DNA microarrays

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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]]<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]])<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<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<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<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<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>.  
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DNA microarrays<ref>http://learn.genetics.utah.edu/content/labs/microarray/</ref>. are used in [[Functional genomics|functional genomics]] to determine the differences in [[Gene expression|gene expression]] levels between a sample and control [[Cell|cell]]<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]])<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<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>. The DNA microarray consists of a flat surface to which [[Oligonucleotides|oligonucleotides]] are bound<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>. These oligonucleotides are complementary to specific [[CDNA|cDNA]] sequences<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<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>. . The [[MRNA|mRNA]] [[Molecules|molecules]] within the sample and the control are converted into labelled cDNA molecules with the use of [[Reverse transcriptase|reverse transcriptase]] 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<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<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]]<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<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<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;<br>
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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<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 mixture and unbound cDNA is washed away<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 microarray consists of spots of colour that is imaged using a [[Confocal fluorescence scanner|confocal fluorescence scanner]]<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 between the sample and control<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]] 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<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 microarrays] are not so useful in determining gene 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>.  
  
 
=== An Application of Microarray Experiment  ===
 
=== An Application of Microarray Experiment  ===
  
An experiment by Lagogue ''et al''. in 2006 showed that resveratrol (an anti-aging component, contained in the skin of red grapes) is able to shift the high-calorie driven pathway in the mice<ref>Lagouge et al (2006) "Resveratrol improves mitochondrial function and protects against metabolic disease by activating Sirt1 and PGC-1alpha". Cell 127: 1109-1122</ref>.  
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An experiment by Lagogue ''et al''. in 2006 showed that resveratrol (an anti-ageing component, contained in the skin of red grapes) is able to shift the high-calorie driven pathway in the mice<ref>Lagouge et al (2006) "Resveratrol improves mitochondrial function and protects against metabolic disease by activating Sirt1 and PGC-1alpha". Cell 127: 1109-1122</ref>.  
  
The [[MRNA|mRNA]] sample from mice with high calorie diet and from mice with high resveratrol diet were taken. Both were then tested by DNA Microarray to monitor and to compare the level of [[Gene expression|gene expressions]]. After analysing using DNA Microarray, it was found that resveratrol was able to reverse the effect of high calorie diet on 144 out of 153 significantly altered pathways in mice.  
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The [[MRNA|mRNA]] sample from mice with high-calorie diet and from mice with high resveratrol diet were taken. Both were then tested by DNA Microarray to monitor and to compare the level of [[Gene expression|gene expressions]]. After analysing using DNA Microarray, it was found that resveratrol was able to reverse the effect of high-calorie diet on 144 out of 153 significantly altered pathways in mice.  
  
 
The DNA Microarray technology enables the researchers to monitor the level of gene expressions quickly and more efficiently.  
 
The DNA Microarray technology enables the researchers to monitor the level of gene expressions quickly and more efficiently.  
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=== References  ===
 
=== References  ===
  
<references />&nbsp;
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<references />

Latest revision as of 16:30, 7 December 2018

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].

An Application of Microarray Experiment

An experiment by Lagogue et al. in 2006 showed that resveratrol (an anti-ageing component, contained in the skin of red grapes) is able to shift the high-calorie driven pathway in the mice[5].

The mRNA sample from mice with high-calorie diet and from mice with high resveratrol diet were taken. Both were then tested by DNA Microarray to monitor and to compare the level of gene expressions. After analysing using DNA Microarray, it was found that resveratrol was able to reverse the effect of high-calorie diet on 144 out of 153 significantly altered pathways in mice.

The DNA Microarray technology enables the researchers to monitor the level of gene expressions quickly and more efficiently.

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
  5. Lagouge et al (2006) "Resveratrol improves mitochondrial function and protects against metabolic disease by activating Sirt1 and PGC-1alpha". Cell 127: 1109-1122
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