Self-assembly of molecular superstructures studied by in situ scanning tunneling microscopy: DNA bases on Au(111)

We have studied the DNA bases adenine, thymine, guanine, and cytosine adsorbed onto Au(111) using in situ scanning tunneling microscopy (STM), atomic force microscopy (AFM), and cyclic voltammetry. Adenine, guanine, and cytosine adsorbed spontaneously onto the electrode with the counter electrode disconnected and yielded stable images over a range of electrode potentials. Thymine was not adsorbed until an electron-transfer reaction occurred at +0.4 V (SCE). Adenine and guanine formed polymeric aggregates in which the bases stacked with repeat distances of 3.4 ± 0.2 Å (adenine) and 3.3 ± 0.3 Å (guanine). Adenine aggregates aligned along the Au[110] directions and also formed a complex that decorated the path of the p × √3 (p ≃ 23) reconstruction. Guanine aggregates were disordered with respect to the underlying gold. Cytosine formed an oblique lattice with a = 10.5 ± 0.2 Å, b = 9.5 ± 0.2 Å, and γ = 103 ± 3°, oriented at 30° to the Au[110] directions. It is fitted well by a model in which every other molecule inverted to bond O₂ to N4 and N1 to N3, followed by N4 to O2 and N3 to N1. Thymine also formed an oblique lattice with a = 6.5 ± 0.5 Å, b = 7.1 ± 0.5 Å, and γ = 105 ± 5°. The STM corrugation measured over adenine, cytosine, and guanine adsorbates was ∼1 Å but only ∼0.1 Å over thymine. Thymine contrast also changed with the electrochemical potential of the electrode. We discuss the possibility of a connection between electrochemical electron transfer and STM contrast.