Nucleic acids ligands

Oldfield TJ. A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent. Acta Cryst 2001 057 82-94. 

Stoltenburg, R. Reinemann, C. Strehlitz, B. SELEX - A (r)evolutionary method to generate high-affmity nucleic acid ligands. Biomol. Eng. 2007, 24, 381 03. 

Stereochemical probes of the specificity of substrates, products, and effectors in enzyme-catalyzed reactions, receptor-ligand interactions, nucleic acid-ligand interactions, etc. Most chirality probe studies attempt to address the stereospecificity of the substrates or ligands or even allosteric effectors. However, upon use of specific kinetic probes, isotopic labeling of achiral centers, chronfium-or cobalt-nucleotide complexes, etc., other stereospecific characteristics can be identified, aU of which will assist in the delineation of the kinetic mechanism as well as the active-site topology. A few examples of chirality probes include ... 

SELEX is a widely used technique for screening of aptamers which are nucleic acid ligands. According to this method, a pool of DNA with a random sequence region attached to a constant chain is constituted by amplification then transcribed to RNA. RNA pool is separated according to the affinity of RNA molecules to a target protein. DNA molecules obtained by reverse transcription from retarded RNA molecules are amplified and the cycle is repeated. 

Green, L.S., Jellinek, D., Bell, C., Beebe, L.A., Feistner, B.D., Gill, S.C., Jucker, F.M. and Janjic, N. (1995) Nuclease-resistant nucleic acid ligands to vascular permeability factor/vascular endothelial growth factor, Chem. Biol. 2, 683-695. 

Potyrailo, R.A., Conrad, R.C., Ellington, A.D. andHieftje, G.M. (1998) Adapting selected nucleic acid ligands (aptamers) to biosensors, Anal. Chem. 70, 3419-3425. 

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... 

In addition to the thermodynamic stability of metal - nncleic acid complexes, the rates at which nucleic acid ligands dissociate from a metal-ion coordination sphere are as important as the thermodynamic stability of the metal-nncleic acid bond. 

We see that DFT is increasingly used to model a wide range of weak interactions in protein-ligand and nucleic acid-ligand systems. Often, DFT is the only method that can incorporate all electron correlated calculations and that can be applied in... 

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... 

Minimizes the co-selection of nnwanted nucleic acid ligands (e.g., for immobilization matrix)... 

Goringer, H. U., Homann, M., Lorger, M. (2003). In vitro selection of high-afflnity nucleic acid ligands to parasite target molecules. Int J Parasitol 33, 1309-1317. 

McGown, L. B., Joseph, M. J., Pittner, J. B., Vonk, G. P., Linn, C. P. (1995). The nucleic acid ligand. A new tool for molecular recognition. Anal Chem 67, 663A-668A. 

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