Surface analysis and engineering of two-dimensional assemblies of purines and pyrimidines on gold

During evolution, nature selected purines and pyrimidines as the basis of life on earth, partly because they allowed high fidelity DNA replication and DNA self-assembly through molecular recognition events, yet left ample possibilities for mutations. It is this richness that inspired the author to select and investigate purines and pyrimidines for their possible use in engineered, two-dimensional assemblies. The ability to engineer highly ordered assemblies with considerable molecular recognition capabilities could, for example, lead to high speed DNA sequencing.; Self-assembled monolayers, prepared from dilute solutions of purines and pyrimidines that chemisorbed to gold surfaces are investigated. The adsorbed layers were imaged with scanning tunneling microscopy (STM) and analyzed with electron spectroscopy for chemical analysis (ESCA) and static secondary ion mass spectrometry (SSIMS). The results indicate monolayer adsorption and highly ordered assemblies of several purines and pyrimidines including the four DNA bases. Mechanisms leading to the monolayer formations will be discussed. Furthermore, the kinetics and energetics of the self-assembly are presented.; The self-assembling DNA bases have been used to functionalize planar gold surfaces and gold coated atomic force microscope (AFM) tips. Directional hydrogen bonding interaction between the tip and the molecular films can be measured only when opposite base-pair coatings are used. The directional interactions can be inhibited by excess nucleotides in solution. Using coated AFM tips, surface chemistry-sensitive recognition AFM can be performed. This chemical imaging technique is potentially useful for DNA sequencing.; Finally, a novel lithographic technique is described using AFM tip scraping of a pattern into a plasma deposited films. The engraved areas can be used for chemical derivatization such as self-assembled film growth. By carefully choosing substrate, film and chemical derivatization, patterned substrates that preferentially adsorb protein or DNA can be designed. Examples of patterning will be presented, including the patterning of the DNA base adenine with the subsequent reading of the pattern using a chemically functionalized thymine AFM tip, and the spatially confined adsorption of lysozyme.