The Thrombin Binding Aptamer

Figure 11.1 G-quadruplex structure of the thrombin-binding aptamer. [From Bock et al. (1992) and Kelly et al. (1996).]...

One of the most preeminent examples of the in vitro selection of DNA oligonucleotides for targeting a specific protein is the thrombin-binding aptamer (TBA). Thrombin is a serine protease and a coagulation protein in the blood stream that has many effects in the coagulation mechanism. Because of its importance in anticlotting therapeutics, TBA has been studied extensively and has also been used for the development of TBA-electrochemical biosensors for the detection of thrombin [40, 41]. 

Different reporter groups have been attached to C5 of uracil, e.g., a number of fluorophores including naphthalene, pyrene, fluor-ene, benzofuran ° and the biaryl derivative (36) that also has an NMR label ( F). The structure of an RNA-DNA hybrid has been examined by EPR using a spin label attached to C5 of du/ A terpyridine moiety has been attached to C5 to chelate metal ions/ Different carbohydrates have been attached via a linker to C5 of dU and the resultant DNA was hybridised to form a three-way junction with the carbohydrate displayed on each arm to probe binding to lectin/ Two nitroimidazole derivatives attached to C5 via a methylene bridge have been described where they form interstrand crosslinks under hypoxic conditions/ The acyclic pyrimidine analogue (37) has been incorporated into the thrombin-binding aptamer where it was found to increase the efficacy of the aptamer/ ... 

Fig. 8.2 Nyquist plot of impedimetric sensor (Section 8.4.3.3). The redox couple ferro/ ferricyanide recorded at (a) bare Au electrode (b) Au electrode modified with thrombin-binding aptamer (c) Au/aptamer electrode with added 2-mercapto ethanol and (d) electrode with bound complementary thrombin/aptamer complex. Each plot was obtained separately (adapted from Radi etal.,2005)...

P. Schultze, R.F. Macaya and J. Feigon, Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGTTGGTGTGG TTGG), J. Mol. Biol, 1994, 235, 1532-1547. 

Figure 4.6 Thrombin biosensor based on a ferrocene-labeled aptamer. In the absence of thrombin, the aptamer (green) displays a random coil strnctnre, allowing contact between the ferrocene label (striped ball) and the electrode. Addition of thrombin forces the aptamer into the thrombin-binding structure, thus removing the redox label from the electrode, allowing no further electrochemical contact. (See insert for color representation.)...

Other is an AES whose inhibitory activity is decreased upon binding to adenosine. In this system the adenosine-binding aptamer connects to the thrombin-inhibiting aptamer and the thrombin enzymatic activity is measured. 

We are presently in the early days of the emerging technology of using aptamers and nanomaterials to modify biosensors. So far, thrombin-binding aptamer has been the topic of numerous reports, but although many improvements are required in reproducibility and sensitivity, there is no doubt that a growing number of aptamers and, it is to be hoped, nanomaterial-based label-free aptasensors will soon be used for the diagnosis and therapeutic follow-up of diseases. 

Figure 12.7 Principle of the multifunctional aptasensor. ABA, ATP-binding aptamer TBA, a-thrombin-binding aptamer MBA, strand containing the aptamers PCS, strand partly complementary to MBA. [From Du et al. (2008).]...

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