A DNA Aptamer That Binds Adenosine and ATP

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Abstract

We have used in vitro selection to isolate adenosine/ATP-binding DNA sequences from a pool of ≈2 × 1014different random-sequence single-stranded DNA molecules. One of these aptamers has been characterized and binds adenosine in solution with a dissociation constant of 6 ± 3 µM. Experiments with ATP analogs indicate that functional groups on both the base and the sugar of ATP are involved in the ligand/aptamer interaction. The binding domain of this aptamer was localized to a 42 base sequence by deletion analysis. A pool of mutagenized versions of this sequence was then synthesized and screened for functional adenosine binding sequences; comparison of the selected variants revealed two highly conserved guanosine-rich regions, two invariant adenosine residues, and two regions of predominantly Watson-Crick covariation. This data led us to propose a model of the ATP-binding DNA structure which is based on a stable framework composed of two stacked G-quartets. The two highly conserved adenosine residues may stack between the top G-quartet and the two short stems, forming a pocket in which the adenosine or ATP ligand binds. Site-directed mutagenesis, base analog substitution studies, and the design of highly divergent but functional sequences provide support for this model. © 1995, American Chemical Society. All rights reserved.

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Huizenga, D. E., & Szostak, J. W. (1995). A DNA Aptamer That Binds Adenosine and ATP. Biochemistry, 34(2), 656–665. https://doi.org/10.1021/bi00002a033

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