Synthesis and characterization of DNA-single molecule-DNA triblock structures [electronic resource] : as a novel approach towards single-molecule electronics

A precise and reproducible electrical contact between a single molecule and the electrodes is the first step in studying single-molecule electronics, which uses individual molecules as active electronic components. One potentially promising strategy to make the electrical contact to a single molecule is to use DNA as a template. DNA has emerged as a good scaffold in the field of nanoelectronics because DNA is easily aligned over large areas, and can be employed as a conducting nanowire with micrometer-scaled length after metallization using metal ions. Moreover, oligodeoxynucleotide (ODN) can be readily linked to a single organic molecule, and its length can be further increased to several micrometer scales through DNA extension techniques. To build DNA-assist single-molecule device structures, I investigated the reactivity of ODN to synthesize organic molecule-bis(ODN) triblock oligomers through three separate cross-coupling routes, such as amide-coupling reaction, isothiourea-bond formation, and "click" chemistry. Specifically, the amide-coupling reaction is scrutinized to enhance its reactivity since it affords the highest yield among the cross-coupling reactions. The optimized amide-coupling reaction is also employed to incorporate functional organic molecules, involving a fluorophore and a conjugated polymer, into ODNs. Organic molecule-bis(ODN) triblock oligomers were characterized by denaturing gel electrophoresis and electrospray ionization mass spectrometry. The ODNs of the triblock oligomers are elongated by polymerase chain reaction (PCR) or DNA hybridization/ligation methods. PCR is a fast and precise method to construct organic molecule-bis(1.5 kbp dsDNA) triblock structures from the triblock oligomers. On the other hand, DNA hybridization/ligation affords longer length of the ODN using micrometer-sized DNA fragments, which are prepared from lambda DNA using restriction enzymes and a phosphatase. Thus, organic molecule-bis(micrometer-sized DNA) triblock structures are assembled to obtain fully stretched DNA strands. To characterize the triblock structures, fluorophore-bis(micrometer-sized DNA) triblock structure was synthesized through DNA hybridization/ligation, and then directly imaged by combined atomic force and single-molecule fluorescence microscopy. For the purpose of building a single-molecule transistor device, a conjugated polymer-bis(micrometer-sized DNA) triblock structure was metallized by palladium metal ion. The metallized triblock structure is characterized by scanning electron microscopy (SEM) to monitor a nanogap from the conjugated polymer (contour length: ~7 nm). Unfortunately, the nanogap is not observed, due to overgrowth of metal ions during the DNA metallization. To overcome the problem, I also describe the synthesis of a micrometer-sized DNA-conjugated polymer-gold nanoparticle asymmetric triblock structure.

Keywords: Chemistry
Advisor: Bao Zhenan primary advisor. Thesis advisor
Chidsey Christopher E. D. (Christopher Elisha Dunn)
Waymouth Robert M. advisor. Thesis advisor