The Circular Dichroism and Differential Scanning Calorimetry Study of the Properties of DNA Aptamer Dimers

Slavomíra Poniková (1) , Katarína Tlučková (2) , Marián Antalík (2, 3) , Viktor Víglaský (2) , Tibor Hianik (1)

1 Faculty of Mathematics
2 Faculty of Science
3 Department of Biophysics

We have applied circular dichroism (CD), temperature-gradient gel electrophoresis (TGGE) and differential scanning calorimetry (DSC) to study the properties of novel bioengineered DNA aptamer dimers sensitive to fibrinogen (F) and heparin (H) binding sites of thrombin and compared them with canonical single stranded aptamer sensitive to fibrinogen binding site of thrombin (Fibri). The homodimer (FF) and heterodimer (FH) aptamers were constructed based on hybridization of their supported parts. CD results showed that both FF and FH dimers form stable guanine quadruplexes in the presence of potassium ions like those in Fibri. The thermal stability of aptamer dimers was slightly lower compared to those of canonical aptamers, but sufficient for practical applications. Both FF and FH aptamer dimers exhibited a potassium-dependent inhibitory effect on thrombin-mediated fibrin gel formation, which was on average two-fold higher than those of canonical single stranded Fibri aptamers.

Mots clés: DNA aptamer dimers; Guanine quadruplex; Thrombin; Circular dichroism; Differential scanning calorimetry; Temperature-gradient gel electrophoresis

Domaines: Chimie-Physique [physics.chem-ph]

Slavomíra Poniková, Katarína Tlučková, Marián Antalík, Viktor Víglaský, Tibor Hianik. The Circular Dichroism and Differential Scanning Calorimetry Study of the Properties of DNA Aptamer Dimers. Biophysical Chemistry, 2011, 155 (1), pp.29. ⟨10.1016/j.bpc.2011.02.004⟩. ⟨hal-00734583⟩