Aptamers to Small Molecules

Abstract

fluence on binding. Furthermore, the sizes of the RNA and DNA aptamers to ATP were similar (40 versus 42, respectively), so one could draw the conclusion that aptamers (of similar complexity) for one target molecule can be isolated from both RNA and DNA pools. However, the selected RNA and DNA aptamers had significantly different sequences and fold into different structures because the DNA lacks the 2l-hydroxyl group of the RNA. This was demonstrated when the DNA version of the RNA aptamer for ATP and the RNA version of the DNA aptamer for ATP were tested for binding, respectively, and neither recognized ATP. A difference between the RNA and DNA aptamers was detected by nuclear magnetic resonance (NMR) studies of the aptamers, revealing that the DNA aptamer binds two ATP molecules, while the RNA aptamer binds just one (Lin and Patel, 1997). Kiga et al. (1998) isolated an RNA aptamer binding xanthine and guanine ( Fig. 4.1). The aptamers were selected via affinity chromatography with xanthine agarose; bound RNA was eluted with free xanthine. A representative RNA aptamer was truncated to 32 nucleotides and turned out to bind xanthine with a K d of 3.3 mmol/L. Guanine was bound by the aptamer as well, while adenenine, cytosine, and uracil were not bound.RNA aptamers that exhibited a new mode of purine recognition were published by Meli et al. (2002). The aptamer contained two relatively independent secondary structure elements, which formed a bipartite RNA structure that bound adenine with a K d of 10 mmol/L. In this aptamer the imidazole moiety of adenine is not trapped in the binding side, as it is in other adenine/ATP-binding aptamers. Hence this aptamer could be supposed to be a cofactor-binding site in a complex ribozyme.In 2004 RNA aptamers that recognized the triphosphate of ATP were selected in the laboratory of Jack W. Szostak (Sazani et al., 2004). By employing a restrictive selection protocol containing AMP-agarose for counterselection and washing the selection column (ATP-agarose) with free AMP prior to elution of ATP-bound RNA, they could isolate aptamers that strongly interacted with the b and g phosphate. The K d -value of a 57-nucleotide minimized aptamer was 11 mmol/L for ATP and 1700 mmol/L for AMP. In contrast to other ATP aptamers, this aptamer showed binding to GTP, UTP, and CTP, also. The aptamer was not isolated in an earlier selection for ATP aptamers, although it had an affinity comparable to other ATP aptamers. That might be due to its more complex structure. Therefore, this triphosphate-binding aptamer could first be isolated after counterselection for the simpler ATP-binding molecules. 96 4 Aptamers to Small MoleculesFig. 4.1 Xanthine and guanine. The RNA aptamer selected for xanthine also binds guanine, while adenine, cytosine, and uracil are not bound.97 Aptamers to Cofactors

Electrochemical Aptasensors – Recent Achievements and Perspectives

“…In principle, there is no restriction in the type of target for which the aptamer can be selected. To date, aptamers with affinity to various ligands were synthesized, including metal ions, organic dyes, drugs, amino acids, cofactors [22], antibiotics [23] and nucleic acid structures [24]. Special interest was focused on the development of aptamers for the detection of proteins including enzymes, antibodies, prions, growth factors, gene regulatory factors, cell adhesion molecules and lectins.…”

Carbohydrate recognition by boronolectins, small molecules, and lectins

“…Naturally, the same methods have also been used for the selection of aptamers that bind carbohydrates. Till now, aptamers to carbohydrates were selected for two purposes: (1) as purification tags for RNA or ribonucleoparticles from RNA mixtures74,331,332 and (2) to identify and/or block specific sugars on cell surfaces 333. Herein we mainly focus on the application of aptamers for cell surface carbohydrate recognition and inhibition.…”

Aptasensors for Small Molecule Detection

“…Since plenty of aptamers directed against diverse small molecules have already been published [41,42], this restriction of aptasensors to mainly three analytes is quite surprising. Within the young and further developing field of aptasensors, many researchers have focused on the well-characterized aptamers directed against ATP and cocaine for the development of aptasensors, and other targets will likely follow in the near future.…”