Thrombin Binding Aptamer, More than a Simple Aptamer: Chemically Modified Derivatives and Biomedical Applications

Abstract

The thrombin binding aptamer (TBA) is a well characterized chair-like, antiparallel quadruplex structure that binds specifically to thrombin at nanomolar concentrations and therefore it has interesting anticoagulant properties. In this article we review the research involved in the development of new TBA derivatives with improved anticoagulant properties as well as the use of the TBA as a model compound for the study of quadruplex structures. Specifically, we describe the impact of modified nucleosides and non-natural backbones in the guanine tetrads or in the loops and the introduction of pendant groups at the 3' or 5'-ends. The modified oligonucleotides are shown to be excellent tools for the understanding of the molecular structure of the TBA and its folding properties. Finally, we review the use of the TBA-Thrombin recognition system for the development of analytical tools based on the TBA folding.

Biosensing with optical fiber gratings

“…Among all the selected aptamers, the thrombin one is the most studied and used as a model system for aptamerbased biosensors [78,79]. This aptamer has been coupled to TFBGs, used as platform for the implementation of a sensor based on SPR [35].…”

The effect of l-thymidine, acyclic thymine and 8-bromoguanine on the stability of model G-quadruplex structures

“…(Table 1). This position is very permissive to be modified [3]. However, thymidine located in position 9 although is present in the same TGT upper loop is very sensitive to the modification as the substitution of T by GNAT at this position decreases the thermal stability in 9.5 ºC.…”

“…It is possible to modulate the diverse biological functions of nucleic acids by the incorporation of site-specific chemical modifications. In this regard, thrombin binding aptamer (TBA) has attracted considerable attention and several modifications have been described to improve their thermal stability, nuclease resistance and affinity for the target thrombin [3,4]. TBA is a 15-base sequence, d(GGTTGGTGTGGTTGG) with anticoagulant properties.…”

“…We recently demonstrated that a higher-order structure of TBA can be stabilized by simple specific loop modifications [9]. Nucleotides with special structural or physicochemical properties have been specifically substituted by natural nucleotides of TBA [3]. For example, locked nucleic acids (LNA) [10,11], unlocked nucleic acids (UNA) [12] or 2'-deoxy-2'-fluoro-β-D-arabinonucleic acid (2'F-ANA) [13] are derivatives with interesting backbone features that 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 have been introduced in different positions of TBA.…”

Anomeric DNA quadruplexes

“…TBA specifically inhibits thrombin in vivo at nanomolar concentrations. 9 The drawback of using an unmodified TBA oligonucleotide is its sensitivity to serum nucleases and fast clearance in the kidneys.…”