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Assembly of DNA Rotaxanes for AFM Based DNA Sequencing

Q. Spadola, S. Qamar, L. Lin, B. Ashcroft, P. Zhang and S.M. Lindsay
The Biodesign Institute at Arizona State University, US

Keywords:
rotaxanes, DNA, AFM, sequencing

Abstract:
The desire to sequence DNA is fueled by the knowledge that the information locked inside of genomes can help fields as varied as molecular medicine, bioarcheology, forensics, and environmental science. The challenge is to establish a method that is more cost effective and faster than the ones currently available. Many new sequencing technologies are being developed to achieve these goals. Our technique takes advantage of the atomic force microscope’s (AFM) ability to detect piconewton scale forces in order to read off sequencing information based on the interaction of nucleotides with a cyclodextrin. We have successfully completed two of the major pieces needed to sequence DNA with an AFM. The problem of nonspecific adhesion of single-stranded DNA with both hydrophobic and hydrophilic surfaces was overcome by using poly (ethylene glycol) passivation layer. The creation of a rotaxane to put on the surface was accomplished involving DNA with a carbon chain, cyclodextrin that will thread the chain, and a stopper. We are also able to successfully model the complex behavior of cyclodextrin sliding over the DNA.

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