STRUCTURE OF HYDRATED OLIGONUCLEOTIDES STUDIED BY IN-SITU SCANNING-TUNNELING-MICROSCOPY

We have used the scanning tunneling microscope (STM) to image several synthetic oligonucleotides adsorbed onto a positively charged Au(111) electrode. The molecules were deposited and imaged in aqueous electrol yte under potential control, a procedure that eliminated the problem o f the substrate artifacts that had limited some previous STM studies. Experiments were carried out with two types of single-stranded molecul es (11 and 20 bases long) and three types of double-stranded molecules (20 and 61 base pairs and 31 bases with 25 bases paired and 6-base '' sticky'' ends). The molecules lie along symmetry directions on the rec onstructed (23 x square-root 3) gold surface, and length measurements indicate that they adopt simple base-stacked structures. The base stac king distances are, within experimental uncertainty, equal to the 0.33 nm measured for polymeric aggregates of stacked purines by direct ima ging in identical conditions. The images show features consistent with helical structures. Double helices have a major-groove periodicity th at is consistent with a 36-degrees twist. The single helices appear to be more tightly twisted. A simple tunneling model of STM contrast gen erates good agreement between measured and calculated images.