[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"$fxLN3MUwXCdr5RPjwZYIDpOj8CHyjOmngWTgoKXPtZbg":3,"$f1s7Kmkc3E0gnuFTOITCLkYf4xiZqY_g_0OwmSNrEp24":32,"$f3Ft0rKFJHppdzE-vuveecxx1BUcg9iOlMLtyzf_MJDg":47},[4,8,12,16,20,24,28],{"title":5,"slug":6,"path":7},"About Microbeonline.com","about-microbeonline-com","\u002Fabout-microbeonline-com\u002F",{"title":9,"slug":10,"path":11},"About Me","about-me","\u002Fabout-microbeonline-com\u002Fabout-me\u002F",{"title":13,"slug":14,"path":15},"Advertise with Us","advertise-us","\u002Fadvertise-us\u002F",{"title":17,"slug":18,"path":19},"Privacy Policy","privacy-policy","\u002Fprivacy-policy\u002F",{"title":21,"slug":22,"path":23},"Abbreviations","abbreviations","\u002Fabbreviations\u002F",{"title":25,"slug":26,"path":27},"Microbes","microbes","\u002Fmicrobes\u002F",{"title":29,"slug":30,"path":31},"Books","recommended-books","\u002Frecommended-books\u002F",{"type":33,"data":34},"blog",{"slug":35,"title":36,"description":36,"seoTitle":37,"seoDescription":37,"author":38,"createdDate":39,"lastUpdatedDate":40,"draft":41,"category":42,"image":37,"body":43,"faq":44,"tags":45,"related":46},"microarray-scanner-principle-and-parts","Microarray Scanner: Principle and Parts",null,"Ashma Shrestha","2022-06-30","2025-12-29",false,"lab-equipment","A microarray is an instrument that helps to detect the expression of thousands of genes at the same time. The microarray is called gene chips or DNA (deoxyribonucleic acid) chips because the slide consists of tiny spots for embedding DNA like the microchip. The DNA molecules in each slide act as a probe for detecting gene expression. The probe DNA molecule is also called the transcriptome.\n\n> Probe DNA are single stranded DNA that helps to detect target complementary DNA by hybridization.\n\nMicroarray scanners are laboratory equipment that helps to measure the fluorescent areas of DNA microarray, revealing information about the activity of thousands of genes. It helps to determine the quality of gene expression or overexpression of genes during particular disease.\n\n![ - DNA Chip and microarray scannerImagecredit:https:\u002F\u002Fwww.news-medical.net\u002Flife-sciences\u002FDNA-microarray.aspx.](https:\u002F\u002Fassets.microbeonline.com\u002Fblogs\u002FMicroarray-scanner.png)\n\u003Cfigcaption>Figure: DNA Chip and microarray scannerImagecredit:https:\u002F\u002Fwww.news-medical.net\u002Flife-sciences\u002FDNA-microarray.aspx.\u003C\u002Ffigcaption>\n\n## Procedure of Microarray\n\nThe **basic principle** of **DNA microarray** is “**nucleic acid hybridization**.” Nucleic acid hybridization means joining two complementary DNA by hydrogen bonds to form a double-stranded molecule. The procedure of microarray has the following steps:\n\n### Preparation of DNA chip\n\nThere are many ways to prepare a microarray chip. The DNA chip was designed using photolithographic methods in the early days. Nowadays, photoactivated chemistry and masking help obtain DNA probes which are also available for purchase commercially. Also another commercially available way is an already designed probe attached to a fine needle printed on a chemical matrix surface by a robot.\n\n### Nucleic acid hybridization\n\nFor hybridizing the nucleic acid, the following steps are performed:\n\n- **Sample collection:** Two samples of healthy as well as infected tissue for comparison are preferred.\n- **Isolating RNA (ribonucleic acid):** Isolate mRNA from the collected sample using the column or solvent method.\n- **Labeled cDNA preparation:** Prepare labeled cDNA (complementary DNA) from the isolated RNAs. Labeling is done by using fluorescent dyes like Cy3 and Cy5.\n- **Hybridization:** Now, place the prepared, labeled cDNAs into the DNA chips\u002Fmicroarray trays with the required probe for hybridization.\n\n### Analysis of DNA chip\n\nA microarray scanner helps collect the data of thus hybridized chip\u002Fmicroarray tray after the tray is rinsed thoroughly to remove the unbound\u002Funhybridized DNAs. The intensity of the color is measured, and the difference helps analyze the genes.\n\n## Principle of Microarray Scanner\n\nThe lasers of the microarray scanner excite the fluorescent-labeled genes in the microarray tray. Likewise, the camera and microscope help form the image of excited genes. Then a program helps calculate the red to green ratio or subtract background data for each spot in the microarray using the digitalized image of the hybridized gene.\n\n## Parts of Microarray Scanner\n\nThe parts of a microarray scanner are broadly classified into two parts:\n\n- **Scanner:** It consists of the laser for exciting the labeled hybridized DNA and a photomultiplier tube for reading each chip spot one by one.