Structural Insight into Protein Recognition by RNA Aptamers

Padlan, Frances-Camille S.; Girvin, Mark E.; Brenowitz, Michael; Levy, Matthew; Almo, Steven C.; Malashkevich, V.N.

doi:10.1016/j.bpj.2012.11.1427

Cited by 1 publication

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“…As previously observed by us and others with aptamers, initial tests indicated that the lowest energy predicted structure, Full.a, did not accurately reflect the actual structure in solution, as truncations using this fold as a guide only-yielded inactive molecules (for example, see ref. 27 ; data not shown). The first suboptimal predicted structure, Full.b, which has a predicted ΔG 0.5 kcal/mole higher than Full.a, was used as a guide for minimization where sections of the aptamer were removed by polymerase chain reaction (PCR) while maintaining the 5' T7 promoter and the 3' constant region.…”

Section: Characterization Of Waz a Novel Noncompetitive Anti-htfr Apmentioning

confidence: 83%

A New Transferrin Receptor Aptamer Inhibits New World Hemorrhagic Fever Mammarenavirus Entry

Maier

Jangra

Shieh

et al. 2016

Molecular Therapy - Nucleic Acids

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Pathogenic New World hemorrhagic fever mammarenaviruses (NWM) utilize Glycoprotein 1 (GP1) to target the apical domain of the human transferrin receptor (hTfR) for facilitating cell entry. However, the conservation between their GP1s is low. Considering this and the slow evolutionary progression of mammals compared to viruses, therapeutic targeting of hTfR provides an attractive avenue for cross-strain inhibition and diminishing the likelihood of escape mutants. Aptamers present unique advantages for the development of inhibitors to vial entry, including ease of synthesis, lack of immunogenicity, and potentially cold-chain breaking solutions to diseases endemic to South America. Here, recognizing that in vivo competition with the natural ligand, transferrin (Tf), likely drove the evolution of GP1 to recognize the apical domain, we performed competitive in vitro selections against hTfR-expressing cells with supplemented Tf. The resultant minimized aptamer, Waz, binds the apical domain of the receptor and inhibits infection of human cells by recombinant NWM in culture (EC50 ~400 nmol/l). Aptamer multimerization further enhanced inhibition >10-fold (EC50 ~30 nmol/l). Together, our results highlight the ability to use a competitor to bias the outcome of a selection and demonstrate how avidity effects can be leveraged to enhance both aptamer binding and the potency of viral inhibition.

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Section: Characterization Of Waz a Novel Noncompetitive Anti-htfr Apmentioning

confidence: 83%