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Related Concept Videos

Restriction Enzymes01:11

Restriction Enzymes

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Restriction enzymes are bacterial enzymes used to cut DNA in a sequence-specific manner. To cleave DNA, they bind to specific palindromic sequences called restriction sites. Such palindromic DNA sequences or inverted repeats are commonly found in regions of functional significance, such as the origin of replication, gene operator sites, and regions containing transcription termination signals.
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Conservative Site-specific Recombination and Phase Variation02:53

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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Base Excision Repair01:54

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One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
The first step of...
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Sanger Sequencing01:57

Sanger Sequencing

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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Homologous Recombination02:31

Homologous Recombination

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The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair
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Sequence-specific DNA nicking endonucleases.

Shuang-yong Xu

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    |September 10, 2015
    PubMed
    Summary
    This summary is machine-generated.

    Newly discovered small HNH nicking endonucleases (NEases) from phage genomes offer versatile DNA targeting for genome engineering and diagnostics. These enzymes, with specificities ranging from 3 to 16 bp, enable applications in optical mapping, diagnostics, and gene editing.

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    Area of Science:

    • Molecular Biology
    • Enzymology
    • Genomics

    Background:

    • Small HNH nicking endonucleases (NEases) from phage genomes recognize short DNA sequences (3-5 bp) requiring Mg2+ or Mn2+.
    • The N.ϕGamma enzyme's minimal nicking domain can be engineered into chimeric NEases with novel specificities.
    • HNH endonucleases have demonstrated roles in phage DNA packaging and are found in restriction systems or engineered from type IIS enzymes.

    Purpose of the Study:

    • To explore the diversity and applications of HNH nicking endonucleases.
    • To highlight the potential of engineered chimeric NEases for novel DNA targeting.
    • To review the current applications of DNA nicking technologies in various biological and diagnostic fields.

    Main Methods:

    • Bioinformatic analysis of phage and prophage genomes to identify novel HNH NEases.
    • Protein engineering to create chimeric NEases by fusing nicking domains with DNA-binding partners.
    • Literature review of existing applications of DNA nicking enzymes.

    Main Results:

    • Discovery of small HNH NEases with specificities for short DNA sites (3-16 bp).
    • Demonstration of engineered chimeric NEases with tailored DNA recognition.
    • Established applications of DNA nicking in optical mapping, diagnostics, and genome editing using CRISPR-Cas9 systems.

    Conclusions:

    • HNH NEases represent a versatile class of enzymes with significant potential in molecular biology and biotechnology.
    • Engineered NEases and nicking technologies offer powerful tools for genome manipulation, diagnostics, and synthetic biology.
    • Further research into HNH NEases will likely uncover new enzymes and expand their applications.