The proof of concept for a novel approach to DNA sequencing

This dissertation presents work on a novel approach to DNA sequencing, Sequencing By Recognition (SBR). SBR is based on the chemical recognition of DNA bases via enhanced electrical current when Watson-Crick hydrogen bonded base pairs form between a base-functionalized probe and a base on a DNA to be read. One important aspect of this method is to prove that it is possible to tunnel across a DNA molecule. Tunneling currents that can identify different bases are detected via hydrogen bonds facilitated transport when the immobilized guanidinium grabs the phosphate group connected to a base that forms Watson-Crick bonds with the closest complementary base attached to the other electrode. Using Scanning Tunneling Microscope (STM), results show that electrode-tethered guanidinium ions form hydrogen bonds which enable the transverse tunneling through native DNA. Bases were identified with a high accuracy via current-distance measurements in hydrogen-bonded tunnel junctions between bases and nucleosides. However, the limited resolution of the present approach makes it unsuitable for DNA sequencing applications where single-base resolution is required. Thus another "telegraph noise" method was developed to measure the tunnel conductance of single hydrogen bonded pair. Experiments results determined the absolute tunnel conductance for adenine-thymidine, 2-amino-8mercaptoadenine-thymidine and guanine-deoxythymidine spanning gold electrodes. The distributions of switching times clearly allow identification of both H-bond and molecule-metal contact breaking. According to all the preliminary results, shorter tunneling path is required to obtain higher gap conductance so as to make SBR method become possible