The application of scanning tunneling microscopy (STM) and related techniques to the study of organic and biomolecular targets
Scanning tunneling microscopy (STM) has been used to study: (a) Self-assembled monolayers and sub-monolayers of butanethiol adsorbed onto highly uniform Au/mica films, (b) DNA adsorbates on different substrates prepared by different deposition techniques. In addition, surface preparation techniques have been investigated. Two strongly oxidizing solutions (sulfochromic and piranha acids) have been studied for the elimination of residual organic adsorbates on the Au/mica substrate. Treatment of the Au/mica surface with piranha acid leads to extensive and uncontrolled etching of the surface, and severe disruption of the surface topography. Limited exposure of the Au/mica surfaces to sulfochromic acid leads to the formation of permanent etch pits of the surface that are exclusively one Au layer deep; extended exposure leads to progressive lateral etching of the surface, ultimately leading to the formation of 3.3-3.6 A high islands on the otherwise flat surface. STM images taken of fully-equilibrated butanethiol monolayer films show molecularly resolved features that are believed to correspond to the methyl terminations of the organic surface. Large domains of organized adsorbates and a variant of the previously reported $p\times\surd3$ superlattice structure is observed on these surfaces; using this nomenclature, the basic repeat unit of the structure reported herein corresponds to a $7\times\surd3$ superlattice. The study of sub-monolayer films shows the island-like formations of SAMs on the gold surface; each island has same molecular structure as observed in monolayer films. Natural plasmids of different lengths together with chemically modified oligonucleotide sequences are adsorbed onto graphite and Au/mica surfaces and studied using the STM. High resolution images were obtained with clearly resolved helical structures.