Oligodeoxyribonucleotide probe accessibility on a three-dimensional DNA microarray surface and the effect of hybridization time on the accuracy of expression ratios

BACKGROUND: DNA microarrays are now routinely used to monitor the transcript levels of thousands of genes simultaneously. However, the array fabrication method, hybridization conditions, and oligodeoxyribonucleotide probe length can impact the performance of a DNA microarray platform. RESULTS: We demonstrate solution-phase hybridization behavior of probe:target interactions by showing a strong correlation between the effect of mismatches in probes attached to a three dimensional matrix of a microarray and solution-based, thermodynamic duplex melting studies. The effects of mismatches in the probes attached to the microarray also demonstrate that most, if not all, of the oligodeoxyribonucleotide is available for hybridization. Kinetic parameters were also investigated. As anticipated, hybridization signals increased in a transcript concentration-dependent manner, and mismatch specificity increased with hybridization time. Unexpectedly, hybridization time increased the accuracy of fold changes by relieving the compression observed in expression ratios, and this effect may be more dramatic for larger fold changes. CONCLUSIONS: Taken together, these studies demonstrate that a three-dimensional surface may enable use of shorter oligodeoxyribonucleotide probes and that hybridization time may be critical in improving the accuracy of microarray data

Acetyl Fluoride

International audienc

Dip pen nanolithography stamp tip

A simple and novel method for fabricating poly(dimethylsiloxane) (PDMS)-coated dip pen nanolithography (DPN) stamp tips was developed. These kinds of tips absorb chemicals (“inks”) easily and allow one to generate molecule-based patterns in a conventional DPN experiment. The generated patterns also can be imaged with the same DPN stamp tips. This method is a type of scanning probe contact printing but provides the ability to generate higher resolution structures than one can obtain with the conventional technique, which thus far has only enabled micron scale patterning. Sub-100 nm resolution patterning with 16-mercaptohexadecanoic acid (MHA) as an ink is demonstrated with these novel tips and is comparable to what one can obtain with a conventional ink-coated Si3N4 probe tip. Proof-of-concept is also demonstrated with 1-octadecanethiol (ODT), dendrimers and cystamine as inks

Microstructure array on Si and SiOx generated by micro-contact printing, wet chemical etching and reactive ion etching

A method, combining micro-contact printing (μCP), wet chemical etching and reactive ion etching (RIE), is reported to fabricate microstructures on Si and SiOx. Positive and negative structures were generated based on different stamps used for μCP. The reproducibility of the obtained microstructures shows the methodology reported herein could be useful in Micro-Electro-Mechanical Systems (MEMS), optical and biological sensing applications

Dip pen nanolithography and its potential for nanoelectronics

Dip pen nanolithography (DPN) is a patterning technique for nanoscale science and engineering based on scanning probe microscopy. Its main advantages are very high resolution, the unique capability to deposit many different materials directly onto a substrate and low cost of ownership. We present here new research and development efforts that demonstrate the potential of DPN as a tool to produce nanoelectronic devices and circuits. We show the direct deposition of electronic materials as well as the use of external accessories to accelerate the development phase of nanoelectronic components.Accepted versio