Dna chips and microarrays


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Dna chips and microarrays

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Dna chips and microarrays

  1. 1. DNA chips and microarrays Biotechnology (FST 2163) Group no: 02 108018 108019 108078
  2. 2. Content o Introduction o Principle o Types of microarray o Applications o Advantages and disadvantages o Summery o References
  3. 3. Introduction DNA chips and microarrays … o Made with thousands of nucleotide attached to a chip o Contains a particular cDNA sequence known as “probe” o Probes are deposited on a solid support, either positively charged nylon or glass slide o Probes occupy a particular “spot” on the chip
  4. 4. Spots
  5. 5. Principle The core principle behind microarrays is hybridization Samples are labeled using fluorescent dyes At least two samples are hybridized to chip Complementary nucleic acid sequences get pair via hydrogen bonds Washing off of non-specific bonding sequences
  6. 6. Principle cont… Fluorescently labeled target sequences that bind to a probe sequence generate a signal The signal depends on The hybridization conditions, ex: temperature washing after hybridization Total strength of the signal, depends upon the; amount of target sample
  7. 7. Principle cont… Microarrays use relative quantization in which the intensity of a spot is compared to the intensity of the same spot under a different condition Identity of the spot is known by its position
  8. 8. Scanning the arrays Laser scanners Excellent spatial resolution Good sensitivity, but can bleach fluorochromes Still rather slow CCD scanners Low resolution Sensitivity easily adjustable (exposure time) Faster and cheaper than lasers In all cases, raw data are images showing fluorescence on surface of chip
  9. 9. Types of Microarrays The types of DNA microarrays most widely used today can be broadly divided into another two categories cDNA arrays Oligonucleotide arrays.
  10. 10. Produces by Affymetrix An oligonucleotide array The most commonly used type of DNA microarray Each array contain hundreds of thousands of probe spots The Affymetrix Gene Chip
  11. 11. Each of these spots contain millions of copies of an individual 25 base long DNA oligonucleotide
  12. 12. cDNA microarrays Each spot corresponds entirely to a specific gene Measure complementary DNA , as it is more stable than mRNA at large sizes. mRNA from the original sample is reverse transcribed in a laboratory to create an equivalent number of the cDNA
  13. 13. These cDNAs are usually more than 500 bases long
  14. 14. Applications Gene expression analysis Not all the genes in the human genome are active at all times used to detect DNA , or detect RNA that may or may not be translated into proteins. The process of measuring gene expression via cDNA is called expression analysis
  15. 15. Thousand genes are simultaneously assessed Study the effects of certain treatments, diseases, and developmental stages on gene expression. E.g.: identify genes expression changes due to pathogens or other organisms by comparing with uninfected cells or tissues
  16. 16. Help to investigate about different diseases E.g.: Earlier cancers classified on the basis of the organs in which the tumors develop. Now, classify the types of cancer on the basis of the patterns of gene activity in the tumor cells. Help to produce very effective drugs Disease diagnosis
  17. 17. Extensive application in Pharmacogenomics Comparative analysis of the genes Help the identification of the specific proteins produce by diseased cells Information used to synthesize drugs which combat with these proteins and reduce their effect. Drug Discovery
  18. 18. Toxicological Research A rapid platform for the research of the impact of toxins on the cells and their passing on to the progeny. Important for Toxicogenomic studies
  19. 19. Small microarrays to check IDs of organisms in food and feed (like GMO) and mycoplasms in cell culture Mostly combining PCR and microarray technology Gene ID
  20. 20. Nutrigenomic research Study variations in the genes related to the influence of diets. These variations, known as single nucleotide polymorphism
  21. 21. E.g.: Studies are followed to reveal, Effects of calorie restriction on gene expression Obesity and high-fat diets Genes responds to gluten and soy protein
  22. 22. Advantages and disadvantages Advantages Provides data for thousands of genes One experiment instead of many Fast and easy to obtain results Huge step closer to discovering cures for diseases and cancer Different parts of DNA can be used to study gene expresion
  23. 23. Disadvantages Correlations in results do not mean causation Very little knowledge is available about many genes Just because mRNA is "turned on" doesn't mean proteins are made  The findings may lead to unethical medical procedures Scientists have no standardized way to share results
  24. 24. Web links http://www.gene-chips.com/ http://www.bio.davidson.edu/courses/geno mics/chip/chip.html http://www.cs.washington.edu/homes/jbuhl er/research/array