Nanoscale patterning of self-assembled monolayer (SAM)-functionalised substrates with single molecule contact printing

Abstract

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.

Structural stability of DNA origami nanostructures under application-specific conditions

“…DNA origami nanostructures are also increasingly employed in various materials science applications. Many studies have used DNA origami nanostructures as templates or lithography masks in order to transfer their shapes into other biological [ 22 , [91] , [92] , [93] ], organic [ [94] , [95] , [96] , [97] ], and especially inorganic materials [ 21 , 23 , 29 , 30 , [98] , [99] , [100] , [101] ]. Even if this requires conditions that deviate from the usual solution conditions, the shapes of the DNA origami templates are often transferred in a single processing step, so that their structural stability is usually of little concern.…”

Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability

“…Since the first demonstration by Rothemund in 2006 [2], DNA origami nanostructures have found their way into many different fields of fundamental and applied research [3]. For instance, DNA origami nanostructures are currently employed as drug delivery vehicles [4,5,6,7,8], sensors [9,10,11,12], templates for the fabrication of nanoelectronic [13,14,15,16] and plasmonic devices [17,18,19,20,21], substrates for single-molecule studies [22,23,24,25,26,27], and masks in molecular lithography [28,29,30,31,32]. While all these applications crucially rely on an intact DNA origami shape, many of them subject the employed DNA origami nanostructures to rather harsh treatments.…”

The Art of Designing DNA Nanostructures with CAD Software

“…In the early years, it was a major accomplishment to even design and construct simple wireframe structures from a small number of oligonucleotides [9,104]. Nowadays, large, often intricately complex, structures consisting of several hundred or more strands, which can template the positions of large collections of accessory molecules, are used for applications that range from synthetic vaccines [105] to the nanofabrication of inorganic materials and substrates [54,95,[106][107][108][109], or measurements of molecular forces that are exerted by single proteins [107].…”