\n- **Imager:** It consists of a laser for exciting the DNA, a camera and a microscope for capturing the image of the gene.  \n- **Analyzer:** It is a software program that helps analyze the data generated after scanning by comparing the color contrast.\n\n## Benefits of Microarray\n\n### Analysis of multiple samples\n\nSince a single chip consists of thousands of spots for DNA hybridization, a single chip can analyze multiple samples simultaneously. It is also beneficial in separating the non-cancerous cells from the cancerous cells.\n\n### Uniformity\n\nThe microarray technique helps produce consistent data, which increases the speed of analysis in comparison to other nucleic acid hybridization techniques.\n\n### Microscale analysis\n\nCompared to conventional assays, the area or scale used in the microarray is minimal, reducing reagents, minimizing research volumes, and increasing the speed of reaction and sample concentrations.\n\n## Limitation of Microarray\n\n### Qualitative result\n\nThe result generated by microarray is usually qualitative; that is, quantifying the data obtained is impossible.\n\n### Non-reproducible results\n\nEven though the used probe is the same, sometimes the result can differ from the original one. Similarly, posttranscriptional monitoring can affect the translation.\n\n### Not applicable for proteins and lipids\n\nMost gene expression techniques have been modified to accommodate the detection of end products like proteins and lipids. Still, microarray only deals with the detection of targeted genes\u002FDNA.\n\n## How to Choose a Microarray Scanner\n\nThe answer to choosing a microarray scanner fit for your laboratory is checking all the following requirements:\n\n- **Sensitivity:** The microarray scanner’s sensitivity must be high to avoid any DNA analysis errors.\n- **Resolution:** The microarray scanner must have a camera with good resolution to magnify the microscopic image.\n- **Scan area:** The scan area of microarray depends on the number of spots usually analyzed in your laboratory. Possibly a slightly larger area than the spots generally analyzed because the number of samples to analyze might increase in the future.\n- **Scanning speed:** The scanning speed highly determines the correct microarray scanner for your laboratory. You should prefer a microarray scanner with the highest scanning speed because it determines the speed to completion of the microarray process.\n- **Other considerations:** Other considerations like how easy is it to use, do you require multiple laser and filter options, and whether it is upgradable according to future needs are also necessary.\n\nSurescan Dx by [Agilent Technologies](https:\u002F\u002Fwww.agilent.com\u002F%5C) and GeneChip 3000 7G by [ThermoFisher Scientific](http:\u002F\u002Fthermofisher.com\u002Fen\u002Fhome.html) fulfill the basic requirements of a microarray scanner.  \n\n**References**\n\n- Agilent.com. Retrieved 30 June 2022, from [https:\u002F\u002Fwww.agilent.com\u002Fcs\u002Flibrary\u002Fbrochures\u002F5989-8555en_lo.pdf](https:\u002F\u002Fwww.agilent.com\u002Fcs\u002Flibrary\u002Fbrochures\u002F5989-8555en_lo.pdf).\n- *microarray | Learn Science at Scitable*. Nature.com. Retrieved 30 June 2022, from [https:\u002F\u002Fwww.nature.com\u002Fscitable\u002Fdefinition\u002Fmicroarray-202\u002F](https:\u002F\u002Fwww.nature.com\u002Fscitable\u002Fdefinition\u002Fmicroarray-202\u002F).\n- *Microarray Scanners Information*. Engineering 360. Retrieved 30 June 2022, from [https:\u002F\u002Fwww.globalspec.com\u002Flearnmore\u002Flabware_scientific_instruments\u002Fclinical_research_labware\u002Fmicroarray_scanners](https:\u002F\u002Fwww.globalspec.com\u002Flearnmore\u002Flabware_scientific_instruments\u002Fclinical_research_labware\u002Fmicroarray_scanners).\n- Stoakes, Shelley Farrar. (2019, May 24). How Do Microarrays Work?. News-Medical. Retrieved on June 29, 2022 from [https:\u002F\u002Fwww.news-medical.net\u002Flife-sciences\u002FHow-Do-Microarrays-Work.aspx](https:\u002F\u002Fwww.news-medical.net\u002Flife-sciences\u002FHow-Do-Microarrays-Work.aspx).\n- Wiltgen, M., & Tilz, G. (2007). DNA microarray analysis: Principles and clinical impact. *Hematology*, *12*(4), 271-287. [https:\u002F\u002Fdoi.org\u002F10.1080\u002F10245330701283967](https:\u002F\u002Fdoi.org\u002F10.1080\u002F10245330701283967)\n- Perkel, J. (2004). *The Microarray Scanner*. The Scientist. Retrieved 30 June 2022, from [https:\u002F\u002Fwww.the-scientist.com\u002Fhow-it-works\u002Fthe-microarray-scanner-49856](https:\u002F\u002Fwww.the-scientist.com\u002Fhow-it-works\u002Fthe-microarray-scanner-49856).