Nanoscale Positioning of Individual DNA Molecules by an Atomic Force Microscope

Abstract

Here we report a method to assemble nanoscale DNA structures with single-molecule precision. This assembly is accomplished by performing nanografting in the presence of short, thiolated DNA strands that have been diluted by a positively charged alkanethiol. The expected number of DNA molecules per patch can be modulated by the application of an electric potential to the surface during patterning. Our ability to position individual DNA within a controlled nanoscale environment and observe these molecules in situ will allow us to understand and potentially decouple the heterogeneity caused by the local environment from the intrinsic properties in single-molecule biophysical measurements. Additionally, our approach can potentially be extended to the molecule-by-molecule assembly of larger artificial test structures of nucleic acids or proteins.

Molecular dynamics simulations of nanoscale engravings on an alkanethiol monolayer

“…The structural parameters of the hole were calculated by averaging over 500 snapshots taken from 60 to 70 ns. The average tilt angle, q, was 24 , agreeing with the typical experimental values of the bulk monolayers (20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30). 50 The percentage of trans conformations was 97% on average.…”

“…The ultimate size limit and spatial resolution of a nanoscale engraving on a thiol monolayer are unknown, even though these monolayers are used widely in many applications. 5,28,29 Various patterns engraved on the monolayers of alkanethiol are utilized as resists for pattern transfers, 1,2 the templates for biomolecules, [3][4][5][6] and the circuit components in molecular electronic devices. 10,11 Given the feature sizes of these negative patterns become smaller and smaller, a fundamental design principle for fabricating such patterns is desired.…”

From the bottom up: dimensional control and characterization in molecular monolayers

“…301,304–307 Nanografting has been used to regulate and to study reaction mechanisms, 308 and to fabricate multicomponent nanostructures for molecular electronic and biological applications. 274,301,309–311 …”

Liquid‐Mediated Three‐Dimensional Scanning Probe Nanosculpting

“…The present reported LSPN process has a similar liquid cell setup with nanoshaving/nanografting developed by Liu et al39 Nanoshaving/nanografting has been widely used in the construction/disruption of highly‐defined nanopatterns of self‐assembled monolayers (SAMs) of small molecules, such as thiols, lipids, and proteins, which sever as promising templates for the studies of molecular assembly/interactions, and nanoscale confined biological reactions 40–48. In contrast, the LSPN can be considered as a variant of the nanoshaving/nanografting technique in a way that it is especially developed for polymer brushes to form 2D/3D‐patterned functional polymer brush surfaces.…”