Aptamers have been selected against a variety of important biodefense targets, including protein toxins such as ricin and pepocin and antigens from pathogenic bacteria such as Yersinia spp. and F. tularemia. To ensure that reagents can be created for any of a variety of chemical and biological agents, including new biological agents, selection methods need to be streamlined. The cost of chemical and enzymatic synthesis of many RNA or modified RNA aptamers remains prohibitive for their development as therapeutics, which limit their application in diagnostic and biosensor applications. The cheapest and best alternative method is to synthesize short DNA aptamers. Unfortunately, short DNA aptamers frequently do not bind their targets with high affinities and specificities, because the surface area between the aptamer and target is too small to ensure multiple contacts. We propose a novel selection method that will both generate high affinity aptamers in a single step and significantly reduce the cost of synthesis of these aptamers. Deliverables for this project will be short aptamers that can bind as networks to MS2 bacteriophage or B. subtilis with affinities in the nanomolar range. The specificities of these aptamer networks will be measured by determining whether they bind to non-cognate targets.
Keywords: Aptamers, Rna, Dna, Polyvalent Aptamer Networks, Sequencing, B. Subtilis
