A 2′FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein

Shambhavi Shubham; Jan Hoinka; Soma Banerjee; Emma Swanson; Jacob A Dillard; Nicholas J Lennemann; Teresa M Przytycka; Wendy Maury; Marit Nilsen-Hamilton

doi:10.1038/s41598-018-30590-8

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A 2′FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein

Journal article

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A 2′FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein

Shambhavi Shubham, Jan Hoinka, Soma Banerjee, Emma Swanson, Jacob A Dillard, Nicholas J Lennemann, Teresa M Przytycka, Wendy Maury and Marit Nilsen-Hamilton

Scientific reports, Vol.8(1), 12373

12/01/2018

DOI: 10.1038/s41598-018-30590-8

PMCID: PMC6098113

PMID: 30120364

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Abstract

With properties such as stability to long-term storage and amenability to repetitive use, nucleic acid aptamers are compatible with many sensing/transducing platforms intended for use in remote locations. Sensors with these properties are important for quickly identifying ebolavirus outbreaks, which frequently start in locations that lack sophisticated equipment. Soluble glycoprotein (sGP), an excellent biomarker for ebolaviruses, is produced from the same gene as the ebolavirus glycoprotein GP1,2 that decorates the surface of the viral particle and is secreted in abundance into the blood stream even during the early stages of infection. Here, we report the selection and properties of a 2′fluoro pyrimidine (2′FY)-modified RNA aptamer, 39SGP1A, that specifically binds sGP. We demonstrate by computational and biochemical analysis that the recognition motif of 39SGP1A is a novel polypyrimidine-rich sequence. Replacement of -F by -OH in the 2′ position of the ribose resulted in complete loss of affinity for sGP. The protein motif to which the aptamer binds requires an intact sGP dimer and binds to an epitope conserved between Ebola virus (EBOV) and Sudan virus (SUDV) sGP, the most divergent Ebolavirus species. This identifies 39SGP1A as an excellent option for integration on a sensor platform to detect ebolavirus infections.

Details

Title: Subtitle: A 2′FY-RNA Motif Defines an Aptamer for Ebolavirus Secreted Protein
Creators: Shambhavi Shubham - Ames, IA USA
Jan Hoinka - Bethesda, MD USA
Soma Banerjee - Aptalogic Inc., Ames, IA USA
Emma Swanson - Ames, IA USA
Jacob A Dillard - Iowa City, IA USA
Nicholas J Lennemann - Iowa City, IA USA
Teresa M Przytycka - Bethesda, MD USA
Wendy Maury - Iowa City, IA USA
Marit Nilsen-Hamilton - Ames, IA USA
Resource Type: Journal article
Publication Details: Scientific reports, Vol.8(1), 12373
DOI: 10.1038/s41598-018-30590-8
PMID: 30120364
PMCID: PMC6098113
NLM abbreviation: Sci Rep
ISSN: 2045-2322
eISSN: 2045-2322
Publisher: Nature Publishing Group UK
Language: English
Date published: 12/01/2018
Academic Unit: Microbiology and Immunology
Record Identifier: 9984083268102771

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