DNA fingerprinting

(noun)

A method of isolating and mapping sequences of a cell's DNA to identify it.

Examples of DNA fingerprinting in the following topics:

  • Classification of Microorganisms

    • Classification of microorganisms has been largely aided by studies of fossils and recently by DNA sequencing.
    • The most widely employed methods for classifying microbes are morphological characteristics, differential staining, biochemical testing, DNA fingerprinting or DNA base composition, polymerase chain reaction, and DNA chips.

  • Genetic Maps

    • The term linkage was used before the discovery of DNA.
    • The exchange of DNA between homologous pairs of chromosomes is called genetic recombination, which occurs by the crossing over of DNA between homologous strands of DNA, such as nonsister chromatids.
    • RFLPs (sometimes pronounced "rif-lips") are detected when the DNA of an individual is cut with a restriction endonuclease that recognizes specific sequences in the DNA to generate a series of DNA fragments, which are then analyzed by gel electrophoresis.
    • The DNA of every individual will give rise to a unique pattern of bands when cut with a particular set of restriction endonucleases; this is sometimes referred to as an individual's DNA "fingerprint."
    • Non-coding DNA has no known biological function; however, research shows that much of this DNA is actually transcribed.

  • DNA Analysis Using Genetic Probes and PCR

    • Hybridization of the sequence with a complementary sequence of DNA or RNA, follows cleavage of the double-stranded DNA of the microorganism in the specimen.
    • At the national or international level, fingerprinting allows strains from different geographic areas to be compared, and the movement of individual strains to be tracked.
    • Fingerprinting technique requires high-quality genomic DNA, which is not only difficult to prepare but also requires culturing of the organism, resulting in a long turnaround time.
    • In addition, fingerprint interpretation and matching can be complicated and require sophisticated computer software for large-scale analysis.
    • However, spoligotyping has significantly less discriminatory power than fingerprinting.

  • Amplifying DNA: The Polymerase Chain Reaction

    • DNA cloning for sequencing; DNA-based phylogeny, or functional analysis of genes
    • The identification of genetic fingerprints (used in forensic sciences and paternity testing)
    • 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
    • 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.

  • 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.

  • Whole-Genome DNA-Binding Analysis

    • Whole-genome DNA-binding analysis is a powerful tool for analyzing epigenetic modifications and DNA sequences bound to regulatory proteins.
    • After cell lysis, the DNA is fragmented by sonication.
    • 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.

  • 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.