ChIP sequencing

Different variations of ChIP experiments are now rapidly evolving. This is mainly due to the rapid progress in the field of microarrays and next-generation sequencing that can be used for the analysis of the immunopreciptated DNA. We discuss here the most important variations of the standard ChIP protocol with a focus on ChIP-on-chip and ChIP-sequencing technologies. 

Metallization. Integrated circuits require conductive layers to form electrical connections between contacts on a device, between devices on a chip, between metal layers on a chip, and between chips and higher levels of interconnections needed for packaging the chips. It is critical to the success of IC fabrication that the metallization be stable throughout the process sequence in order to maintain the correct physical and electrical properties of the circuit. It must also be possible to pattern the blanket deposition. 

SoLidiern, E. M., 1996. DNA chips Analysing sequence by hybridization to oligoiiLicleoddes on a large scale. Trends in Genetics 12 110-115. 

DNA microarrays, or DNA chips consist of thousands of individual DNA sequences arrayed at a high density on a single matrix, usually glass slides or quartz wafers, but sometimes on nylon substrates. Probes with known identity are used to determine complementary binding, thus allowing the analysis of gene expression, DNA sequence variation or protein levels in a highly parallel format. 

A developing application of DNA technology uses a DNA chip that contains many small segments of bases of known sequence. Such DNA chips are being used to attack cancers. Cancers occur when defective genes cause cells to divide uncontrollably, but usually the process of protein synthesis also is modified. Different types of cancer result in different modifications to protein synthesis, depending on how the DNA... 

As the schematic illustration shows, a segment containing a particular base sequence molecule will bind to an area of the chip that contains its complementary sequence, but it will not bind to any area that has a mismatched sequence. 

When the chip is rinsed, fluorescent DNA remains bound to all those areas of the chip that have complementaiy sequences. Areas of the chip whose sequences are not complementary do not bind to the DNA. When the chip is rinsed and subsequently exposed to ultraviolet light, the areas with bound DNA fluoresce, generating light from each area to which the DNA has bound, hi contrast, areas of the chip that contain noncomplementary sequences remain dark. The fluorescence pattern reveals which protein synthesis processes have been modified in the cancerous cell, and this in turn helps physicians determine what treatment is most likely to be effective against the cancer. 

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