Two-dimensional ordering of the DNA base guanine observed by scanning tunneling microscopy.

Abstract

Guanine, one ofthe four DNA bases, has been observed by tunneling microscopy to form a two-dimensional ordered structure on two crystalline substrates, graphite and MoS2. The two-dimensional lattice formed by guanine is nearly identical on the two surfaces, and heteroepitaxy appears to be the growth mechanism in both cases. Although the resolution of molecular details is superior for the graphite substrate, the simpler results on MoS2 are not only easier to interpret but also facilitate the understanding of the more complex images on graphite. We propose that the interfacial structure is composed of linear chains of hydrogen-bonded molecules aligned into a closely packed two-dimensional array.Several recent studies have examined the possibility of imaging DNA by scanning tunneling microscopy (STM) (1-3). However, the ultimate goal-to read the code contained in the strands-has not yet been achieved. To do so it must be possible to recognize clearly and distinguish between the four bases of the genetic code. One essential requirement for imaging small organic molecules by STM is to find experimental preparation conditions whereby the molecules stick firmly to the substrate and form a highly stable layer. This is necessary to withstand the forces of the STM tip during imaging. Compared to the binding of complete DNA strands to the basal planes of MoS2 or graphite, the adsorption of "naked" nucleotide bases is favored by their greater hydrophobicity and, as is shown in this report, by their ability to register with the substrate, thus forming a stable twodimensional ordered array. No signs of mobility were observed during investigations, which lasted up to 1 h in a single region. That such an array can form is probably due to the intermolecular hydrogen bonding capability of the DNA bases (4).Ordered molecular layers of organic molecules, such as benzene (5), alkanes (6), or liquid crystals (7,8), are the most prominent examples to have been imaged recently by STM at atomic resolution. STM results of adenine, one of the four DNA bases, have recently been obtained on graphite by Allen et al. (9). Using a sample preparation technique similar to theirs (9), we prepared samples of guanine on the surfaces of natural MoS2 crystals and highly oriented pyrolytic graphite. We often observed steps from the bare substrate to monolayers of guanine. The results presented in this paper were obtained on such monolayer islands. The character of the steplines provides additional information since the orientation of the molecular lattice with respect to the substrate can be measured there. In the STM images the bases look quite different depending on whether they are deposited on MoS2 (Fig. 1) or on graphite (see Fig. 3). The main differences are that on MoS2 the bases appear as distinct well-isolated nearly structureless blobs; on graphite more details become visible, although it is still not possible to determine the 8003The publication costs of this article were defrayed in part by page charge payment. This article must ...

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