Scientific Reports (May 2021)

Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate

  • Iman Jeddi,
  • Leonor Saiz

DOI
https://doi.org/10.1038/s41598-021-88796-2
Journal volume & issue
Vol. 11, no. 1
pp. 1 – 12

Abstract

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Abstract Aptamer interactions with a surface of attachment are central to the design and performance of aptamer-based biosensors. We have developed a computational modeling approach to study different system designs—including different aptamer-attachment ends, aptamer surface densities, aptamer orientations, and solvent solutions—and applied it to an anti MUC1 aptamer tethered to a silica biosensor substrate. Amongst all the system designs explored, we found that attaching the anti MUC1 aptamer through the 5′ terminal end, in a high surface density configuration, and solvated in a 0.8 M NaCl solution provided the best exposure of the aptamer MUC1 binding regions and resulted in the least amount of aptamer backbone fluctuations. Many of the other designs led to non-functional systems, with the aptamer collapsing onto the surface. The computational approach we have developed and the resulting analysis techniques can be employed for the rational design of aptamer-based biosensors and provide a valuable tool for improving biosensor performance and repeatability.