Light-induced formation of silver(I)-mediated base pairs in DNA: Possibilities and limitations

Naskar, Shuvankar; Hebenbrock, Marian; Müller, Jens

doi:10.1016/j.ica.2020.119856

Cited by 7 publications

(9 citation statements)

References 75 publications

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“…A similar observation had been made for duplexes with NPP-protected cytidine residues in comparison to unmodified cytidine moieties. 29 This stabilizing effect is likely due to a geometrical orientation of the NPP moiety that allows its engagement in π stacking interactions with the neighboring nucleobases. The addition of Cu(II) to duplex II does not significantly influence its T m .…”

Section: ■ Results and Discussionmentioning

confidence: 99%

“…It was achieved recently in the case of Hg(II)-and Ag(I)-mediated base pairs. 28,29 To evaluate the possibility of expanding the repertoire of light-inducible metal-mediated base pairs to include also Cu(II)-mediated pairs, the deoxyribonucleoside H comprising the ligand 3-hydroxy-2-methylpyridin-4(1H)-one was chosen to be modified with a photocleavable protecting group. analog.…”

Section: ■ Introductionmentioning

confidence: 99%

“…In this context, metal-dependent DNAzymes and an aptamer were reported. − The capacity to trigger metal-mediated base pair formation by light represents a likewise important goal. It was achieved recently in the case of Hg(II)- and Ag(I)-mediated base pairs. , …”

Section: Introductionmentioning

confidence: 99%

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Triggering Copper(II)-Mediated Base Pair Formation by Light

Naskar

Müller

2021

Inorg. Chem.

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Metal-mediated base pairs enable a site-specific incorporation of transition metal ions into nucleic acid structures. The resulting nucleic acid−metal complex conjugates are of interest in the context of functionalized nucleic acids, as they bear metalbased functionality. It is desirable to devise nucleic acids with an externally triggered metal-binding affinity, as this may allow regulating this functionality. Toward this end, a caged deoxyribonucleoside analog H NPP was devised for the site-specific binding of copper(II) ions upon irradiation by light, based on the ligand 3hydroxy-2-methylpyridin-4(1H)-one (H) and the photocleavable 2-(2-nitrophenyl)propoxy protecting group (NPP). The formation of both H−Cu(II)−H homo base pairs and H−Cu(II)−X hetero base pairs (involving a second artificial deoxyribonucleoside X, based on imidazole-4-carboxylate) was achieved upon irradiation of DNA duplexes bearing the respective H NPP :H NPP or H NPP :X mispairs in the presence of copper(II) ions. The H−Cu(II)−X pair shows an exceptional DNA duplex stabilization of up to 43 °C upon its formation, exceeding that of the H−Cu(II)−H pair. It therefore represents one of the most stabilizing Cu(II)-mediated base pairs reported so far. Our findings expand the scope of light-triggered metal-mediated base pair formation by introducing a copper(II)-binding ligand.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

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Triggering Copper(II)-Mediated Base Pair Formation by Light

Naskar

Müller

2021

Inorg. Chem.

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“…Efforts to expand DNA molecular recognition have taken advantage of noncanonical structures such as guanine quadruplexes or i-motifs. − To assemble new structural motifs, artificial base pairs can be synthetically introduced into the DNA backbone . Similarly, to introduce new function into DNA nanostructures, DNA strands are typically modified with synthetic groups, such as metal–organic complexes − and hydrophobic, − photoresponsive, − or biologically active units. − The latter methods introduce relatively few functional groups in a DNA strand, typically a single end modification . The dense introduction of multiple functional groups into DNA requires synthetically demanding and relatively costly multiple nucleotide modifications , or relies on uniform ionic coatings …”

Section: Introductionmentioning

confidence: 99%

Tuning DNA Supramolecular Polymers by the Addition of Small, Functionalized Nucleobase Mimics

et al. 2021

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Nucleobase mimicking small molecules able to reconfigure DNA are a recently discovered strategy that promises to extend the structural and functional diversity of nucleic acids. However, only simple, unfunctionalized molecules such as cyanuric acid and melamine have so far been used in this approach. In this work, we show that the addition of substituted cyanuric acid molecules can successfully program polyadenine strands to assemble into supramolecular fibers. Unlike conventional DNA nanostructure functionalization, which typically end-labels DNA strands, our approach incorporates functional groups into DNA with high density using small molecules and results in new DNA triple helices coated with alkylamine or alcohol units that grow into micrometer-long fibers. We find that small changes in the small molecule functional group can result in large structural and energetic variation in the overall assembly. A combination of circular dichroism, atomic force microscopy, molecular dynamics simulations, and a new thermodynamic method, transient equilibrium mapping, elucidated the molecular factors behind these large changes. In particular, we identify substantial DNA sugar and phosphate group deformations to accommodate a hydrogen bond between the phosphate and the small-molecule functional groups, as well as a critical chain length of the functional group which switches this interaction from intra- to interfiber. These parameters allow the controlled formation of hierarchical, hybrid DNA assemblies simply through the addition and variation of small, functionalized molecules.

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“…The metal-mediated base pair chosen for this study is based on the artificial imidazole 2'-deoxyribonucleoside (Im). This nucleoside is well known to form highly stabilizing Ag(I)-mediated Im-Ag(I)-Im base pairs ( Figure 1) [30][31][32][33] and has already been proposed for a use in various applications [34][35][36]. A slight disadvantage of using this metal-mediated base pair could be the fact that Ag(I) is known to have an affinity to adenine derivatives (such as ATP, i.e., the target molecule of the aptamer) [37,38].…”

Section: Introductionmentioning

confidence: 99%

Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

Heddinga¹,

Müller²

2020

Beilstein J. Org. Chem.

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For the first time, a metal-mediated base pair has been used to modulate the affinity of an aptamer towards its target. In particular, two artificial imidazole 2’-deoxyribonucleosides (Im) were incorporated into various positions of an established ATP-binding aptamer (ATP, adenosine triphosphate), resulting in the formation of three aptamer derivatives bearing Im:Im mispairs with a reduced ATP affinity. A fluorescence spectroscopy assay and a binding assay with immobilized ATP were used to evaluate the aptamer derivatives. Upon the addition of one Ag(I) ion per mispair, stabilizing Im–Ag(I)–Im base pairs were formed. As a result, the affinity of the aptamer derivative towards ATP is restored again. The silver(I)-mediated base-pair formation was particularly suitable to modulate the aptamer function when the Im:Im mispairs (and hence the resulting metal-mediated base pairs) were located close to the ATP-binding pocket of the aptamer. Being able to trigger the aptamer function opens new possibilities for applications of oligonucleotides.

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Light-induced formation of silver(I)-mediated base pairs in DNA: Possibilities and limitations

Cited by 7 publications

References 75 publications

Triggering Copper(II)-Mediated Base Pair Formation by Light

Triggering Copper(II)-Mediated Base Pair Formation by Light

Tuning DNA Supramolecular Polymers by the Addition of Small, Functionalized Nucleobase Mimics

Incorporation of a metal-mediated base pair into an ATP aptamer – using silver(I) ions to modulate aptamer function

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