Probe array density

Troesch A et al. Mycobacterium species identification and rifampin resistance testing with high-density DNA probe arrays. J Clin Microbiol 1999 37 49-55. 

Mahadevappa, M. and Warrington, J.A., A high-density probe array sample preparation method using 10- to 100-fold fewer cells. Nature Biotechnol., 17, 1134-1136, 1999. 

As the density of information derived from efforts to sequence, map and identify human genes increased, so did the demand for analytical tools capable of exploiting this information. DNA microarrays were developed in response to this demand. Southern(69) was the first to describe parallel, in situ ohgonucleotide synthesis as a means of generating oligonucleotide probe arrays on solid supports for highly parallel hybridization analysis. Southern s method uses standard nucleotide synthetic reactions to synthesize the oligonucleotides. The reactions are carried out in a movable chamber, which provides a physical barrier between the reaction chamber and the intended synthesis area. 

The next step in miniaturization within proteomics is the development of protein nanoarrays. In nanoarrays of proteins, the size is within an mm2 range, spot size (feature) is 3-1000 nm, and the array density (probes/mm2) is <1 x 106/mm2. There are also some initial studies on attovial arrays, in which the miniaturization of the array components is beyond our imagination (e.g., attovial arrays use 6 (0 200nm) to 4000 aL (0 5 pm) sized vials, at a density of 225 vials/mm2 (tentative densities of 90,000-225,000 vials/mm2) (Wolbers et al. 2006b). 

Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C. Transcriptome analysis of Escherichia coh using high-density ohgonucleotide probe arrays. Nucleic Acids Res. 2002 30(17) 3732-3738. 

A new method for the removal of the 5 -0-DMT group during the synthesis of ODNs on a microarray has been studied" which uses all the steps involved in phosphoramidite synthesis, but uses a photogenerated acid (PGA) rather than trichloroacetic acid to deprotect. The photolabile 3 -0- [2-(2-nitrophenyl)propoxy]carbonyl -protected 5 -phosphoramidites (5) have been prepared for the 5 ->3 light-directed synthesis of DNA on microarrays." Developments for the synthesis of high-density DNA probe arrays employ nucleoside monomers protected with 5 -(a-methyl-6-nitropiperonyloxycarbonyl) (MeN-POC) with proximity photolithography, which is currently capable of printing 10 m probe features at a density of 10 probes/cm. "... 

High-Density GeneChip Oligonucleotide Probe Arrays... 

McGall, G.H., Christians, P.C. High-Density GeneChip Oligonucleotide Probe Arrays. Vol. 77,... 

The peculiar maximum near 100 nM in the measured adsorption isotherms remains a puzzle. Although fluorescence quenching appears to be an unlikely explanation, detailed measurements of the fluorescence quantum yield as a function of adsorbed density have not been carried out and are warranted to address this issue. In any case, the anomalous behavior of the isotherms occurs at concentrations far higher than typically employed in biological applications of the probe arrays (1 pM to 10 nM) and is therefore not expected to be relevant to them. 

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