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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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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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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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AID Recognizes Structured DNA for Class Switch Recombination.

Qi Qiao1, Li Wang1, Fei-Long Meng2

  • 1Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.

Molecular Cell
|August 1, 2017
PubMed
Summary
This summary is machine-generated.

Activation-induced cytidine deaminase (AID) prefers structured DNA, like G-quadruplexes, for antibody diversification. Disrupting AID

Keywords:
AIDAPOBECCSRG-quadruplexactivation-induced cytidine deaminaseclass switch recombinationcrystal structure

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Area of Science:

  • Immunology
  • Molecular Biology
  • Structural Biology

Background:

  • Activation-induced cytidine deaminase (AID) is crucial for antibody diversification through class switch recombination (CSR) and somatic hypermutation (SHM).
  • The precise mechanisms of AID targeting and catalysis are not fully understood, despite its importance in immunity and potential role in tumorigenesis.
  • Understanding AID function is critical for both basic immunology and therapeutic strategies.

Purpose of the Study:

  • To elucidate the substrate recognition and catalytic mechanisms of human Activation-induced cytidine deaminase (AID).
  • To investigate the role of DNA secondary structures, particularly G-quadruplexes (G4s), in AID targeting.
  • To determine the structural basis for AID's preference for structured substrates and its implications in class switch recombination (CSR).

Main Methods:

  • Production of active human AID for biochemical assays.
  • In vitro deamination assays using various DNA substrates, including G4-containing sequences.
  • X-ray crystallography to determine the structures of AID alone and in complex with deoxycytidine monophosphate.
  • Structure-based mutagenesis to assess the functional importance of identified structural features.
  • Analysis of CSR in splenic B cells following targeted mutations in AID.

Main Results:

  • Human AID preferentially recognizes and deaminates structured DNA substrates, with G-quadruplex (G4) structures being particularly effective.
  • Crystal structures revealed a unique bifurcated substrate-binding surface on AID, enabling simultaneous capture of two adjacent single-stranded overhangs.
  • G4 substrates were found to induce cooperative oligomerization of AID.
  • Structure-based mutations disrupting the bifurcated binding surface or AID oligomerization significantly impaired CSR in B cells.

Conclusions:

  • Activation-induced cytidine deaminase (AID) possesses an intrinsic preference for structured DNA substrates, including G-quadruplexes.
  • The identified bifurcated substrate-binding surface and AID oligomerization are critical for efficient G4 recognition and function in CSR.
  • These findings provide structural insights into AID's mechanism and highlight the importance of DNA secondary structures in antibody diversification.