Label-less probes for microarrays - Nano-scaled Polystyrene films
Blog Post for Second BIOC6006 Presentation
Microarray Analysis using disiloxyl 70mer oligonucleotides
Microarrays are one of the most powerful tools in modern biology. A single chip, containing thousands of probes can provide data on the regulation of thousands of genes. A microarray works via the principle of hybridization.
Each microarray chip contains hundreds to thousands of tiny holes. In each hole (or spot) is a cDNA (or sometimes cRNA) sequence from a particular gene. The cDNA is can be taken from a wild type organism living in normal conditions, as a background in a comparison-type experiment, or it can be synthesized. This background or synthesized cDNA (or cRNA) is labelled (usually with a fluorescent, red probe) and placed into the wells. cDNA or cRNA is obtained (by Reverse Transcription) from the organism when it has been exposed to the conditions we are testing. These probes are labelled with a different kind of probe (usually a fluorescent green probe). The cDNA (cRNA) taken from the test organism is mixed with the spots containing the background cDNA or synthetic probes. They are placed in conditions in which the test organisms’ cDNA will hybridize with the probes already in the well. All non-specific stuff will wash off.
After this is done, each well will have an amount of background or neutral cDNA (cRNA) and an amount of cDNA (cRNA) from the organism that was tested. If the gene was more upregulated in the neutral/background organism, then the spot will glow red. If the gene was more upregulated in the test organisms, then the spot will glow green. If the gene is regulated in a similar manner in both, then it will glow yellow.
In this paper “Label-less fluorescence based method to detect hybridization with applications to DNA micro array”, by Sanjun Niu, Gaurav Singh and Ravi. F. Saraf, examines (as the title will tell you), examines how it is possible to make DNA probes fluorescence without having to add fluorescent labels, which takes time, and money and could interfere with the functioning of the probe.
By analysing how immobilized ssDNA probes scatter light, the group were able to create a fluorescent polystyrene film , whose thickness is determined at the nano-meter scale, that the probes will be immobilized to. Binding of DNA to the probes will create dsDNA and change the scattering of light, creating a fluorescence contrast which is extremely sensitive. The team calculates that it will increase the detection of binding by an entire order.
By Mark Phillipps
40995867
Microarray Analysis using disiloxyl 70mer oligonucleotides
Microarrays are one of the most powerful tools in modern biology. A single chip, containing thousands of probes can provide data on the regulation of thousands of genes. A microarray works via the principle of hybridization.
Each microarray chip contains hundreds to thousands of tiny holes. In each hole (or spot) is a cDNA (or sometimes cRNA) sequence from a particular gene. The cDNA is can be taken from a wild type organism living in normal conditions, as a background in a comparison-type experiment, or it can be synthesized. This background or synthesized cDNA (or cRNA) is labelled (usually with a fluorescent, red probe) and placed into the wells. cDNA or cRNA is obtained (by Reverse Transcription) from the organism when it has been exposed to the conditions we are testing. These probes are labelled with a different kind of probe (usually a fluorescent green probe). The cDNA (cRNA) taken from the test organism is mixed with the spots containing the background cDNA or synthetic probes. They are placed in conditions in which the test organisms’ cDNA will hybridize with the probes already in the well. All non-specific stuff will wash off.
After this is done, each well will have an amount of background or neutral cDNA (cRNA) and an amount of cDNA (cRNA) from the organism that was tested. If the gene was more upregulated in the neutral/background organism, then the spot will glow red. If the gene was more upregulated in the test organisms, then the spot will glow green. If the gene is regulated in a similar manner in both, then it will glow yellow.
In this paper “Label-less fluorescence based method to detect hybridization with applications to DNA micro array”, by Sanjun Niu, Gaurav Singh and Ravi. F. Saraf, examines (as the title will tell you), examines how it is possible to make DNA probes fluorescence without having to add fluorescent labels, which takes time, and money and could interfere with the functioning of the probe.
By analysing how immobilized ssDNA probes scatter light, the group were able to create a fluorescent polystyrene film , whose thickness is determined at the nano-meter scale, that the probes will be immobilized to. Binding of DNA to the probes will create dsDNA and change the scattering of light, creating a fluorescence contrast which is extremely sensitive. The team calculates that it will increase the detection of binding by an entire order.
By Mark Phillipps
40995867
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