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:

  • Uses of Genome Sequences

    • Genome sequences and expression can be analyzed using DNA microarrays, which can contribute to detection of disease and genetic disorders.
    • DNA microarrays are methods used to detect gene expression by analyzing an array of DNA fragments that are fixed to a glass slide or a silicon chip to identify active genes and identify sequences .
    • Almost one million genotypic abnormalities can be discovered using microarrays, whereas whole-genome sequencing can provide information about all six billion base pairs in the human genome.
    • DNA microarrays can be used to analyze gene expression within the genome.

  • 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

  • Basic Techniques in Protein Analysis

    • The basic techniques used to analyze proteins are mass spectrometry, x-ray crystallography, NMR, and protein microarrays.
    • The basic technique for protein analysis, analogous to DNA sequencing, is mass spectrometry.
    • Protein microarrays have also been used to study interactions between proteins.
    • Generally, the transcription factor is split into a DNA-binding domain (BD) and an activation domain (AD).
    • In this method, a transcription factor is split into a DNA-binding domain (BD) and an activation domain (AD).

  • DNA Replication in Prokaryotes

    • Prokaryotic DNA is replicated by DNA polymerase III in the 5' to 3' direction at a rate of 1000 nucleotides per second.
    • In prokaryotes, three main types of polymerases are known: DNA pol I, DNA pol II, and DNA pol III.
    • DNA pol III is the enzyme required for DNA synthesis; DNA pol I and DNA pol II are primarily required for repair.
    • DNA polymerase III uses this primer to synthesize the daughter DNA strand.
    • DNA polymerase I replaces the RNA primer with DNA.

  • 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.

  • Basics of DNA Replication

    • DNA replication uses a semi-conservative method that results in a double-stranded DNA with one parental strand and a new daughter strand.
    • Watson and Crick's discovery that DNA was a two-stranded double helix provided a hint as to how DNA is replicated.
    • In dispersive replication, after replication both copies of the new DNAs would somehow have alternating segments of parental DNA and newly-synthesized DNA on each of their two strands.
    • DNA from cells grown exclusively in 15N produced a lower band than DNA from cells grown exclusively in 14N.
    • So each "daughter" DNA actually consists of one "old"  DNA strand and one newly-synthesized strand.

  • Characteristics of Eukaryotic DNA

    • Eukaryotic DNA is packed into bundles of chromosomes, each consisting of a linear DNA molecule coiled around basic (alkaline) proteins called histones, which wind the DNA into a more compact form.
    • In addition, prokaryotes have plasmids, which are smaller pieces of circular DNA that can replicate separately from prokaryotic genomic DNA.
    • A major DNA difference between eukaryotes and prokaryotes is the presence of mitochondrial DNA (mtDNA) in eukaryotes.
    • The mtDNA is composed of significantly fewer base pairs than nuclear DNA and encodes only a few dozen genes, depending on the organism.
    • Eukaryotic DNA is stored in a nucleus, whereas prokaryotic DNA is in the cytoplasm in the form of a nucleoid.

  • 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.