Coverage Dependence of DNA Hybridization in Nanostructured Monolayers: a Nanografting AFM Study

author: Loredana Casalis, ELETTRA - Sincrotrone Trieste
published: Feb. 12, 2008,   recorded: October 2007,   views: 4334


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One of the main challenges in the development of new analytical methods for life sciences is to dramatically reduce the minimum amount of DNA and RNA that can be directly and precisely characterized. Micro-arrays can not operate in this limit, and generally need the use of enzymatic amplification processes, that introduce statistical uncertainties, crucially affecting the performance of the device. Towards this end, new techniques at the nano-scale for amplification-free and label-free detection of DNA hybridization need to be explored. We use nanografting (an atomic force microscopy (AFM) based nanolithography technique) to fabricate nanopatches of self-assembled monolayers of single stranded DNA (ss-DNA) within a "matrix" of other thiols on gold surfaces. By opportunely varying the nanografting parameters, we establish a relative scale for the surface coverage of the ss-DNA spots. We find that the height of the patches grows with growing coverage reaching a "saturation" regime at very high ss-DNA coverage, and that the height of each patch increases upon hybridization. Not surprisingly, maximum sensitivity for hybridization has been obtained before the height of the grafted patch reaches saturation, and therefore high packing densities. Surprisingly, however, in the height/packing saturation regime the compressibility of hybridized ss-DNA grafted patches is much smaller than the one of ss-DNA patches, but the same as that of ds-DNA patches grafted as such. We conclude that, in contrast with several statements present in the current literature, in our nanopatches DNA has little trouble in hybridizing even at high surface densities. The level of molecular order in the nanopatches, with respect to that in spontaneously assembled ss-DNA monolayers, is responsible for the different hybridization efficiencies. Our findings provide new insights on the recombination of short DNA fragments on surfaces, with important consequences for the field of solid surface supported DNA hybridization detection.

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