Nucleic acids ligand binding

In addition to antibodies, it is possible to use artificial nucleic acids ligands, known as aptamers, for the selective detection of proteins. The tight binding properties make aptamers attractive candidates as molecular recognition elements in a wide range of bioassays and for the development of protein arrays. Electrochemistry has been shown useful for monitoring aptamer-protein interactions (66). 

Nucleic acids that can perform a wide variety of binding reactions have been selected from random sequence pools by affinity immobilization. Oliphant et al. [2] selected DNA molecules that could bind to the yeast transcriptional activator GCN4 from a random-sequence DNA pool that spanned nine positions. Since then, aptamers (nucleic acid ligands) have been selected against a variety of protein targets that naturally bind to nucleic acids, such as EF-Tu, ribosomal proteins, QP replicase, and reverse transcriptase (reviewed in Ref. 3). In addition, aptamers have been selected against intracellular and... 

Comparisons of various ligand-binding aptamer structures with proteins which bind related molecules showed that nucleic acids and proteins use strikingly similar strategies for the formation of well-defined binding pockets. Structures of nucleic acid/ligand complexes that have been published so far are summarized in Table 9.1. 

Fluorescent dyes can also bind with nucleic acid ligands. McGown et al... 

Fig. 2.5 Thermodynamic cycle for the ligand (D)—nucleic acid (NA) binding process...

When the sites on nucleic acids which bind a ligand are of a single type and behave independently of each other, the binding process can be described in simple mass-action terms, giving ... 

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