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

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.

Current Perspectives on Aptamers as Diagnostic Tools and Therapeutic Agents

“…In another study, an RNA aptamer, 39SGP1A, functionalized with 2’ fluoropyrimidine (2’FY) was developed, which was explicitly bound to a soluble glycoprotein (sGP) of the Ebola virus (EBOV). The motif of 39SGP1A aptamer was found to be a novel polypyrimidine-rich sequence that had a role in the recognition of sGP [ 65 ]. The aptamer was useful for the diagnosis of two Ebola virus species, Ebola virus (EBOV) and Sudan virus (SUDV, by binding to a conserved epitope present in both species.…”

Aptamers for Anti-Viral Therapeutics and Diagnostics

“…sGP is a good biomarker for EBOV because it is secreted in abundance into the bloodstream, even during the early stages of infection. The isolated aptamer was specifically bound to sGP with high affinity and was demonstrated to be an excellent diagnostic tool for the detection of EBOV infection [ 155 ]. Hong et al developed DNA aptamers against EBOV GP and NP using a highly efficient aptamer selection platform in which they used magnetism-controlled selection chips to select aptamers.…”

Aptamers for Detection and Diagnostics (ADD) is a proposed mobile app acquiring optical data from conjugated quantum nanodots to identify molecules indicating presence of SARS-CoV-2 virus: Why public health and healthcare need smartphone sensors as a platform for early detection and prevention

“…Single stranded (ss) DNA aptamers (ssRNA 7 are equally useful 8 but susceptible to degradation by ribonuclease) bind with specificity to SARS-CoV-2 9 proteins (Nucleocapsid, Spike, Nsp1).…”