Aptamers

James, W.

doi:10.1002/9780470027318.a1402

Cited by 14 publications

(11 citation statements)

References 183 publications

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“…Some of the reported RNA aptamers, including aptamer 93, had increased affinities for a refolded -sheet rich form of the prion protein, and showed little binding to the -helix rich form. These results were promising, although RNA aptamers have a number of disadvantages, including their pleomorphism, their large molecular weight and the restricted range of site that are suitable for RNA binding (James, 2000). The synthetic chemical ligands described here can be obtained inexpensively with high purities, are durable, and able to withstand harsh sterilization techniques.…”

Section: Discussionmentioning

confidence: 88%

The design, synthesis and evaluation of affinity ligands for prion proteins

Renou

Gupta

Young

et al. 2004

J of Molecular Recognition

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Bifunctional affinity ligands based on a triazine scaffold were rationally designed to target prion protein and shown to bind recombinant prion protein with high affinity and selectivity. The ligands were capable of discriminating between prion protein glycoforms and monomeric and dimeric forms of the prion protein. The ligands also discriminate between conformational differences in the prion protein, resulting from point mutations in the prion protein gene. These results suggest that derived compounds could be used selectively to detect the disease-associated form of the prion protein, and as such, could provide diagnostic or therapeutic tools for prion diseases.

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Section: Discussionmentioning

confidence: 88%

The design, synthesis and evaluation of affinity ligands for prion proteins

Renou

Gupta

Young

et al. 2004

J of Molecular Recognition

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“…Aptamers are short nucleic acid sequences typically identified through an experimental technique, the Systematic Evolution of Ligands by EXponential enrichment (SELEX) [32,33]. Aptamers can bind to specific molecular targets including small molecules, proteins, nucleic acids, phospholipids and can also be targeted to complex structures such as cells, tissues, bacteria and other organisms.…”

Section: Aptamer Designmentioning

confidence: 99%

“…Aptamers can bind to specific molecular targets including small molecules, proteins, nucleic acids, phospholipids and can also be targeted to complex structures such as cells, tissues, bacteria and other organisms. Because of their strong and specific binding through molecular recognition, aptamers are promising tools in molecular biology and have both therapeutic and diagnostic clinical applications [32][33][34][35]. Unfortunately, some limitations of the SELEX technique have seriously slowed down the progress of discovering aptamers [36].…”

Section: Aptamer Designmentioning

confidence: 99%

Maximum Entropy in Drug Discovery

Tseng

Tuszyński

2014

Entropy

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Drug discovery applies multidisciplinary approaches either experimentally, computationally or both ways to identify lead compounds to treat various diseases. While conventional approaches have yielded many US Food and Drug Administration (FDA)-approved drugs, researchers continue investigating and designing better approaches to increase the success rate in the discovery process. In this article, we provide an overview of the current strategies and point out where and how the method of maximum entropy has been introduced in this area. The maximum entropy principle has its root in thermodynamics, yet since Jaynes' pioneering work in the 1950s, the maximum entropy principle has not only been used as a physics law, but also as a reasoning tool that allows us to process information in hand with the least bias. Its applicability in various disciplines has been abundantly demonstrated. We give several examples of applications of maximum entropy in different stages of drug discovery. Finally, we discuss a promising new direction in drug discovery that is likely to hinge on the ways of utilizing maximum entropy.

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“…Aptamers are DNA or RNA molecules that can be selected from random pools based on their ability to bind other molecules [4][5][6][7]. Aptamers have been selected to bind other nucleic acids, proteins, small organic compounds, and even entire organisms.…”

Section: Introductionmentioning

confidence: 99%

Evaluation of the structure–activity relationship of thrombin with thrombin binding aptamers by voltammetry and atomic force microscopy

Diculescu¹,

Chiorcea-Paquim²,

Eritja³

et al. 2011

Journal of Electroanalytical Chemistry

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a b s t r a c tThe structure-activity relationship of the complex between thrombin and thrombin binding aptamers (TBA) was evaluated by differential pulse voltammetry at a glassy carbon electrode and atomic force microscopy at a highly oriented pyrolytic graphite electrode. The effects on the interaction with thrombin of TBA primary and secondary structures as well as of its folding properties in the presence of alkaline metals were investigated. The complex between thrombin and single stranded aptamers involved the coiling of the single stranded molecules around thrombin structure leading to the formation of a robust TBA-thrombin complex that maintains the symmetry and conformation of the thrombin molecule. Monitoring both thrombin and TBA oxidation peaks, showed that the thrombin oxidation peaks occur at more positive potentials after TBA-thrombin complex formation. In the presence of K + ions, the aptamers fold into quadruplex structures that facilitate the interaction with thrombin molecules. The TBAthrombin complex adsorbs at the surface with the aptamer quadruplex always in preferential contact with the surface, and the thrombin molecules on top of the aptamer quadruplex structure, thus being less accessible to the electrode surface leading to the occurrence of thrombin oxidation peaks at less positive potentials.

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Aptamers

Cited by 14 publications

References 183 publications

The design, synthesis and evaluation of affinity ligands for prion proteins

The design, synthesis and evaluation of affinity ligands for prion proteins

Maximum Entropy in Drug Discovery

Evaluation of the structure–activity relationship of thrombin with thrombin binding aptamers by voltammetry and atomic force microscopy

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