Supramolecular Nanopatterns Self-Assembled by Adenine−Thymine Quartets at the Liquid/Solid Interface

Abstract

By means of scanning tunneling microscopy (STM), we have observed for the first time well-ordered supramolecular nanopatterns formed by mixing two complementary DNA bases: adenine (A) and thymine (T), respectively, at the liquid/solid interface. By mixing A and T at a specific mixing molar ratio, cyclic structures that were distinctly different from the structures observed by the individual base molecules separately were formed. From an interplay between the STM findings and self-consistent charge density-functional based tight-binding (SCC-DFTB) calculation method, we suggest formation of A-T-A-T quartets constructed on the basis of A-T base pairing. The formation of the A-T-A-T quartets opens new avenues to use DNA base pairing as a way to form nanoscale surface architecture and biocompatible patterned surfaces particularly via host-guest complexation that might be suitable for drug design, where the target can be trapped inside the cavities of the molecular containers.

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

“…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.…”

Ordering and Stabilization of Metal–Organic Coordination Chains by Hierarchical Assembly through Hydrogen Bonding at a Surface

“…[1][2][3][4][5][6] Specific supramolecular architectures can be designed by choosing molecular building blocks with distinct size, geometry, and bonding interaction, as has been demonstrated extensively in solution-based coordination chemistry [7][8][9][10] and, in recent years, on surfaces. [11][12][13][14][15] The technological potential of controlled structural and chemical patterning of surfaces has driven an interest in the rational design of highly ordered and regular networks at solid surfaces, which require selective and directional bonding interactions, such as hydrogen bonding [16][17][18] or metal-organic coordination. [11,13,19,20] Reversible (noncovalent) bonding motifs allow for efficient error-correction during the growth process and long-range structural order in the resulting supramolecular architecture.…”

Surface modification and pattern formation by nucleobases and their coordination complexes

“…It was suggested that such structures might offer applications in biocompatible nanopatterned surfaces and for targeted drug delivery. 65 Coadsorption of guanine and cytosine also resulted in ordered assemblies at 1-octanol/graphite interface, where one of the phases consisted of hydrogen-bonded guanine-cytosine dimers (Fig. 7).…”

“…65 Interestingly, thymine on Au(111) substrate leads to randomly oriented 1D laments, when viewed at low surface coverage, which gets morphed to 2D island-like growth patterns on increasing the coverage area, supported by weak van der Waals forces. The 2D islands could be reverted to 1D laments through STM tip perturbation, suggesting that 2D islands were loosely held compared to more stable laments (Fig.…”