Direct microcontact printing of oligonucleotides for biochip applications

Abstract

BackgroundA critical step in the fabrication of biochips is the controlled placement of probes molecules on solid surfaces. This is currently performed by sequential deposition of probes on a target surface with split or solid pins. In this article, we present a cost-effective procedure namely microcontact printing using stamps, for a parallel deposition of probes applicable for manufacturing biochips.ResultsContrary to a previous work, we showed that the stamps tailored with an elastomeric poly(dimethylsiloxane) material did not require any surface modification to be able to adsorb oligonucleotides or PCR products. The adsorbed DNA molecules are subsequently printed efficiently on a target surface with high sub-micron resolution. Secondly, we showed that successive stamping is characterized by an exponential decay of the amount of transferred DNA molecules to the surface up the 4th print, then followed by a second regime of transfer that was dependent on the contact time and which resulted in reduced quality of the features. Thus, while consecutive stamping was possible, this procedure turned out to be less reproducible and more time consuming than simply re-inking the stamps between each print. Thirdly, we showed that the hybridization signals on arrays made by microcontact printing were 5 to 10-times higher than those made by conventional spotting methods. Finally, we demonstrated the validity of this microcontact printing method in manufacturing oligonucleotides arrays for mutations recognition in a yeast gene.ConclusionThe microcontact printing can be considered as a new potential technology platform to pattern DNA microarrays that may have significant advantages over the conventional spotting technologies as it is easy to implement, it uses low cost material to make the stamp, and the arrays made by this technology are 10-times more sensitive in term of hybridization signals than those manufactured by conventional spotting technology.

Increasing the sensitivity of DNA microarrays by metal-enhanced fluorescence using surface-bound silver nanoparticles

“…Also, the nanoparticles may cause the solvent to be pinned at multiple points within the print area, not just at the perimeter. For comparison, DNA arrays made by direct microcontact printing, a ‘dry’ method that does not involve droplet evaporation, yield uniform spots (35). Additionally, ring formation is not observed with oligonucleotide arrays fabricated by in situ synthesis (e.g.…”

Interaction of biomolecules sequentially deposited at the same location using a microcantilever-based spotter

“…Whatever the technique, the size of the spots produced by these types of commercial devices ranges between 50 and 500 μm in diameter, depending on the type and the surface chemistry of the substrate (nylon membranes, glass slides, silicon, etc.). An alternative method for the parallel deposition of molecules on functionalized surface is the microcontact printing (μCP), which uses polydimethylsiloxane (PDMS) stamps exhibiting micrometer to nanometer size engraved patterns over large areas (Renault et al 2003;Thibault et al 2005). For higher size reduction, dip-pen lithography or nanodispensing techniques (NADIS) are today the most suitable techniques to reach nanometer scale dimensions.…”

Automated and Multiplexed Soft Lithography for the Production of Low-Density DNA Microarrays

“…All of these processes require the chemical functionalization of the reticulated PDMS stamp surface and are not straightforward. Thibault et al [27] showed that, contrary to expectation, unmodified reticulated PDMS stamp surface can retain nucleic acids which can then be transferred onto the substrate surface, enabling a facile route for the production of DNA microarrays. To account for this patterning process using unmodified reticulated PDMS surfaces, these authors showed that DNA transferred onto the target surface originated from nucleic acids retained by low molecular weight (LMW) siloxane fragments present within and at the surface of the cured PDMS stamp [28].…”