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DNA microarrays<ref>http://learn.genetics.utah.edu/content/labs/microarray/</ref> are used in [[Functional genomics|functional genomics]]&nbsp;to determine the differences in [[Gene expression|gene expression]]&nbsp;levels&nbsp;between a sample and control [[Cell|cell]]&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The sample cell can be: from a different tissue, at a different stage of development, at a different stage of the [[Cell cycle|cell cycle]], or be under different conditions (for example, exposure to a [[Toxin|toxin]])&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. In the DNA microarrays, there are closely packed gene-specific sequences are exist and they are bound to the surface of a glass microscope slide&nbsp;<ref>Lodish H., Berk A., Kaiser C A., Krieger M., Bretscher A., Ploegh H., Amon A., Scott M P. (2013) Molecular Cell Biology, 7th Edition, New York: W.H. Freeman and Company</ref>.&nbsp;The DNA&nbsp;microarray consists of a flat surface to which [[Oligonucleotides|oligonucleotides]] are bound&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>.&nbsp;These oligonucleotides&nbsp;are complementary to specific&nbsp;[[CDNA|cDNA]] sequences&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. Additionally, the oligonucleotides generally around 20 nucleotides lenght and they are synthesised from the previously attached gene-specific sequences to the glass microscope slide&nbsp;<ref name="3" />. &nbsp;The&nbsp;[[MRNA|mRNA]] [[Molecules|molecules]] within the sample and the control are converted into labelled cDNA&nbsp;molecules with the use of [[Reverse transcriptase|reverse transcriptase]]&nbsp;and fluorescently-labelled [[Nucleotide|nucleotides]]<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>.  
DNA microarrays<ref>http://learn.genetics.utah.edu/content/labs/microarray/</ref> are used in [[Functional genomics|functional genomics]]&nbsp;to determine the differences in [[Gene expression|gene expression]]&nbsp;levels&nbsp;between a sample and control [[Cell|cell]]&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The sample cell can be: from a different tissue, at a different stage of development, at a different stage of the [[Cell cycle|cell cycle]], or be under different conditions (for example, exposure to a [[Toxin|toxin]])&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. In the DNA microarrays, there are closely packed gene-specific sequences are exist and they are bound to the surface of a glass microscope slide&nbsp;<ref>Lodish H., Berk A., Kaiser C A., Krieger M., Bretscher A., Ploegh H., Amon A., Scott M P. (2013) Molecular Cell Biology, 7th Edition, New York: W.H. Freeman and Company</ref>.&nbsp;The DNA&nbsp;microarray consists of a flat surface to which [[Oligonucleotides|oligonucleotides]] are bound&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>.&nbsp;These oligonucleotides&nbsp;are complementary to specific&nbsp;[[CDNA|cDNA]] sequences&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. Additionally, the oligonucleotides generally around 20 nucleotides lenght and they are synthesised from the previously attached gene-specific sequences to the glass microscope slide&nbsp;<ref>Lodish H., Berk A., Kaiser C A., Krieger M., Bretscher A., Ploegh H., Amon A., Scott M P. (2013) Molecular Cell Biology, 7th Edition, New York: W.H. Freeman and Company</ref>&nbsp;.&nbsp; The&nbsp;[[MRNA|mRNA]] [[Molecules|molecules]] within the sample and the control are converted into labelled cDNA&nbsp;molecules with the use of [[Reverse transcriptase|reverse transcriptase]]&nbsp;and fluorescently-labelled [[Nucleotide|nucleotides]]<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>.  


