DESIGN AND CHARACTERIZATION OF SSDNA APTAMER CANDIDATES TO BIND BACTEROIDES FRAGILIS TOXIN SUBTYPES BFT-1 AND BFT-2

Enterotoxigenic Bacteroides fragilis (ETBF) is a diarrheal pathogen that secretes a twenty kilo-dalton protein toxin, Bacteroides fragilis toxin (BFT) which binds to an uncharacterized receptor on the surface of epithelial resulting in junctional cleavage causing chronic colitis. ETBF has also associated in colorectal cancer and irritable bowel disease patients. Magnetic bead based SELEX was used to generate aptamer pools with enriched binding specificity to BFT subtypes BFT-1 and BFT-2. A SYBR Green based Real-Time PCR assay was developed to monitor the enrichment of aptamer pools against BFT. Publicly available GUI based analyzed Illumina MiSeq sequencing aptamer pools. Secondary structure prediction algorithms and phylogeny trees of aptamer pool multiple sequence alignment data characterized eleven BFT binding aptamer candidates for future studies. These experiments demonstrate a simplified and easily adaptable set of methods for generating candidate ssDNA aptamers against bacterial protein toxins