Boron-Implanted Silicon Substrates for Physical Adsorption of DNA Origami

Abstract

DNA nanostructures routinely self-assemble with sub-10 nm feature sizes. This capability has created industry interest in using DNA as a lithographic mask, yet with few exceptions, solution-based deposition of DNA nanostructures has remained primarily academic to date. En route to controlled adsorption of DNA patterns onto manufactured substrates, deposition and placement of DNA origami has been demonstrated on chemically functionalized silicon substrates. While compelling, chemical functionalization adds fabrication complexity that limits mask efficiency and hence industry adoption. As an alternative, we developed an ion implantation process that tailors the surface potential of silicon substrates to facilitate adsorption of DNA nanostructures without the need for chemical functionalization. Industry standard 300 mm silicon wafers were processed, and we showed controlled adsorption of DNA origami onto boron-implanted silicon patterns; selective to a surrounding silicon oxide matrix. The hydrophilic substrate achieves very high surface selectivity by exploiting pH-dependent protonation of silanol-groups on silicon dioxide (SiO2), across a range of solution pH values and magnesium chloride (MgCl2) buffer concentrations.

Correlative Super-Resolution and Atomic Force Microscopy of DNA Nanostructures and Characterization of Addressable Site Defects

“…While we do not attempt to elucidate the chemical composition of the surface postcleaning, it was observed that DNA origami adsorption does not occur in the absence of divalent cations and at pH less than 7. This behavior is similar to prior observations of DNA origami adsorption to piranha/HF-cleaned, thermally grown silica, for which it was postulated that pH-dependent adsorption resulted from the deprotonation of silanol groups generated during cleaning …”

“…DNA-directed self-assembly offers precise spatial control when arranging molecules and particles at the nanoscale. − The utility of DNA origami has been demonstrated through multiple applications, such as plasmonic and photonic devices, − localized chemical reaction networks for sensing and DNA computation, − lithographic masks for semiconductor devices, − and protein/enzyme-based biosensors. ,,,,, Many of these applications rely on the inclusion of addressable sites, typically single-stranded (ss) DNA tethers, for postassembly modification. The availability of such sites on the origami is critical to the synthesis of functional structures.…”

Nuclease resistance of DNA nanostructures

“…Demonstrations of the applications of DNA in different fields have increased exponentially in the past decade 50,51 . In materials science, DNA can serve as a copolymer for creating integrated chips 52,53 , pooled DNA libraries are used in data storage and molecular computation 54,55 , and DNA-based moulds have been used for the assembly of metallized nanosheets and electrical nanowires 56,57 . In chemistry, DNA has been used in directing polymer construction 58 and site-specific chemical reactions 59 36 , objects such as polyhedra 35,144 , periodic 2D lattices 145 , DNA origami 37 and DNA bricks 38 .…”

Low-cost, bottom-up fabrication of large-scale single-molecule nanoarrays by DNA origami placement

“…DNA origami nanotechnology is modular and spatially-programmable [17][18][19][20][21][22] ; an assembled origami unit being capable of carrying up to 200 individually addressable molecules-of-interest [23][24][25][26] . In the last decade, origami nanostructures have been utilized for a myriad of applications ranging from electronic- 27,28 and optical-devices 14,26,29,30 , to single-molecule biophysics [9][10][11]31,32 , biosensing [33][34][35] , and nanofabrication [36][37][38][39][40] . Being synthesized in solution, spatial stochasticity is intrinsically linked with the deposition of planar origami and their payload on glass substrates for optical experiments.…”