Journal Article10.1021/BI00002A033
A DNA aptamer that binds adenosine and ATP.
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TL;DR: A model of the ATP-binding DNA structure which is based on a stable framework composed of two stacked G- Quartets is proposed, which may stack between the top G-quartet and the two short stems, forming a pocket in which the adenosine or ATP ligand binds.
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Abstract: We have used in vitro selection to isolate adenosine/ATP-binding DNA sequences from a pool of approximately 2 x 10(14) different 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 microM. 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.
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Citations
Highly selective dual sensing of ATP and ADP using fluorescent ribonucleopeptide sensors
TL;DR: Highly selective fluorescent sensors for ATP and ADP were constructed from RNA aptamers by applying a modular design of a ribonucleopeptide scaffold to enable facile and quantitative detection of ATP andADP simultaneously in a solution and enable monitoring of the time-course changes of ADP concentrations in an enzymatic reaction.
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Unlocking G-quadruplex: Effect of unlocked nucleic acid on G-quadruplex stability
TL;DR: It is shown using CD spectroscopy that UNA modifications can cause structural transitions in some cases although they retain the inherent G-quadruplex signature, and a greater serum stability of the modified oligonucleotides in comparison with unmodified ones is demonstrated.
15
Microarrays as Model Biosensor Platforms to Investigate the Structure and Affinity of Aptamers
TL;DR: This study investigated the binding of multiple aptamer/target pairs immobilized on a commercially available microarray as a model system mimicking biosensor applications and indicated a minimum distance from the surface and thymine nucleobase linker provides reproducible binding across varying conditions.
Plasmonic aptamer-gold nanoparticle sensors for small molecule fingerprint identification.
Jorge L. Chávez,Juliann K. Leny,Suzanne E. Witt,Grant M. Slusher,Joshua A. Hagen,Nancy Kelley-Loughnane +5 more
TL;DR: The utilization of the plasmonic response of aptamer-gold nanoparticle conjugates (Apt-AuNPs) to design cross-reactive arrays for fingerprint identification of small molecular targets was demonstrated for the first time, and it was observed that it was not necessary to select an aptamer per analyte of interest to generate differentiable signatures.
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