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| The basic unit of CombiMatrix chip is microelectrodes arranged
on the silicon wafer. The advantage of the semiconductor chip is that it can be used to direct oligonucleotide synthesis and to detect
signals from the hybridized microelectrodes using ElectraSense™ detector. |
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 Chemistry of in-situ oligonucleotide synthesis on microelectodes. |
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The CombiMatrix chips are produced in a form that the protected
thymines are attached on the surface of each electrode. |
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By computer-controlled electronics, selected electrodes are turned on to form effective acidic
local environment around the corresponding electrodes. The protection groups on thymines are cleaved off in the acidic environment. |
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Microfluidic device supplies amidite solutions which couples to the deprotected nucleotide to
form phosphodiester bond. |
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The chip surface is washed to remove any free amidite on the solution. |
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The repetition of selected deprotection-couple-wash step results in the synthesis of
oligonucleotides with custom-designed sequence. |
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Two platform shares the in-situ nature of the oligonucleotide synthesis, but they are differ in the principle of deprotecting the protecting group of amidites. In constrast to CombiMatrix where the electric signal controls the deprotection chemistry, Affymetrix chip uses photolithographic principle where the photomasks are used to selectively illuminate the position where the next coupling should be performed.
The synthesis of Affymetrix chip needs set of photomasks designed and synthesized before the actual synthesis of the chip. Thus, the change of custom design is more time- and resource-consuming compared to CombiMatrix chip where the only thing you need to do is to change the sequence file for the synthesis software. Moreover, the state-of-art microfulics design and electronic controls enables the exact synthesis chemistry that CombiMartrix offers precise synthesis of oligonucleotide up to 50-mer, compared to 25-mer of Affymetrix.
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The stripping of CombiMatrix chip is based on chemical denaturation of DNA:DNA and DNA:RNA hybrids.
The stripping enables for users to perform hybridization up to 3 times.
Probes that are longer than 40mer may not be stripped completely.
Optimized for DNA and RNA targets labeled with biotin, and with cy5
Microarrays must be kept wet for re-usage.
The figures 1-3 illustrate the efficiency of stripping. |
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