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Related Concept Videos

DNA-only Transposons02:57

DNA-only Transposons

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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
The donor site from where the transposon is excised is either degraded or...
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Transposons01:24

Transposons

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Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...
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Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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LTR Retrotransposons03:08

LTR Retrotransposons

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LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
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Translesion DNA Polymerases02:10

Translesion DNA Polymerases

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Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
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Repressible Operon: trp Operon01:21

Repressible Operon: trp Operon

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The trp operon in Escherichia coli exemplifies a repressible operon. It regulates the synthesis of tryptophan through repressor-mediated transcriptional control and attenuation. This dual regulatory mechanism ensures tryptophan biosynthesis occurs only when needed, conserving cellular resources.Structure of the trp OperonThe trp operon consists of five structural genes (trpE, trpD, trpC, trpB, and trpA) that encode enzymes for tryptophan biosynthesis. These genes are transcribed as a single...
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Related Experiment Video

Updated: Dec 11, 2025

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
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Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

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G-quadruplex structures bind to EZ-Tn5 transposase.

Simone L Cree1, Eng Wee Chua1, Jennifer Crowther2

  • 1Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand.

Biochimie
|August 18, 2020
PubMed
Summary
This summary is machine-generated.

Nextera transposase shows bias in DNA sequencing, avoiding G-quadruplex structures. These structures bind strongly to the transposase, suggesting they are preferential sites for transposition and viral integration.

Keywords:
DNA:Protein interactionG-quadruplexG4Non-B DNATn5 transposase

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Single-molecule Manipulation of G-quadruplexes by Magnetic Tweezers
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Area of Science:

  • Genomics
  • Molecular Biology
  • Biochemistry

Background:

  • Next-generation sequencing (NGS) is crucial for analyzing pharmacogenes like CYP2D6.
  • Transposase enzymes, such as Nextera, are used in NGS library preparation.
  • G-quadruplexes are non-canonical DNA structures found in the genome with potential regulatory roles.

Purpose of the Study:

  • To investigate the observed low sequencing coverage bias in CYP2D6 amplicons.
  • To determine if G-quadruplex structures influence Nextera transposase activity.
  • To explore the implications of G-quadruplex interactions with transposases in genomic processes.

Main Methods:

  • Analysis of sequencing coverage data from CYP2D6 amplicons.
  • In vitro formation and characterization of G-quadruplex structures.
  • Binding affinity assays between EZ-Tn5 transposase and G-quadruplex DNA.

Main Results:

  • Sequencing coverage was significantly lower at predicted G-quadruplex forming sites within the CYP2D6 amplicon.
  • G-quadruplex structures were confirmed to form in vitro within the CYP2D6 gene.
  • The hyperactive Tn5 transposase (EZ-Tn5) exhibited high-affinity binding to G-quadruplex DNA.

Conclusions:

  • G-quadruplex structures may act as preferential integration sites for transposons.
  • These findings provide evidence for the role of G-quadruplexes in transposition and viral integration.
  • Transposase targeting bias can be influenced by secondary DNA structures.