Virtual screening of truncated single stranded DNA aptamers for Staphylococcal enterotoxin type A

Abstract

Single stranded DNA (ssDNA)/RNA aptamers, are screened through the labor intensive, iterative Systematic Evolution of Ligand by Exponential Enrichment process (SELEX) method. Complete sequence of screened aptamers never interacts with target or participates in final structure. Hence, in silico tools can be used to redesign a short length aptamer from previously reported aptamers which can have high affinity and specificity to the target. This approach is fast, cost effective, and less laborious than in vitro SELEX towards finding an aptamer sequence with better affinity with the target. Here, Staphylococcal enterotoxin type A (SEA) was used as target. A total of nine aptamers reported for different Staphylococcal food poisoning (SFP) enterotoxins were used as a starting pool. The aptamers were variously truncations and thoroughly analyzed through in silico methods. Three truncated aptamers namely AptSEA1.4, AptSEA2.4 and AptSEA8.4 were found to show higher affinity with target SEA. The computational data was also validated with DOT BLOT assay complemented with image analysis. These results also confirmed that the % specific binding and the dissociation constant (Kd) of truncated aptamers AptSEA1.4, AptSEA2.4 and AptSEA8.4 was better than their original counterparts. The truncated aptamers showed great promise to be used as a capture reagent in developing a sensitive assay for detection of SEA.

Communicated by Ramaswamy H. Sarma

Keywords:

• Aptamer
• DOT BLOT
• truncation
• SELEX
• Staphylococcal enterotoxin

Author contributions

Seema Nara: conceptualization, methodology, investigation, and writing—review and editing. Smriti Singh: methodology, investigation, and writing—review and editing. Papia Chowdhury: methodology and writing. Arabinda Ghosh: methodology.

Acknowledgements

We sincerely acknowledge Motilal Nehru National Institute of Technology Allahabad, India and Ministry of Human Resource and Development (MHRD), India for providing all necessary facilities and support for this research work. We would also like to acknowledge DST-FIST for their support to our department.

Disclosure statement

No potential conflict of interest was reported by the authors.

Funding

The author(s) reported there is no funding associated with the work featured in this article.