Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia.
J Biomol Struct Dyn. 2012;30(5):524-31. doi: 10.1080/07391102.2012.687518. Epub 2012 Jun 26.
A number of thrombin-binding DNA aptamers have been developed during recent years. So far the structure of just a single one, 15-mer thrombin-binding aptamer (15TBA), has been solved as G-quadruplex. Structures of others, showing variable anticoagulation activities, are still not known yet. In this paper, we applied the circular dichroism and UV spectroscopy to characterize the temperature unfolding and conformational features of 31-mer thrombin-binding aptamer (31TBA), whose sequence has a potential to form G-quadruplex and duplex domains. Both structural domains were monitored independently in 31TBA and in several control oligonucleotides unable to form either the duplex region or the G-quadruplex region. The major findings are as follows: (1) both duplex and G-quadruplex domains coexist in intramolecular structure of 31TBA, (2) the formation of duplex domain does not change the fold of G-quadruplex, which is very similar to that of 15TBA, and (3) the whole 31TBA structure disrupts if either of two domains is not formed: the absence of duplex structure in 31TBA abolishes G-quadruplex, and vice versa, the lack of G-quadruplex folding results in disallowing the duplex domain.
近年来，已经开发出了许多凝血酶结合 DNA 适体。到目前为止，只有一种 15 -mer 凝血酶结合适体（15TBA）的结构已被确定为 G-四链体。其他具有不同抗凝活性的结构仍然未知。在本文中，我们应用圆二色性和紫外光谱学来表征 31-mer 凝血酶结合适体（31TBA）的热解折叠和构象特征，其序列具有形成 G-四链体和双链区的潜力。双链区和 G-四链区这两个结构域在 31TBA 及其几个不能形成双链区或 G-四链区的对照寡核苷酸中独立监测。主要发现如下：（1）双链和 G-四链区都存在于 31TBA 的分子内结构中，（2）双链区的形成不会改变 G-四链区的折叠，这与 15TBA 非常相似，（3）如果不形成两个结构域中的任何一个，整个 31TBA 结构都会被破坏：31TBA 中双链结构的缺失会使 G-四链体失活，反之亦然，G-四链体折叠的缺失会导致双链结构不能形成。
