Atomic force microscopy reveals two phases in single stranded DNA self-assembled monolayers

Abstract

We have investigated the structure of single-stranded (ss) DNA self-assembled monolayers (SAMs) on gold by combining peak force tapping, Kelvin probe and phase contrast atomic force microscopy (AFM) techniques. The adhesion, surface potential and phase shift signals show heterogeneities in the DNA film structure at two levels: microscale and nanoscale; which cannot be clearly discerned in the topography. Firstly, there is multilayer aggregation covering less than 5% of the surface. The DNA multilayers seem to be ordered phases and their existence suggests that DNA end-to-end interaction can play a role in the self-assembly process. Secondly, we find the formation of two phases in the DNA monolayer, which differ both in surface energy and surface potential. We relate the two domains to differences in the packing density and in the ssDNA conformation. The discovered heterogeneities in ssDNA SAMs provide a new scenario in our vision of these relevant films that have direct consequences on their biological, chemical and physical properties.

Functionalised microscale nanoband edge electrode (MNEE) arrays: the systematic quantitative study of hydrogels grown on nanoelectrode biosensor arrays for enhanced sensing in biological media

“…It is interesting that is also a signicant increase in R ct , since it has been established that this charge transfer response is largely determined by redox reaction through pinhole defects in the SAM layer formed on multicrystalline electrode surfaces. [26][27][28] This suggests that the local enhanced pH change and hydrogel growth increases the observed charge transfer resistance through constricting the size, and/or blocking at least some, of these pinholes as a result of the creation of hydrogel anchor points to the underlying electrode, which is consistent with the previously observed adherence of the hydrogel. The nal sensing step again resulted in the expected signicant increase in R ct (without a change in R nl ), due to the formation of the more blocking PNA-DNA duplex SAM lm at the electrode surface.…”

Hydration Induced Stress on DNA Monolayers Grafted on Microcantilevers

“…17,18 The final strand density in self-assembled monolayers plays a critical role in nanomechanical sensing 9 and it is indeed far from being fully controllable. 19,[20][21][22][23] One singularly limiting difficulty has been to accomplish the anchoring of the ssDNA probes with a well-defined uniform density and a standing up conformation. 19,24 For such purpose, sophisticated nanografting methods need to be applied.…”

“…19,[20][21][22][23] One singularly limiting difficulty has been to accomplish the anchoring of the ssDNA probes with a well-defined uniform density and a standing up conformation. 19,24 For such purpose, sophisticated nanografting methods need to be applied. 25,26 Alternatively, the gold layer needs to comply with very restrictive conditions regarding surface roughness 13 and surface electrostatics, 16 while long incubation times are also applied, 24 which bans the use of technologies for high multiplexing, such as ink-jet low volume dispensing.…”

Crowding-induced Cooperativity in DNA Surface Hybridization

“…Moreover, surface heterogeneity can widen the melting curve, enhancing the negative cooperativity12. On the other side, aggregation on the surface was reported during the preparation of both dsDNA and ssDNA monolayers, giving dense and spare domains424344. This implies the existence of favourable interactions between same kind of DNA, which would promote positive cooperativity and phase separation.…”