DNA microarray

(noun)

a collection of microscopic DNA spots attached to a solid surface forming an array; used to measure the expression levels of large numbers of genes simultaneously

Related Terms

Examples of DNA microarray in the following topics:

  • Microarrays and the Transciptome

    • The study of transcriptomics, also referred to as expression profiling, examines the expression level of mRNAs in a given cell population, often using high-throughput techniques based on DNA microarray technology.
    • DNA microarrays can provide a genome-wide method for comparison of the abundance of DNAs in the same samples.The DNA in spots can only be PCR products specific for individual genes.
    • A DNA copy of RNA is made using the enzyme reverse transcriptase.
    • Sequencing is now being used instead of gene arrays to quantify DNA levels, at least semi-quantitatively.
    • The core principle behind microarrays is hybridization between two DNA strands, the property of complementary nucleic acid sequences to specifically pair with each other by forming hydrogen bonds between complementary nucleotide base pairs.

  • Whole-Genome DNA-Binding Analysis

    • The method of chromatin immunoprecipitation, combined with microarrays (ChIP-Chip), is a powerful tool for genome-wide analysis of protein binding.
    • DNA bound by the protein will be coprecipitated and enriched, compared to DNA not bound by the respective protein.
    • Two different fluorescence labels are used to label the IP DNA, and a hybridization-control DNA, respectively.
    • Usually, total DNA before IP (input DNA) is used as hybridization control.
    • The two differentially-labeled DNAs are hybridized to the same microarray and the difference in fluorescence intensity gives a measure of the enrichment .

  • Genetic Analysis

    • Viruses differ from other microbes as they can carry either DNA or RNA.
    • DNA cloning is another technique fundamental to molecular biology that requires adaptation in order to be useful in studying DNA at a whole genome scale.
    • Microarray hybridization is another technique used to characterize the dynamic nature of gene expression within a microbial cell.
    • Microarray technology allows whole organism gene expression to be investigated.
    • Summarize the techniques used to study genomes: PFGE. ordered clone approach, direct shotgun sequencing and microarray hybridization

  • DNA Protection Analysis

    • DNA protection or "footprinting" analysis is a powerful technique for identifying the nucleotides involved in a protein-DNA interaction.
    • DNA protection or footprinting is a technique from molecular biology/biochemistry that detects DNA-protein interaction using the fact that a protein bound to DNA will often protect that DNA from enzymatic cleavage.
    • This makes it possible to locate a protein binding site on a particular DNA molecule.
    • The cleavage pattern of the DNA in the absence of a DNA binding protein, typically referred to as free DNA, is compared to the cleavage pattern of DNA in the presence of a DNA binding protein.
    • If the protein binds DNA, the binding site is protected from enzymatic cleavage.

  • DNA Sequencing Based on Sanger Dideoxynucleotides

    • The classical chain-termination method requires a single-stranded DNA template, a DNA primer, a DNA polymerase, normal deoxynucleotidetriphosphates (dNTPs), and modified nucleotides (dideoxyNTPs) that terminate DNA strand elongation .
    • Following rounds of template DNA extension from the bound primer, the resulting DNA fragments are heat denatured and separated by size using gel electrophoresis.
    • The DNA bands may then be visualized by autoradiography or UV light and the DNA sequence can be directly read off the X-ray film or gel image.
    • Automated DNA-sequencing instruments (DNA sequencers) can sequence up to 384 DNA samples in a single batch (run) in up to 24 runs a day.
    • The four DNA bases are represented by different colours which are interpreted by the software to give the DNA sequence above.

  • Obtaining DNA

    • When cloning genomic DNA, the DNA to be cloned is extracted from the organism of interest.
    • For cloning of genomic DNA, the DNA to be cloned is extracted from the organism of interest.
    • DNA for cloning experiments may also be obtained from RNA using reverse transcriptase (complementary DNA or cDNA cloning), or in the form of synthetic DNA (artificial gene synthesis). cDNA cloning is usually used to obtain clones representative of the mRNA population of the cells of interest, while synthetic DNA is used to obtain any precise sequence defined by the designer.
    • Typically, this is done by cleaving the vector DNA and foreign DNA with the same restriction enzyme.
    • The two resulting DNA strands make up the template DNA for the next cycle, thus doubling the amount of DNA duplicated for each new cycle.

  • Supercoiling

    • DNA supercoiling refers to the over- or under-winding of a DNA strand, and is an expression of the strain on that strand.
    • DNA supercoiling refers to the over- or under-winding of a DNA strand, and is an expression of the strain on that strand .
    • DNA supercoiling is important for DNA packaging within all cells.
    • Supercoiling of DNA reduces the space and allows for much more DNA to be packaged.
    • Because DNA must be unwound for DNA and RNA polymerase action, supercoils will result.

  • Amplifying DNA: The Polymerase Chain Reaction

    • DNA cloning for sequencing; DNA-based phylogeny, or functional analysis of genes
    • PCR is used to amplify a specific region of a DNA strand (the DNA target).
    • DNA template that contains the DNA region (target) to be amplified
    • It causes DNA melting of the DNA template by disrupting the hydrogen bonds between complementary bases, yielding single-stranded DNA molecules.
    • The two resulting DNA strands make up the template DNA for the next cycle, thus doubling the amount of DNA duplicated for each new cycle.

  • Recombinant DNA Technology

    • Recombinant DNA technology also referred to as molecular cloning is similar to polymerase chain reaction (PCR) in that it permits the replication of a specific DNA sequence.
    • The cloning vector is treated with a restriction endonuclease to cleave the DNA at the site where foreign DNA will be inserted.
    • Typically, this is done by cleaving the vector DNA and foreign DNA with the same restriction enzyme, for example EcoRI.
    • For cloning of genomic DNA, the DNA to be cloned is extracted from the organism of interest.
    • DNA of interest is ligated into a vector.

  • Molecular Products from Microbes

    • These enzymes have the ability to cut DNA at specific recognition sequences and have served as invaluable tools in DNA modification and manipulation.
    • DNA ligase plays a key role in molecular biology processes due to its ability to insert DNA fragments into plasmids.
    • The process of DNA ligation is defined as the ability of DNA ligase to covalently link, or ligate, fragments of DNA together.
    • In molecular biology -- specifically, during the process of developing recombinant DNA -- DNA ligase can be used to ligate a fragment of DNA into a plasmid vector .
    • The most commonly used DNA ligase is derived from the T4 bacteriophage and is referred to as T4 DNA ligase.