The circular dichroism and differential scanning calorimetry study of the properties of DNA aptamer dimers

• Published in: Biophysical chemistry 2011-04, Vol.155 (1), p.29-35
• Main Authors: Poniková, Slavomíra, Tlučková, Katarína, Antalík, Marián, Víglaský, Viktor, Hianik, Tibor
• Format: Article
• Language: English
• Subjects: Aptamers, Nucleotide - chemistry; Binding Sites; Calorimetry, Differential Scanning; Chemical Physics; Circular Dichroism; Differential scanning calorimetry; Dimerization; DNA aptamer dimers; Fibrinogen - chemistry; Guanine quadruplex; Heparin - chemistry; Physics; Temperature; Temperature-gradient gel electrophoresis; Thrombin; Thrombin - chemistry
• ISSN: 0301-4622; 1873-4200
• DOI: 10.1016/j.bpc.2011.02.004

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. We studied the properties of DNA aptamer dimers sensitive to fibrinogen (F) and heparin (H) binding sites of thrombin. The homodimer (FF) and heterodimer (FH) aptamer dimers form stable guanine quadruplexes in the presence of potassium ions and exhibited a two-fold higher inhibitory effect on thrombin-mediated fibrin gel formation in comparison with canonical single stranded aptamers. [Display omitted] ► We showed that the simple molecular engineering of DNA aptamers sensitive to the thrombin based on hybridization of their supporting part resulted in formation of aptamers dimers that maintain the 3D conformation of the binding site – the guanine quadruplexes. ► The aptamer dimers had higher affinity to the thrombin as it has been demonstrated by their approximately two-fold stronger inhibitory effect on cleavage the fibrinogen by thrombin in comparison with those of canonical monomeric aptamers. ► We showed that the molecular engineering can be used as effective tool for improvement of the aptamer properties.