Specificity of Watson–Crick Base Pairing on a Solid Surface Studied at the Atomic Scale

Abstract

Surface Watson–Crick base pairing makes binary mixtures of the complementary nucleobases guanine (G) and cytosine (C) on Au(111) thermally stable up to the desorption temperature of the bases, whereas binary mixtures of the noncomplementary adenine (A) and cytosine segregate on heating (see STM images with DFT structures).

Supramolecular Porous Network Formed by Molecular Recognition between Chemically Modified Nucleobases Guanine and Cytosine

“…It is reasonable to expect that higher efficiency and accuracy in the molecular recognition process exist between the biomimetically modified nucleobases compared to the nucleobases C and G alone, because fewer competitive hydrogen-bonded configurations are available for the modified nucleobases. This is indeed confirmed by our previous experiments [8] performed with the unmodified bases C and G, where we found that Watson-Crick G-C pairs were only randomly embedded into a C filament and characteristic fivefold ring structures without higher ordering. In summary, we have demonstrated that Watson-Crick hydrogen bonding can indeed play a vital role in driving natural molecular recognition between complementary nucleobases on a noble gold surface, even under well-controlled UHV conditions.…”

“…In support of this postulation, molecular recognition between complementary bases, most likely driven by hydrogen bonding alone, has already been observed both at the liquid/solid (HOPG) interface and on the noble Au(111) surface under extreme ultrahigh vacuum (UHV) conditions. [8][9][10] These previous experiments were, however, conducted with nucleobases alone, and hence did not take the presence of deoxyribose into account. It is therefore of utmost importance to explore the role that Watson-Crick hydrogen bonding plays at surfaces in chemical structures that mimic nucleotides so as to address the fundamental question of how the polymerization of nucleotides may have started in the prebiotic soup in the absence of enzymes.…”

“…Adsorption of such chemically modified nucleobases on a noble Au(111) surface under well-controlled UHV conditions constitutes an interesting model system that may give unique insight into the fundamental driving forces behind molecular recognition between complementary nucleobases. The Au-(111) surface served as a template to ensure that the nucleobases adopt a flat adsorption geometry [8,[18][19][20][21][22] that mimics the base-stacking situation in natural double-stranded nucleic acids (see the Supporting Information), and the wellcontrolled ultraclean UHV conditions provide an idealized environment without water, salts, metal ions, etc. The main determinants for intermolecular interactions between the nucleobases under these extreme conditions are limited to hydrogen bonding and possible van der Waals interactions between the aryl groups.…”

Role of van der Waals interaction in forming molecule-metal junctions: flat organic molecules on the Au(111) surface

“…However, in many cases, e.g. for DNA bases 8,11,12,14,16 and melamine molecules on the Au(111) surface, 15,28 perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride (PTCDA) molecules on the Ag(111) surface, 19,22,23 benzene 26 and PTCDA 30 molecules on the Au(111), Cu(111) and Ag(111) surfaces the calculated adsorption energies are too small (of the order of 0.1-0.2 eV) which is inconsistent with experimental observations of the desorption temperatures for these molecules (around 100-300 1C). This failure of standard generalized gradient approximation (GGA) functionals, such as e.g.…”

Fabrication of a Complex Two-Dimensional Adenine–Perylene-3,4,9,10-tetracarboxylic Dianhydride Chiral Nanoarchitecture through Molecular Self-Assembly

“…21,22 Molecular size and geometry, as well as interaction between molecules, are some of the key parameters determining whether or not molecular self-assembly is possible and what the final outcome will be. For instance, it has been shown that the mixture of adenine and cytosine, both DNA bases, does not lead to the formation of ordered multicomponent structures, 23 whereas several multicomponent structures have been obtained using semiconducting perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride (PTCDA) molecules mixed pentacene 24 and 2,4,6-triamino-1,3,5-triazine, sym-triaminotriazine. 25 In this paper, we investigate the self-assembly of a nonsymmetric adenine DNA base ( Figure 1a) mixed with symmetric PTCDA molecules (Figure 1b) on a Au(111)-(22 Â √ 3) surface at room temperature in ultrahigh vacuum.…”