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Related Concept Videos

CRISPR01:59

CRISPR

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Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced...
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Bacteria and archaea are susceptible to viral infections just like eukaryotes; therefore, they have developed a unique adaptive immune system to protect themselves. Clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins (CRISPR-Cas) are present in more than 45% of known bacteria and 90% of known archaea.
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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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DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
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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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Related Experiment Video

Updated: Jun 30, 2025

CIRCLE-Seq for Interrogation of Off-Target Gene Editing
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CRISPR-powered quantitative keyword search engine in DNA data storage.

Jiongyu Zhang1,2, Chengyu Hou1,2, Changchun Liu3

  • 1Department of Biomedical Engineering, University of Connecticut Health Center, Farmington, CT, 06030, USA.

Nature Communications
|March 16, 2024
PubMed
Summary
This summary is machine-generated.

We developed SEEKER, a CRISPR-Cas12a system for quantitative DNA data searching. It rapidly finds keywords in DNA archives by measuring fluorescence, enabling efficient data retrieval.

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Area of Science:

  • Synthetic biology
  • Bioinformatics
  • Molecular diagnostics

Background:

  • Archiving vast amounts of data in synthetic DNA is a growing field.
  • Quantitative querying of DNA-stored data remains a significant challenge.

Purpose of the Study:

  • To develop a method for quantitative searching of information stored in synthetic DNA.
  • To enable rapid and accurate retrieval of specific keywords from DNA data archives.

Main Methods:

  • Utilized CRISPR-Cas12a for enzymatic keyword recognition, generating fluorescence upon target detection.
  • Developed non-collision grouping coding for dictionary size reduction and lossless compression.
  • Implemented a 3D-printed microfluidic chip for parallel searching.

Main Results:

  • Successfully identified keywords in 40 files amidst approximately 8000 irrelevant terms using four queries.
  • Demonstrated that fluorescence intensity growth rate is proportional to keyword frequency, enabling quantitative analysis.
  • Achieved simple implementation and rapid result generation for DNA data searching.

Conclusions:

  • SEEKER provides a novel, quantitative approach for parallel searching of complete DNA-stored content.
  • The system offers a practical solution for addressing the challenges of data explosion and DNA data retrieval.
  • SEEKER facilitates efficient and accurate keyword searching in large DNA data repositories.