DNA hybridization

(noun)

Hybridization is the process of establishing a non-covalent, sequence-specific interaction between two or more complementary strands of nucleic acids into a single complex, which in the case of two strands is referred to as a duplex. Oligonucleotides, DNA, or RNA will bind to their complement under normal conditions, so two perfectly complementary strands will bind to each other readily.

Related Terms

Examples of DNA hybridization in the following topics:

  • 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.
    • 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 .

  • The FISH Technique

    • FISH can be used to detect RNA or DNA sequences of interest.
    • The probe must be large enough to hybridize specifically with its target but not so large as to impede the hybridization process.
    • They are anti-sense to the target mRNA or DNA of interest, thus they hybridize to targets.
    • A similar hybridization technique is called a zoo blot.
    • Describe how fluorescent in situ hybridization (FISH) is used in clinical and biomedical studies to detect and localize the presence or absence of specific DNA sequences and to identify pathogens

  • Hybrid Zones

    • An area where two closely-related species continue to interact and reproduce, forming hybrids, is called a hybrid zone.
    • Over time, the hybrid zone may change depending on the fitness strength and the reproductive barriers of the hybrids .
    • Over time, via a process called hybrid speciation, the hybrids themselves can become a separate species.
    • With DNA analysis becoming more accessible in the 1990s, hybrid speciation has been shown to be a fairly common phenomenon, particularly in plants.
    • Discuss how the fitness of a hybrid will lead to changes in the hybrid zone over time

  • Prokaryotic Reproduction

    • The DNA of a prokaryote exists as as a single, circular chromosome.
    • If a nonpathogenic bacterium takes up DNA for a toxin gene from a pathogen and incorporates the new DNA into its own chromosome, it, too, may become pathogenic.
    • The DNA transferred can be in the form of a plasmid or as a hybrid, containing both plasmid and chromosomal DNA.
    • The DNA may remain separate as plasmid DNA or be incorporated into the host genome.
    • In (b) transduction, a bacteriophage injects DNA into the cell that contains a small fragment of DNA from a different prokaryote.

  • Synthesizing DNA

    • DNA) must be understood.
    • DNA must be synthesized to study genes, the sequence of genomes, and many other studies.
    • Here we will focus on chemical synthesis of DNA, which is also known as oligonucleotide synthesis.
    • They are most commonly used as antisense oligonucleotides, small interfering RNA, primers for DNA sequencing and amplification, probes for detecting complementary DNA or RNA via molecular hybridization, tools for the targeted introduction of mutations and restriction sites, and for the synthesis of artificial genes.
    • In contrast, natural DNA replication requires existing DNA templates for synthesizing new DNA.

  • DNA Analysis Using Genetic Probes and PCR

    • Genetic probes are based on the detection of unique nucleotide sequences with the DNA or RNA of a microorganism.
    • 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.
    • The use of molecular technology in the diagnoses of infectious diseases has been further enhanced by the introduction of gene amplication techniques, such as the polymerase chain reaction (PCR) in which DNA polymerase is able to copy a strand of DNA by elongating complementary strands of DNA that have been initiated from a pair of closely spaced oligonucleotide primers.
    • In many PCR-based typing assays, the target DNA of interest is amplified and labeled by PCR, and the labeled products are hybridized to an array of immobilized diagnostic probes.
    • Describe how genetic probes can be used to detect unique nucleotide sequences within the DNA or RNA or a microorganism

  • 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.
    • The level of cDNA is then quantified using high-resolution image scanners.
    • Summarize the techniques used to study genomes: PFGE. ordered clone approach, direct shotgun sequencing and microarray hybridization

  • DNA Sequencing of Insertion Sites

    • These include Southern hybridization, inverse Polymerase Chain Reaction (iPCR), and most recently, vectorette PCR to identify and map the genomic positions of the insertion sequences.
    • Southern hybridization is rather time-consuming and requires additional procedures for localizing ISs.
    • Also, the length of each restriction DNA fragment containing a target sequence must be determined by Southern hybridization followed by sub-genomic fractioning before intramolecular ligation and PCR amplification.
    • These difficulties render Southern hybridization and iPCR impractical as techniques for quickly surveying repetitive elements in genomes.
    • Vectorette PCR (vPCR) is another method used to amplify unknown sequences flanking a characterized DNA fragment.

  • Physical Maps and Integration with Genetic Maps

    • Physical maps display the physical distance between genes and can be constructed using cytogenetic, radiation hybrid, or sequence mapping.
    • There are three methods used to create a physical map: cytogenetic mapping, radiation hybrid mapping, and sequence mapping.
    • Radiation hybrid mapping uses radiation, such as x-rays, to break the DNA into fragments.
    • The creation of genomic libraries and complementary DNA (cDNA) libraries (collections of cloned sequences or all DNA from a genome) has sped up the process of physical mapping.
    • Describe the methods used to physically map genes: cytogenetic mapping, radiation hybrid mapping, and sequence mapping

  • Supercoiling

    • DNA supercoiling refers to the over- or under-winding of a DNA strand, and is an expression of the strain on that strand.
    • For larger molecules, it is common for hybrid structures to form – a loop on a toroid can extend into a plectoneme.
    • 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.