Aptamer Structures

Piganeau, Nicolas; Schroeder, Renée

doi:10.1016/s1074-5521(03)00028-0

Cited by 20 publications

(6 citation statements)

References 7 publications

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“…ssDNA and RNA aptamers selectively bind to their target amino acids, – peptides, proteins, nucleotides, carbohydrates, and other molecules. , The binding of aptamers and their ligand often rely on the secondary and tertiary structural elements of the nucleic acid. Some studies suggest that the in vitro selected aptamers structure is similar to that of the RNA in the bacterium’s biosynthetic pathway, indicating that such small functional RNA motifs may exist in cells . However, the function and evolutionary mechanism of these RNAs are not clear.…”

Section: Introductionmentioning

confidence: 99%

Microcalorimetrics Studies of the Thermodynamics and Binding Mechanism between l-Tyrosinamide and Aptamer

et al. 2008

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In recent years, several high-resolution structures of aptamer complexes have shed light on the binding mode and recognition principles of aptamer complex interactions. In some cases, however, the aptamer complex binding behavior and mechanism are not clearly understood, especially with the absence of structural information. In this study, it was demonstrated that isothermal titration calorimetry (ITC) and circular dichroism (CD) were useful tools for studying the fundamental binding mechanism between a DNA aptamer and L-tyrosinamide (L-TyrNH2). To gain further insight into this behavior, thermodynamic and conformational measurements under different parameters such as salt concentration, temperature, pH value, analogue of L-TyrNH2, and metal ion were carried out. The thermodynamic signature along with the coupled CD spectral change suggest that this binding behavior is an enthalpy-driven process, and the aptamer has a conformational change from B-form to A-form. The results showed that the interaction is an induced fit binding, and the driving forces in this binding behavior may include electrostatic interactions, hydrophobic effects, hydrogen bonding, and the binding-linked protonation process. The amide group and phenolic hydroxyl group of the L-TyrNH2 play a vital role in this binding mechanism. In addition, it should be noted that Mg(2+) not only improves binding affinity but also helps change the structure of the DNA aptamer.

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Section: Introductionmentioning

confidence: 99%

Microcalorimetrics Studies of the Thermodynamics and Binding Mechanism between l-Tyrosinamide and Aptamer

et al. 2008

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“…Their high specificity is reflected in their many different possible modes of target recognition. Excellent work to elucidate the molecular structure of aptamer–ligand interactions has had a great impact on our understanding of aptamer function 1, 82. Most aptamers are very adaptive and flexible when unbound.…”

Section: Advantages and Limitations Of Aptamers—necessary Future Dmentioning

confidence: 99%

“…Aptamers can form specific hydrogen bonds or lie perpendicular to the target. They have been shown to bind only to the surface of antiparallel beta sheets or to encapsulate their target molecule by adopting unusual L‐shaped architectures 1, 35, 82…”

Section: Advantages and Limitations Of Aptamers—necessary Future Dmentioning

confidence: 99%

Nucleic Acid Aptamers as Tools and Drugs: Recent Developments

Rimmele¹

2003

ChemBioChem

143

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Nucleic acid aptamers are molecules that bind to their ligands with high affinity and specificity. Unlike other functional nucleic acids such as antisense oligonucleotides, ribozymes, or siRNAs, aptamers almost never exert their effects on the genetic level. They manipulate their target molecules such as gene products or epitopes directly and site specifically, leaving nontargeted protein functions intact. In a similar way to antibodies, aptamers bind to many different kinds of target molecules with high specificity and can be made to order, but as a result of their different biochemical nature and size they can also be used complementary to antibodies. In some cases, aptamers might be more suitable or more specific than antibody approaches or small molecules, both as scientific and biotechnological tools and as therapeutic agents. Recent examples of characterization of aptamers as tools for scientific research to study regulatory circuits, as tools in diagnostic or biosensor development, and as therapeutic agents are discussed.

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“…They are able to form a myriad of three-dimensional (3D) structures that can bind with high affinity and specificity to various target molecules, aided by electrostatic charges, hydrogen bonding, and van der Waals forces. [3][4][5] Also dubbed "chemical antibodies," aptamers have many advantages compared to antibodies. They are associated with a lower cost of synthesis, are able to undergo reversible denaturation and renaturation, have low-to-no immunogenicity, and are easily functionalized.…”

Section: Introductionmentioning

confidence: 99%

Isolation of a novel DNA aptamer against LipL32 as a potential diagnostic agent for the detection of pathogenic Leptospira

Shien

Tang

Citartan

2022

Biotechnology Journal

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Leptospirosis is a potentially life-threatening zoonosis caused by pathogenic Leptospira and for rapid diagnostics, direct detection is desirable. LipL32 protein is the most suitable biomarker for direct detection. DNA aptamers are sought to be generated against LipL32 by Systemic Evolution of Ligands via Exponential Enrichment (SELEX).LepDapt-5a is the most potent aptamer candidate among all the candidates, as determined by direct Enzyme-linked Aptasorbent Assay (ELASA). LepDapt-5a was predicted to form a G-quadruplex structure as predicted by QGRS Mapper and validated experimentally by direct ELASA. The diagnostic potential of the aptamer was further tested on a direct and sandwich ELASA platform. A LOD of 10 6 mL -1 and 10 5 mL -1 were estimated by direct and sandwich ELASA platforms, respectively, which are within the range associated with leptospiremia levels. The dot blot assay developed was able to attain a LOD of 10 4 CFU mL −1 against pathogenic Leptospira, which is also within the leptospiremia level. This is the first-ever DNA aptamer and hybrid-heterodimeric aptamer constructed against LipL32. The diagnostic potentiality of the LepDapt-5a DNA aptamer was proven on three major diagnostic platforms, which are direct ELASA, sandwich ELASA, and aptamer-based dot assay.

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Aptamer Structures

Abstract: The crystal structure of a streptomycin binding RNA aptamer displays a novel bipartite fold able to clamp the antibiotic. In view of the recent findings that metabolites directly control mRNA translation, we might expect that similar structures exist in natural RNAs.

Cited by 20 publications

References 7 publications

Microcalorimetrics Studies of the Thermodynamics and Binding Mechanism between l-Tyrosinamide and Aptamer

Microcalorimetrics Studies of the Thermodynamics and Binding Mechanism between l-Tyrosinamide and Aptamer

Nucleic Acid Aptamers as Tools and Drugs: Recent Developments

Isolation of a novel DNA aptamer against LipL32 as a potential diagnostic agent for the detection of pathogenic Leptospira

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