Ability of thrombin to act as molecular chaperone, inducing formation of quadruplex structure of thrombin-binding aptamer

Abstract

Single-stranded guanosine (G)-rich oligonucleotides have a propensity to form quadruplex structures stabilized by 4-G quartets. The four guanines of such a quartet array in a square planar conWguration, each G interacting with the adjacent one via two hydrogen bonds and behaving as H acceptor/donor of what is known as a Hoogsteen basepair. These structures are believed to exist only in the presence of certain cations, described to stabilize the quadruplex, presumably by compensating the intermolecular repulsion due to the negative charges of the nucleic acid [1–3]. Proteins able to bind such structures under physiological conditions have been described [3,4], and two of them have even been suggested to promote quadruplex formation [5,6]. The fact that some quadruplex-forming sequences have been described to inhibit proliferation of viruses or cancer cells is being exploited for its potential therapeutic application [1]. The thrombin-binding aptamer (TBA)1 was the Wrst in vitro-selected oligonucleotide targeted toward a protein that has no known physiological binding to nucleic acids. The TBA is known to be in equilibrium between a random and a quadruplex conformation when dissolved in aqueous solution [7]. This quadruplex structure contains two G(syn)-G(anti)-G(syn)-G(anti) quartets and three lateral loops, in what is usually referred to as a “chair structure” [8–11]. The presence of K+ in the medium was believed to be necessary to shift the equilibrium toward the quadruplex conformation, subsequently