The degree of molecular order or morphology of probe molecules has an imperative role in the performance of DNA nano-arrays of unprecedented sensitivity, and needs to be carefully addressed. Towards this, we use “Nanografting” to fabricate well-packed ss-DNA nanopatches within a “carpet matrix” self-assembled monolayers (SAM) of inert thiols on gold surfaces. The DNA surface density is varied by changing the “writing” parameters, for example, tip speed, and number of scan lines. Since ss-DNA is 50 times more flexible than ds-DNA, hybridization leads to a transition to a “standing up” phase. Therefore, accurate height and compressibility measurements of the nanopatches before and after hybridization allow reliable, sensitive, and label-free detection of hybridization.
DNA Nanopatches and S/A:
We have systematically studied the increased height, by using the height of the OEG SAM as a reference (i.e. about 1.5nm from the gold surface), of the ss-DNA nanopatches by varying the number of scanning lines during the nanografting process. i.e., by grafting over the same area more than once, we find increasing heights for ss-DNA-nanopatches written at higher line overlap. We also introduce a line density parameter “S/A” where S is the scanned area and A is the actual area of the final patch. S/A = R·N/L in which R is the width of the tip at the point of contact with the surface, and N/L is the number of scan lines (in the slow scan direction) divided by the length of the patch L (in the same direction). This means that for S/A=1 the nanografted lines do not overlap with each other, while for S/A=3 each spot in the nanopatch has been nanografted 3 times over.
Compressibility of DNA Nanopatches:
We also investigate the height response versus applied load of AFM tip that can provide useful information on the mechanical behavior of the system. The height-to-load response of 3 Nanografted Assembled Monolayers (NAMs) made respectively with ss-DNA, ds-DNA and ds-DNA produced by in-situ full hybridization of ss-DNA-nanopatches, is investigated at S/A = 50. The results reveal three important findings: 1) the elastic response of DNA-nanopatches before (in blue) and after hybridization (in pink) differs sufficiently to allow for easy identification. 2) ds-DNA is almost incompressible with forces below 16 nN which is consistent with the fact that the persistence length of ds-DNA is 50 times larger that that of ss-DNA 3) the stiff mechanical response of the in-situ hybridized DNA nanostructure (in pink) is almost identical to that of the nanografted ds-DNA-nanopatch (in black).
Comparison with Theoretical Studies:
Theoretical studies are also important to better understand the fundamental biophysical aspects of our system (NAMs). We are currently working on this subject in a close collaboration with Prof. C. Micheletti and Alessandro Bosco (PhD student).
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1. Mirmomtaz, E., Castronovo, M., Grunwald, C., Bano, F., Scaini, D., Ensafi, A. A., Scoles, G., Casalis, L. Nano Lett. 2008, 8, 4134.