\n- *DNA Microarray Technology Fact Sheet*. Genome.gov. (2020). Retrieved 30 June 2022, from [https:\u002F\u002Fwww.genome.gov\u002Fabout-genomics\u002Ffact-sheets\u002FDNA-Microarray-Technology](https:\u002F\u002Fwww.genome.gov\u002Fabout-genomics\u002Ffact-sheets\u002FDNA-Microarray-Technology).\n- *DNA microarray*. News-Medical.net. (2019). Retrieved 30 June 2022, from [https:\u002F\u002Fwww.news-medical.net\u002Flife-sciences\u002FDNA-microarray.aspx](https:\u002F\u002Fwww.news-medical.net\u002Flife-sciences\u002FDNA-microarray.aspx).\n- Berhanu, G., & Dula, T. (2020). Types, Importance and Limitations of DNA Microarray. *Global Journal Of Biotechnology & Biochemistry*, *15*(2), 25-31. [https:\u002F\u002Fdoi.org\u002F10.5829\u002Fidosi.gjbb.2020.15.02.15124](https:\u002F\u002Fdoi.org\u002F10.5829\u002Fidosi.gjbb.2020.15.02.15124)",[],[],[],[48,55,61,66,70,74,79,84,88,92],{"slug":49,"name":50,"description":51,"image":52,"body":53,"postCount":54},"acharya-tankeshwar","Acharya Tankeshwar","Editor-in-chief","https:\u002F\u002Fassets.microbeonline.com\u002Fauthors\u002Ftankeshwar-acharya-author-microbeonline.jpg","***Tankeshwar Acharya, MSc (Medical Microbiology)***\n\n*Tankeshwar Acharya is an Assistant Professor in the Department of Microbiology at Patan Academy of Health Sciences (PAHS), Nepal, where he has been teaching and practicing clinical microbiology for over 14 years. He is the founder of Microbe Online, one of the leading free microbiology education resources on the web, covering bacteriology, mycology, parasitology, immunology, and clinical laboratory diagnostics written from direct experience in both the classroom and the diagnostic laboratory.*",433,{"slug":56,"name":38,"description":57,"image":58,"body":59,"postCount":60},"ashma-shrestha","SEO Copywriter and Science Communicator\nKathmandu, Nepal","https:\u002F\u002Fassets.microbeonline.com\u002Fauthors\u002Fashma-shrestha.png","Ashma Shrestha holds a Master of Science in Medical Microbiology from the Institute of Science and Technology (IOST), Tribhuvan University, Nepal, where she developed a strong foundation in virology, molecular biology, and diagnostic microbiology.\n\nShe now works as an SEO Copywriter at Resolution Digital, where she combines her scientific training with research-driven content strategy. She is certified in Google Analytics and Google Business Profile (GBP), and brings a data-informed approach to science communication writing content that is not only accurate but structured to reach and serve the students who need it most.\n\nAt microbeonline, Ashma contributes articles primarily in virology and molecular biology, areas she finds most compelling for their mechanistic depth and their growing clinical relevance. Her writing reflects the same standard the site is built on: factual rigor, clear explanation of the *why* behind microbiology concepts, and content that helps students move from memorization to genuine understanding.\n\nShe is passionate about making complex microbiological concepts accessible without sacrificing accuracy; a skill that sits at the intersection of her scientific training and her professional work in content and SEO.",81,{"slug":62,"name":63,"description":64,"image":37,"body":37,"postCount":65},"sushmita-baniya","Sushmita Baniya","Author \u002F Contributor",32,{"slug":67,"name":68,"description":64,"image":37,"body":37,"postCount":69},"samikshya-acharya","Samikshya Acharya",20,{"slug":71,"name":72,"description":64,"image":37,"body":37,"postCount":73},"alisha-tripathi","Alisha Tripathi",6,{"slug":75,"name":76,"description":77,"image":37,"body":37,"postCount":78},"aastha-shrestha","Aastha Shrestha"," Author \u002F Contributor",10,{"slug":80,"name":81,"description":82,"image":37,"body":37,"postCount":83},"guest-author","Guest Author","Guest Author \u002F Contributor",2,{"slug":85,"name":86,"description":64,"image":37,"body":37,"postCount":87},"srijana-khanal","Srijana Khanal",18,{"slug":89,"name":90,"description":82,"image":37,"body":37,"postCount":91},"dr-poonam-acharya","Dr. Poonam Acharya",1,{"slug":93,"name":94,"description":64,"image":37,"body":95,"postCount":96},"nisha-rijal","Nisha Rijal","**Nisha Rijal** is a microbiologist and quality assurance specialist. She served for nearly 12 years as a microbiologist at the National Public Health Laboratory (NPHL), Nepal's national reference laboratory, and continues to work as a consultant microbiologist in international public health organization. ",51]