Abstract
BackgroundNucleic acid aptamers have long demonstrated the capacity to bind viral envelope proteins and to inhibit the progression of pathogenic virus infections. Here we report on initial efforts to develop and screen DNA aptamers against recombinant envelope proteins or synthetic peptides and whole inactivated viruses from several virulent arboviruses including Chikungunya, Crimean-Congo hemorrhagic fever (CCHF), dengue, tickborne encephalitis and West Nile viruses. We also analyzed sequence data and secondary structures for commonalities that might reveal consensus binding sites among the various aptamers. Some of the highest affinity and most specific aptamers in the down-selected libraries were demonstrated to have diagnostic utility in lateral flow chromatographic assays and in a fluorescent aptamer-magnetic bead sandwich assay. Some of the reported aptamers may also be able to bind viral envelope proteins in vivo and therefore may have antiviral potential in passive immunity or prophylactic applications.ResultsSeveral arbovirus DNA aptamer sequences emerged multiple times in the various down selected aptamer libraries thereby suggesting some consensus sequences for binding arbovirus envelope proteins. Screening of aptamers by enzyme-linked aptamer sorbent assay (ELASA) was useful for ranking relative aptamer affinities against their cognate viral targets. Additional study of the aptamer sequences and secondary structures of top-ranked anti-arboviral aptamers suggest potential virus binding motifs exist within some of the key aptamers and are highlighted in the supplemental figures for this article. One sequence segment (ACGGGTCCGGACA) emerged 60 times in the anti-CCHF aptamer library, but nowhere else in the anti-arbovirus library and only a few other times in a larger library of aptamers known to bind bacteria and rickettsia or other targets. Diagnostic utility of some of the aptamers for arbovirus detection in lateral flow chromatographic assays and a fluorescent sandwich assay on the surface of magnetic microbeads is also demonstrated.ConclusionsThis article catalogues numerous DNA aptamer sequences which can bind various important pathogenic arboviruses and have, in some cases, already demonstrated diagnostic potential. These aptamer sequences are proprietary, patent-pending, and partially characterized. Therefore, they are offered to the scientific community for potential research use in diagnostic assays, biosensor applications or for possible passive immunity and prophylaxis against pathogenic viruses.
Highlights
Nucleic acid aptamers have long demonstrated the capacity to bind viral envelope proteins and to inhibit the progression of pathogenic virus infections
Such is the case with the following body of aptamer sequence, screening, and structural data for aptamers developed against recombinant proteins or synthetic peptides and whole inactivated viruses that were developed as part of several Small Business Innovative Research (SBIR) contracts with the U.S Defense Department for diagnostic applications
While some of the sequences demonstrated diagnostic potential in our enzyme-linked aptamer sorbent assay (ELASA [1,2]), we hypothesize that the highest affinity and most specific aptamers in the screened libraries may have therapeutic, prophylactic, or further diagnostic potential since aptamers have demonstrated antiviral potential in humans and animals against influenza [3,4,5] and a number of other viruses [6,7] beginning with HIV in the earliest days of aptamer research [8]
Summary
Nucleic acid aptamers have long demonstrated the capacity to bind viral envelope proteins and to inhibit the progression of pathogenic virus infections. Some of the reported aptamers may be able to bind viral envelope proteins in vivo and may have antiviral potential in passive immunity or prophylactic applications. The self-professed aim of BMC Research Notes is to “reduce the loss suffered by the research community when results remain unpublished because they do not form a sufficiently complete story to justify the publication of a full research article.” Such is the case with the following body of aptamer sequence, screening, and structural data for aptamers developed against recombinant proteins or synthetic peptides and whole inactivated viruses that were developed as part of several Small Business Innovative Research (SBIR) contracts with the U.S Defense Department (see the Acknowledgments section for contract numbers) for diagnostic applications. Passive aptamer therapy would hold the advantage of low to nonexistent immunogenicity, because nucleic acids are generally nonimmunogenic and do not lead to allergic reactions or serum sickness upon subsequent administration [9,10]
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