Folding and Base Pairing of a Fibrinogen Specific DNA Aptamer

Abstract Nucleic acid aptamers can be directed to bind to a variety of target molecules that range widely in molecular size. Their high specificity and selectivity for their targets, in addition to the relative ease in generating aptamers, have sparked their development as drugs and use in diagnostic applications. The 90-mer DNA aptamer (Ap90), specific for the glycoprotein fibrinogen was analyzed by a combination of gel electrophoresis, secondary structure prediction software and NMR spectroscopy to determine what structural motifs are formed prior to binding to its target. Native gel electrophoresis and structure prediction indicate that the aptamer is partially folded. This was further supported by the NMR studies focusing on base pairing. The NMR experiments revealed that the aptamer only forms a maximum of 4-5 AT and 6-8 GC base pairs. Using several model substrates, the base paired region was identified as a hairpin structure originating from the primer region. Changing the solvent conditions did not elicit additional base pairs or promote stable tertiary structures. These results demonstrate that the majority of the aptamer has no established structure prior to binding and guides the design of more efficient aptamers