Active aptamers

There is a useful public database of functionally active aptamers aptamer. icmb. utexas. edu. 

A more recent application of redox labeled ODNs is redox-active aptamers that exploit molecular recognition between the aptamer and a target analyte. Briefly, aptamers are functional nucleic acids that selectively bind to a variety of targets. Due to a well-defined three-dimensional structure, aptamers can achieve selectivity comparable to that of antibodies but are readily accessible taking advantage of well-known nucleic acid chemistry, polymeric chain reaction and contemporary separation methods, followed by aptamer selection from random pools of nucleic acids (DNA or RNA) by in vitro selection process called systematic evolution of ligands by... 

FIGURE 21.4 Possible mechanism for the action of ligand-regulated aptamers. (a) Addition of the ligand inhibits aptamer function and promotes the dissociation of the aptamer-receptor complex, (b) Addition of the ligand induces formation of the aptamer-receptor complex and activates aptamer function. Inhibitory activity of aptamers is assumed in both cases. L Ligand that controls aptamer activity A inactive aptamer A active aptamer R receptor (aptamer target). 

Figure 10.26 Screening of the biosynthetic ON library L15 for aptamers binding to m -GTP (10.22) the selection/amplification process and the structure of the most active aptamer 10.23.

ELECTROCHEMICAL APTASENSOR BASED ON REDOX-ACTIVE APTAMER MONOLAYERS LINKED TO ELECTRODES... 

Sandwich-type sensing platforms are also nsed widely in electrochemical aptasensors (Willner and Zayats, 2007), especially for common model molecnles such as a-thrombin (Mir et al., 2006 Polsky et al., 2006 Centi et al., 2007) and platelet-derived growth factor (PDGF) (Zhou et al., 2007), which possess two active aptamer-binding sites. This type of sensor usually... 

Townsend L, Devivar R, Turk S, Nassiri M, Drach J (1995) Design, synthesis, and antiviral activity of certain 2,5,6-trihalo-l-(beta-d-ribofuranosyl)benzimidazoles. J Med Chem 38 4098 105 Turlure F, Devroe E, Silver PA, Engelman A (2004) Human cell proteins and human immunodeficiency virus DNA integration. Front Biosd 9 3187-3208 Umehara T, Fukuda K, Nishikawa F, Kohara M, Hasegawa T, NisUkawa S (2005) Rational design of dual-functional aptamers that inhibit the protease and helicase activities of HCV NS3. J Biochem 137 339-347... 

Kleimnan et al. 2008). In addition, synthetic siRNAs are also subject to degradation in vivo by nuclease activity. Besides side effects and instability, the efficient and specific delivery of the RNAi indncers to the target cell still requires optimization. Here we snmmarize the cnrrent statns of nncleic acid-based antiviral therapentics. The focns will be on antiviral strategies nsing antisense and RNAi technology. Additionally, antiviral ribozymes and aptamers will be discussed briefly, with a focus on recent studies. Gene therapy approaches and delivery systems are the subject of Chapter 11 of this book. 

Bridonneau. R, Bunch, S., Tengler, R., Hill, K., Carter, J., Pieken, W., Tinner-meier, D., Lehrman, R., and Drolet, D. W., Purification of a highly modified RNA-aptamer. Effect of complete denaturation during chromatography on product recovery and specific activity, /. Chromatogr. B, 726, 237, 1999. 

While indirect selections work quite well for antibodies they have been less successful in the case of catalytic nucleic acids. There are only three examples which prove that it is possible in principle to obtain a ribo- or deoxyribozyme by selecting an aptamer that binds to a TSA A rotamase ribozyme [7], a ribozyme capable of catalyzing the metallation of a porphyrin derivative [92], and one catalytic DNA of the same function [93]. Another study reported the selection of a population of RNA-aptamers which bind to a TSA for a Diels-Alder reaction but the subsequent screen for catalytic activity was negative for all individual RNAs tested [94]. The attempt to isolate a transesterase ribozyme using the indirect approach also failed [95]. 

Identification of Aptamers as Specific Binders and Moduiators of Ceii-Surface Receptor Activity... 

The aptamers obtained against the nAChR either are biologically active by themselves and inhibit the muscle-type nAChR activity as cocaine does or are by them biologically inactive and, therefore, protect the receptor against inhibition by cocaine (25). 

Figure 12.19 Electrochemical detection of thrombin by the interaction between a nucleic acid and a redox-active oligothiophene polyelectrolyte. The electrical contact between the polyelectrolyte and the electrode by means of the aptamer/thrombin complex is blocked. Parts Reprinted with permission from Ref. 66b. Copyright Wiley-VCH Verlag GmbH Co.

The formation of aptamer-substrate complexes was also followed by the use of redox-active intercalators73 (Fig. 12.18d). A nucleic acid hairpin structure that contained in its single-stranded loop the antithrombin base sequence was assembled on a Au electrode, and methylene blue was intercalated as a redox label in the double-stranded stem of the hairpin structure. The hairpin was, then, opened in the presence of thrombin, by generating the respective G-quadruplex-thrombin complex, and as a result, the redox label was removed from the nucleic structure, showing a decrease in the voltammetric response with the increase in the concentration of thrombin. This method enabled the analysis of thrombin with a detection limit that corresponded to... 

Several electrical aptamer biosensors implemented the biocatalytic hydrolytic activities of thrombin, or the fact that proteins (e.g., thrombin) often include several binding sites for the formation of supramolecular complexes with different aptamers. The bioelectrocatalytic detection of thrombin by an electrical aptasensor was demonstrated by formation of an aptamer-thrombin complex on the electrode, followed by a thrombin-mediated hydrolysis of the nitroaniline-functionalized peptide, (22), yielding the redox-active product nitroaniline, (23), which was analyzed electrochemically76 (Fig. 12.20b). A further bioelectrocatalytic aptasensors configuration is depicted in Fig. 12.20c, where the multidentate formation of aptamer-protein supramolecular complexes was used to analyze thrombin.76 Thrombin includes two different binding sites for aptamers.77 One of the thrombin aptamers... 

FIGURE 2 RNA aptamer that binds ATP. The shaded nucleotides are those required for the binding activity. 

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