A Fresh Look at Adenosine‐Binding DNA Motifs

Barbu, Mihaela; Stojanović, Milan N.

doi:10.1002/cbic.201200024

Cited by 10 publications

(14 citation statements)

References 31 publications

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“…Interestingly, a recently isolated RNA aptamer for cAMP has a 2.5‐fold higher affinity for cAMP over ATP . An ssDNA aptamer for cAMP has an approximately twofold higher affinity for cAMP over ATP …”

Section: Resultsmentioning

confidence: 99%

A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition

2019

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As a ubiquitous second messenger, cyclic adenosine monophosphate (cAMP) mediates diverse biological processes such as cell growth, inflammation, and metabolism. The ability to probe these pathways would be significantly enhanced if we had a DNA‐based sensor for cAMP. Herein, we describe a new, 31‐base long single‐stranded DNA aptamer for cAMP, denoted caDNApt‐1, that was isolated by in vitro selection using systemic evolution of ligands after exponential enrichment (SELEX). caDNApt‐1 has an approximately threefold higher affinity for cAMP than ATP, ADP, and AMP. Using non‐denaturing gel electrophoresis and fluorescence spectroscopy, we characterized the structural changes caDNApt‐1 undergoes upon binding to cAMP and revealed its potential as a cAMP sensor.

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Section: Resultsmentioning

confidence: 99%

A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition

2019

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“…RNA sequences identified from sequence libraries by systematic evolution by exponential enrichment (SELEX). 13 Aptamers for a number of nucleoside phosphates or cofactors, including ATP, 14,15 cAMP, 16 SAM, 17 FAD, 18,19 and GTP 20 are known, and so are ribonucleopeptides 21,22 that bind ATP or GTP.…”

Section: Introductionmentioning

confidence: 99%

Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligands

Vollmer

Richert

2015

Org. Biomol. Chem.

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Triplexes with a gap in the purine strand have been shown to bind adenosine or guanosine derivatives through a combination of Watson-Crick and Hoogsteen base pairing. Rigidifying the binding site should be advantageous for affinity. Here we report that clamps delimiting the binding site have a modest effect on affinity, while bridging the gap of the purine strand can strongly increase affinity for ATP, cAMP, and FAD. The lowest dissociation constants were measured for two-strand triple helical motifs with a propylene bridge or an abasic nucleoside analog, with Kd values as low as 30 nM for cAMP in the latter case. Taken together, our data suggest that improving preorganization through covalent bridges increases the affinity for nucleotide ligands. But, a bulky bridge may also block one of two alternative binding modes for the adenine base. The results may help to design new receptors, switches, or storage motifs for purine-containing ligands.

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“…Noting that the A20G mutation of the same adenosine nucleotide is both expected 6 and (here) observed to allow substantial activity, we surmise that the A20C mutation is simply not as deleterious in the 14JS101 deoxyribozyme context as in the isolated ATP aptamer. Replacing the ATP aptamer module of 14JS101 with the variant MB-1 aptamer that binds only a single molecule of ATP (versus two ATP molecules for the parent aptamer) 13 resulted in no 14JS101 activity under the same assay conditions (<0.5%; data not shown).…”

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confidence: 99%

A modular tyrosine kinase deoxyribozyme with discrete aptamer and catalyst domains

Dokukin

Silverman

2014

Chem. Commun.

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We assess the utility of integrating a predetermined aptamer DNA module adjacent to a random catalytic DNA region for identifying new deoxyribozymes by in vitro selection. By placing a known ATP aptamer next to an N40 random region, an explicitly modular DNA catalyst for tyrosine side chain phosphorylation is identified. The results have implications for broader identification of deoxyribozymes that function with small-molecule substrates.

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A Fresh Look at Adenosine‐Binding DNA Motifs

Abstract: One is enough: For many years an adenosine binding aptamer with two binding sites has been used in DNA devices. We now show that an aptamer with a single binding site may also be used.

Cited by 10 publications

References 31 publications

A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition

A DNA Aptamer for Cyclic Adenosine Monophosphate that Shows Adaptive Recognition

Effect of preorganization on the affinity of synthetic DNA binding motifs for nucleotide ligands

A modular tyrosine kinase deoxyribozyme with discrete aptamer and catalyst domains

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