In situ comparison of hybridization properties of nanografted and self-assembled DNA monolayers

Using a conventional AFM and nano-patterned low and high density single stranded DNA SAMs we have investigated the elastic response of surface tethered DNA molecules after various hybridization times and under different loading forces. Upon hybridization, as expected, only for the low density single stranded DNA SAM a transition to the “standing up” phase is seen. We find that high density DNA SAMs are lacking the capability to hybridize not because of density but because of inherent disorder which is reflected by their low DNA SAM height. Nanografting is known to increase both packing density and molecular order. Therefore we have performed patch-in-a-patch experiments to nano-pattern a conventional low density single stranded DNA SAM with 2 subsequent nanografting processes. First a reference area of HS-C6-OH molecules was created into which in a second process single stranded DNA was nanografted. Thereby an accurate in situ comparison under equivalent conditions between conventional DNA SAMs and nanografted DNA patches becomes accessible. Side by side height and compression measurements can provide valuable biophysical insights on the organization of DNA molecules close to a solid interface e.g. discriminating between molecular order and density effects.