-Schneider, M.J.B. & Maestre, M.F. (1970) Circular dichroism spectra of oriented and unoriented deoxyribonucleic acid films: A preliminary study. J. Mol. Biol. 52, 521-541.
  • 13.Williams, A.P., Longfellow, C.L., Freier, S.M., Kierzek, R. & Turner, D.H. (1989) Laser temperature-jump, spectroscopic and thermodynamic study of salt effects on duplex formation by dGCATGC. Biochemistry 28, 4283-4291.
  • 14.Xia, T., McDowell, J.A. & Turner, D.H. (1997) Thermodynamics of nonsymetric tandem mismatches adjacent to G-C base pairs in RNA. Biochemistry 36, 12486-12497.
  • 15.Dougherty, J.P., Rizzo, C.J. & Breslow, R. (1992) Oligodeoxynucleotides that contain 2',5' linkages: Synthesis and hybridization properties. J. Am. Chem. Soc. 114, 6254- 6255.
  • 16.Hashimoto, H. & Switzer, C. (1992) Self-association of 2',5'-linked deoxynucleotides: meta- DNA. J. Am. Chem. Soc. 114, 6255-6256.
  • 17.Robinson, H., Jung, K.-E., Switzer, C. & Wang, A.H.-J. (1995) DNA with 2'-5' phosphodiester bonds forms a duplex structure in the A-type conformation. J. Am. Chem. Soc. 117, 837-838.
  • 18.Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.H., Neilson, T. & Turner, D.H. (1986) Improved free energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. U.S.A. 83, 9373- 9377.
  • 19.Sugimoto, N., Kierzek, R. & Turner, D.H. (1987) Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry 26, 4554-4559.
  • 20.Quigley, G.J. & Rich, A., (1976) Structural domains of transfer RNA molecules. Science 194, 791-802.
  • 21.Protein Data Bank (http://www.pdb.bnl/gov), Nucleic Acid Data Base (http://ndbserver. ritgers. edu).
  • 22.Burkard, M.E., Kierzek, R. & Turner, D.H. (1999) Thermodynamics of unpaired terminal nucleotides on short RNA helixes correlates with stacking at helix termini in larger RNAs. J. Mol. Biol. 290, 967-982.
  • 23.Sprinzl, M., Horn, C., Brown, M., Ioudovitch, A. & Steinberg, S. (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 26, 148-153.
  • 24.Mathews, D.H., Sabina, J., Zucker, M. & Turner, D.H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940.

Typ dokumentu

Bibliografia

Identyfikatory

Identyfikator YADDA

bwmeta1.element.agro-article-64492f5b-dfe2-45d3-907d-401891083439
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