Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes

Micura, Ronald; Höbartner, Claudia

doi:10.1039/d0cs00617c

Cited by 137 publications

(94 citation statements)

References 311 publications

(406 reference statements)

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“…The involvement of this nitrogen atom in stabilizing the protonated ligand in the ground state was unequivocally confirmed by atomic mutagenesis. This adds an additional role to the versatile functions of guanine nucleobases found in riboswitches and ribozymes 38 , 39 .…”

Section: Discussionmentioning

confidence: 99%

Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine

et al. 2021

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Fluorogenic RNA aptamers are synthetic functional RNAs that specifically bind and activate conditional fluorophores. The Chili RNA aptamer mimics large Stokes shift fluorescent proteins and exhibits high affinity for 3,5-dimethoxy-4-hydroxybenzylidene imidazolone (DMHBI) derivatives to elicit green or red fluorescence emission. Here, we elucidate the structural and mechanistic basis of fluorescence activation by crystallography and time-resolved optical spectroscopy. Two co-crystal structures of the Chili RNA with positively charged DMHBO+ and DMHBI+ ligands revealed a G-quadruplex and a trans-sugar-sugar edge G:G base pair that immobilize the ligand by π-π stacking. A Watson-Crick G:C base pair in the fluorophore binding site establishes a short hydrogen bond between the N7 of guanine and the phenolic OH of the ligand. Ultrafast excited state proton transfer (ESPT) from the neutral chromophore to the RNA was found with a time constant of 130 fs and revealed the mode of action of the large Stokes shift fluorogenic RNA aptamer.

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Section: Discussionmentioning

confidence: 99%

Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine

et al. 2021

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“…For the following closely related topics, we would like to refer readers to other reviews within this themed issue: non-covalent labeling via aptamers (Unrau), labeling with photocages (Deiters), novel DNA base pairs (Hirao), fundamental photophysics of nucleic acids (Seidel) and fundamental studies of ribozymes/DNAzymes. 28 For the detection of natural modifications of DNA and RNA, we would like to refer to an excellent recent review. 29…”

Section: Introductionmentioning

confidence: 99%

Covalent labeling of nucleic acids

2020

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“…Different target analytes were sensed by aptamers, including low-molecularweight compounds, such as cocaine [37][38][39][40], explosives [41][42][43], pesticides [44,45], toxins [46] and antibiotics [47][48][49], and macromolecules such as protein [50][51][52][53][54][55][56][57] and biopolymers [58][59][60]. The specific recognition of metal ions by aptamers, e.g., Mg 2+ , Zn 2+ and Ni 2+ led to the assembly of catalytic nucleic acids, DNAzymes [61][62][63], capable of cleaving oligonucleotides or ligating nucleic acids. In addition, the sequence dictated binding of transition metal complexes, such as catalytic supramolecular Fe(III)-Protoporphyrin IX (hemin) [64], or metal-ion terpyridine complexes, catalyzing chemical transformations such as tyrosine oxidation [65], and the association of chromophores, e.g., Zn (II)-Protoporphyrin IX, to sequence-specific nucleic acids, yielding photocatalysts for artificial photosynthetic transformations [66], were demonstrated.…”

Section: Introductionmentioning

confidence: 99%

Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications

Vázquez‐González

Willner

2021

IJMS

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Sequence-specific nucleic acids exhibiting selective recognition properties towards low-molecular-weight substrates and macromolecules (aptamers) find growing interest as functional biopolymers for analysis, medical applications such as imaging, drug delivery and even therapeutic agents, nanotechnology, material science and more. The present perspective article introduces a glossary of examples for diverse applications of aptamers mainly originated from our laboratory. These include the introduction of aptamer-functionalized nanomaterials such as graphene oxide, Ag nanoclusters and semiconductor quantum dots as functional hybrid nanomaterials for optical sensing of target analytes. The use of aptamer-functionalized DNA tetrahedra nanostructures for multiplex analysis and aptamer-loaded metal-organic framework nanoparticles acting as sense-and-treat are introduced. Aptamer-functionalized nano and microcarriers are presented as stimuli-responsive hybrid drug carriers for controlled and targeted drug release, including aptamer-functionalized SiO2 nanoparticles, carbon dots, metal-organic frameworks and microcapsules. A further application of aptamers involves the conjugation of aptamers to catalytic units as a means to mimic enzyme functions “nucleoapzymes”. In addition, the formation and dissociation of aptamer-ligand complexes are applied to develop mechanical molecular devices and to switch nanostructures such as origami scaffolds. Finally, the article discusses future challenges in applying aptamers in material science, nanotechnology and catalysis.

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Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes

Abstract: This review juxtaposes common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes.

Cited by 137 publications

References 311 publications

Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine

Large Stokes shift fluorescence activation in an RNA aptamer by intermolecular proton transfer to guanine

Covalent labeling of nucleic acids

Aptamer-Functionalized Hybrid Nanostructures for Sensing, Drug Delivery, Catalysis and Mechanical Applications

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