9. You use reverse transcriptase and PCR to amplify the mRNA of a tumor cell and

Question

9. You use reverse transcriptase and PCR to amplify the mRNA of a tumor cell and its normal counterpart. You label the tumor cDNAs with rhodamine, which glows red, and the normal cDNAs with fluoresceine, which glows green. Match the result with the appropriate interpretation of which gene is in the spot.

I. spot glows red

II. spot glows green

III. spot glows yellow

IV. spot doesn’t glow

I

II

III IV

a

normal only

tumor only

both sources

neither source

b

tumor only

normal only

both sources

neither source

c

tumor only

normal only

neither source

both sources

d

tumor only

neither source

normal only

both sources

e

neither source

both sources

tumor only

normal only

IV. spot doesn’t glow

I

II

III IV

a

normal only

tumor only

both sources

neither source

b

tumor only

normal only

both sources

neither source

c

tumor only

normal only

neither source

both sources

d

tumor only

neither source

normal only

both sources

e

neither source

both sources

tumor only

normal only

Explanation / Answer

Option B satisfies for the given condition.

I) Red spot: tumour cDNA

II) Green Spot: normal cDNA

III) Yellow: both the sources

IV) Black: neither of the sources

The given experiment can be analysed using DNA Microarray Technology. Normal cells cDNA are labelled with green dye and cancerous cDNAs are labelled with red dye in this experiment. These cDNA labelled solutions are put on the DNA chip and cDNA hybridises to the cDNA present in the microarray. There is few strands which do not hybridise. Hence four pattern of spots are produced on the DNA chip after carrying out hybridisation and washing of the chip. Finally the chip is scanned on the microarray scanner to recognize the gene expression pattern.

Turning on the green scan of the microarray scanner will show the expression of normal cells in the microarray. We will see that all the spots in the chip will not be green. Hence, all the genes are not expressed in normal or healthy cells. Those genes that are not expressed produce no colour or stay blank or black.

When red scanner is turned on, many spots will show red colour on the chip. But certainly the red pattern will look different. So it will depict that healthy or normal cells have different pattern of gene expression than the cancerous cells.

To analyze the data, red image is merged with the green image which will result in production of three kinds of spots on the chip: the red, green and yellow spots. Yellow coloured spot has a gene which is present in both the healthy and cancer cells as the gene in the spot hybridizes to both the green and red cDNA. Many spots will show yellow colour when red and green scans are merged. Rest many spots will still show green and red colour, they are of importance in respect of gene expression. Whereas, yellow spots are of little interest, as these are genes which get turned on in both the healthy cells as well as the cancerous state.

Red spot will show genes turned up in cancer or the gene is not functioning properly. There is also case that there are so many red spots and has the gene gone bad in all these spots? No, they are red as they are controlled by gene that has gone bad. Hence, gene that has turned bad will have red colour but green colour will be there in the spots which are turned down by this aberrant gene.

Green spots will depict the genes expression of which is turned down in the cancerous state.

Yellow colour normally indicates the genes that are turned on in both healthy and cancerous state. But, if a gene has gone bad and still produces mRNA, this defect will prevent the translation of this mRNA into protein and this will also generate yellow colour on the chip. This can be regarded as one the drawbacks of this technology.

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