Ewa Biała

Publications (4)27.77 Total impact

• Article: Amphiphilic 3'-peptidyl-RNA conjugates.

  Silvia Terenzi, Ewa Biała, Nhat Quang Nguyen-Trung, Peter Strazewski
  Angewandte Chemie International Edition 07/2003; 42(25):2909-12. · 13.45 Impact Factor
• Article: The influence of various modified nucleotides placed as 3'-dangling end on thermal stability of RNA duplexes.

  Krzysztof Ziomek, Elzbieta Kierzek, Ewa Biała, Ryszard Kierzek
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  ABSTRACT: The ribonucleic acids (RNA) form highly folded structures, which behind the helical fragments contain several secondary and tertiary structural motives. All of them have an influence on thermodynamic stability of the RNA. The 5'- and 3'-dangling ends are one of those structural motives, which effect stability of the adjacent helixes. In this paper, we described the influence of 14 different modified nucleotides, placed as 3'-dangling ends, on thermal stability of the RNA duplexes. Collected data demonstrate that: (i) 5-substituents of the uridine have an impact on the 3'-dangling end effect and the largest changes were observed for 5-chloro, bromo and methyl substituents; (ii) position of the methyl group within the uracil residue affect the thermal stability of the duplex; (iii) increasing a size of the heterocycle base placed as the 3'-terminal unpaired nucleotide enhances stabilization of duplexes.
  Biophysical Chemistry 07/2002; 97(2-3):243-9. · 2.20 Impact Factor
• Article: The thermal stability of RNA duplexes containing modified base pairs placed at internal and terminal positions of the oligoribonucleotides.

  Krzysztof Ziomek, Elzbieta Kierzek, Ewa Biała, Ryszard Kierzek
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  ABSTRACT: The presence of various modifications within oligomers changes their thermodynamic stability. To get more systematic data, we measured effects of 5- and 6-substituted uridine on thermal stability of (AUCU(Mod.)AGAU)2 and (AUCUAGAU(Mod.))2. Collected results lead to the following conclusions: (i) 5-halogenated and 5-alkylated substituents of the uridine affect thermal stability of the RNA duplexes differently. Moreover, the 5-fluorouridine changes stability of the RNA duplexes opposite to remaining 5-halogenouridines; (ii) for oligomers containing 5-chloro, 5-bromo or 5-iodouridine stronger hydrogen bond formed between oxygen-4 of the 5-halogenated uracil and 6-amino group of the adenine is presumably responsible for stabilizing effect; (iii) placing of A-U(5R) base pairs closer to the end of the duplex enhance thermal stability relatively to oligomer with central position of this base pair; (iv) the effects of 5-substituents are additive, particularly for substituents which stabilize RNA duplexes; (v) 6-methyluridines (N1 and N3 isomers) as well as 3N-methyluridine present at internal position of A-U(Mod.) inhibit duplexes formation; (vi) 6-methyluridines (N1 and N3 isomers) as well as 3N-methyluridine placed as terminal base pairs stabilize the duplexes mostly via 3'-dangling end effect.
  Biophysical Chemistry 07/2002; 97(2-3):233-41. · 2.20 Impact Factor
• Source

  Available from: unibas.ch

  Article: Internally mismatched RNA: pH and solvent dependence of the thermal unfolding of tRNA(Ala) acceptor stem microhairpins.

  Ewa Biała, Peter Strazewski
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  ABSTRACT: The thermal unfolding of two RNA hairpin systems derived from the aminoacyl accepting arm of Escherichia coli tRNA(Ala) that included all possible single internal mismatches mostly in the third base pair position was measured spectroscopically in 0.1 M NaCl at pH 7.5 and, in part, 5.5. The thermodynamic parameters DeltaH(o), DeltaS(o), DeltaG(o), and T(m) of a total of 36 RNA strands were determined through nonlinear curve fitting of the melting profiles (22 tetralooped 22mers and 14 heptalooped 25mers, same stem sequence). Only three of the 22mers, the A.C-containing variants, were shown to be significantly more stable at pH 5.5. A number of remarkable differences-most likely of more general relevance-between the thermodynamics of certain structurally very similar hairpin variants (e.g., G.C versus A.U, G.U versus I.U) at pH 7.5 are discussed with respect to two possible ways of helix stabilization: pronounced hydration versus low entropic penalty. Four selected 22mers were additionally analyzed in 1 M NaCl and in solvent mixtures containing ethanol, ethylene glycol, and dimethylformamide. The wealth of thermodynamic data suggest that the exothermicity DeltaH(o) and entropic penalty T x DeltaS(o) of folding are strongly dominated by the rearrangement and formation of hydration layers around the solutes, while it is well-known that the stability of folding results only from the difference (DeltaG(o)) and ratio of both parameters (T(m) = DeltaH (o)/DeltaS(o)).
  Journal of the American Chemical Society 05/2002; 124(14):3540-5. · 9.91 Impact Factor