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SignificanceCurrent efforts aimed at constructing complex supramolecular structures often suffer from low yields or require long assembly protocols. We address these problems by demonstrating a facile strategy for optimizing the nucleation step of a multicomponent self-assembly reaction. By tracking the formation of multisubunit clusters in situ, our experiments show that modifying the critical nucleus required to initiate structure growth can broaden the range of conditions over which self-assembly occurs and, consequently, can dramatically improve the final yield of correctly formed structures. Since varying the design of only a small portion of the target structure optimizes its yield, this strategy provides a practical route to improve the speed and accuracy of self-assembly in biomolecular, colloidal, and nanoparticle systems.

We have carried out a systematic study of hydrogen-bonded cyclic A, C, T, and mixed GCGC tetrads resembling conformations occurring in experimental tetraplex structures, using the B3LYP hybrid density functional (DFT) method and the MMFF and AMBER force fields to determine tetrad structures and interaction energies. The results are compared to G and U tetrads analyzed previously, thereby presenting a comprehensive overview of all cyclic tetrads formed from one base type only, in addition to the GCGC data. The DFT calculations indicate that the C tetrad is planar and the GCGC tetrad is nearly planar and correspond to local minima at C 4 h and C i symmetry, respectively. For A tetrads with N6−H6···N7 and with N6−H6···N1 H-bonds and for T tetrads, nonplanar structures are more stable than the planar ones, and among the nonplanar structures, S 4-symmetric conformations are more stable than C 4 structures. Minima confirmed by frequency calculations are found for the planar C tetrad, the C i -symmetric GCGC tetrad, the C 4-symmetric structure of the A tetrad with N6−H6···N7 H-bonds, and the S 4-symmetric T tetrad, in addition to the already known local minima of the S 4-symmetric structure of the G tetrad and the planar U tetrad with C−H···O hydrogen bonds. The interaction energies (ΔE T) corrected for deformation of the bases in the tetrads range from −69.47 kcal/mol for the GCGC tetrad with three pairs of strong Watson−Crick type hydrogen bonds to −11.09 kcal/mol in the planar A tetrad having only a single N6−H62···N1 interbase hydrogen bond. With more than 18%, the largest cooperativity contribution to ΔE is found for the C and G tetrads. The interaction energies derived from the MMFF and AMBER force field are similar to the DFT data for those tetrads having high interaction energies, whereas the relative deviations are much larger for weakly H-bonded tetrads.

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Defined arrangements of individual molecules are covalenty connected ("printed") onto SAM-functionalised gold substrates with nanometer resolution. Substrates were initially pre-functionlised by coating with 3,3'-dithiodipropionic acid (DTPA) to form a self-assembled monolayer (SAM), which was characterised by atomic force microscopy (AFM), contact angle goniometry, cyclic voltammetry and surface plasmon resonance (SPR) spectroscopy. Pre-defined "ink" patterns displayed on DNA origami-based single-use carriers ("stamp") were covalently conjugated to the SAM using 1-ethyl-3-(3-dimethylamino-propyl)carbodiimide (EDC) and N-hydroxy-succinimide (NHS). These anchor points were used to create nanometer-precise single-molecule arrays, here with complementary DNA and streptavidin. Sequential steps of the printing process were evaluated by AFM and SPR spectroscopy. It was shown that 30% of the detected arrangements closely match the expected length distribution of designed patterns, whereas another 40% exhibit error within the range of only 1 streptavidin molecule. SPR results indicate that imposing a defined separation between molecular anchor points within the pattern through this printing process enhances the efficiency for association of specific binding partners for systems with high sterical hindrance. This study expands upon earlier findings where geometrical information was conserved by the application of DNA nanostructures, by establishing a generalisable strategy which is universally applicable to nearly any type of prefunctionalised substrate such as metals, plastics, silicates, ITO or 2D materials.