For example, the cDNA&nbsp;of the sample can have a red fluorescence label whereas the cDNA&nbsp;of the control can have a green fluorescence label&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The DNA microarray is exposed to the cDNA&nbsp;mixture and unbound cDNA&nbsp;is washed away&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The resultant DNA&nbsp;microarray consists of spots of colour that is imaged using a [[Confocal fluorescence scanner|confocal fluorescence scanner]]&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The colour of the spot is indicative of the differences in [[Gene|gene]] expression&nbsp;between the sample and control&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. Following the colour scheme above, a red spot indicates that the sample is overexpressing that particular [[Gene|gene]]&nbsp;compared to the control; a green spot indicates that the sample is underexpressing that particular gene&nbsp;compared to the control; and a yellow spot indicates that there is equal gene expression&nbsp;in the sample and control&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. However, the range of colours is not as discrete as suggested here, it is more of a spectrum covering intermediate differences in [[Gene expression|gene expression]]<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. [http://www.bio.davidson.edu/courses/genomics/chip/chip.html DNA&nbsp;microarrays] are not so useful in determining gene&nbsp;function but can ascertain which genes may have the same regulatory mechanisms<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>.&nbsp;  
For example, the cDNA&nbsp;of the sample can have a red fluorescence label whereas the cDNA&nbsp;of the control can have a green fluorescence label&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The DNA microarray is exposed to the cDNA&nbsp;mixture and unbound cDNA&nbsp;is washed away&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The resultant DNA&nbsp;microarray consists of spots of colour that is imaged using a [[Confocal fluorescence scanner|confocal fluorescence scanner]]&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. The colour of the spot is indicative of the differences in [[Gene|gene]] expression&nbsp;between the sample and control&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. Following the colour scheme above, a red spot indicates that the sample is overexpressing that particular [[Gene|gene]]&nbsp;compared to the control; a green spot indicates that the sample is underexpressing that particular gene&nbsp;compared to the control; and a yellow spot indicates that there is equal gene expression&nbsp;in the sample and control&nbsp;<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. However, the range of colours is not as discrete as suggested here, it is more of a spectrum covering intermediate differences in [[Gene expression|gene expression]]<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>. [http://www.bio.davidson.edu/courses/genomics/chip/chip.html DNA&nbsp;microarrays] are not so useful in determining gene&nbsp;function but can ascertain which genes may have the same regulatory mechanisms<ref name="Daniel L. Hartl">Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.</ref>.&nbsp;  

Revision as of 20:01, 14 October 2013

DNA microarrays[1] are used in functional genomics to determine the differences in gene expression levels between a sample and control cell [2]. The sample cell can be: from a different tissue, at a different stage of development, at a different stage of the cell cycle, or be under different conditions (for example, exposure to a toxin) [2]. In the DNA microarrays, there are closely packed gene-specific sequences are exist and they are bound to the surface of a glass microscope slide [3]. The DNA microarray consists of a flat surface to which oligonucleotides are bound [2]. These oligonucleotides are complementary to specific cDNA sequences [2]. Additionally, the oligonucleotides generally around 20 nucleotides lenght and they are synthesised from the previously attached gene-specific sequences to the glass microscope slide [4] .  The mRNA molecules within the sample and the control are converted into labelled cDNA molecules with the use of reverse transcriptase and fluorescently-labelled nucleotides[2].

For example, the cDNA of the sample can have a red fluorescence label whereas the cDNA of the control can have a green fluorescence label [2]. The DNA microarray is exposed to the cDNA mixture and unbound cDNA is washed away [2]. The resultant DNA microarray consists of spots of colour that is imaged using a confocal fluorescence scanner [2]. The colour of the spot is indicative of the differences in gene expression between the sample and control [2]. Following the colour scheme above, a red spot indicates that the sample is overexpressing that particular gene compared to the control; a green spot indicates that the sample is underexpressing that particular gene compared to the control; and a yellow spot indicates that there is equal gene expression in the sample and control [2]. However, the range of colours is not as discrete as suggested here, it is more of a spectrum covering intermediate differences in gene expression[2]. DNA microarrays are not so useful in determining gene function but can ascertain which genes may have the same regulatory mechanisms[2]. 

References

  1. ↑ http://learn.genetics.utah.edu/content/labs/microarray/
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 Daniel L. Hartl, Elizabeth W. Jones (2009) Genetics Analysis of Genes and Genomes 7th Edition USA, Jones and Bartlett Publishers.
  3. ↑ Lodish H., Berk A., Kaiser C A., Krieger M., Bretscher A., Ploegh H., Amon A., Scott M P. (2013) Molecular Cell Biology, 7th Edition, New York: W.H. Freeman and Company
  4. ↑ Lodish H., Berk A., Kaiser C A., Krieger M., Bretscher A., Ploegh H., Amon A., Scott M P. (2013) Molecular Cell Biology, 7th Edition, New York: W.H. Freeman and Company

 

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