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In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Related Experiment Video

Updated: Jan 31, 2026

Two Methods for Decellularization of Plant Tissues for Tissue Engineering Applications
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Plant DNA Repair Pathways and Their Applications in Genome Engineering.

Qiudeng Que1, Zhongying Chen2, Tim Kelliher2

  • 1Seeds Research, Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA. qiudeng.que@syngenta.com.

Methods in Molecular Biology (Clifton, N.J.)
|January 6, 2019
PubMed
Summary
This summary is machine-generated.

Genome editing technologies like site-directed nucleases and base editors precisely engineer crops. Understanding plant DNA repair pathways is key to improving genome engineering efficiency and directing desired outcomes.

Keywords:
Alternative end joining (altEJ)Base editor (BE)DNA repairDouble-strand break (DSB)Genome engineeringHomology-directed repair (HDR)Nonhomologous end joining (NHEJ)Single-strand break (SSB)Site-directed nuclease (SDN)

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Area of Science:

  • Plant biotechnology
  • Molecular biology
  • Genetics

Background:

  • Advanced genome editing tools, including site-directed nucleases (SDNs) and base editors (BEs), enable precise modification of plant DNA sequences for novel crop characteristics.
  • Current genome editing outcomes are influenced by DNA damage type, host repair machinery, and donor DNA presence, leading to unpredictable insertions/deletions with SDNs.
  • While base editing offers higher precision, its efficiency is variable, depending on the editor type and endogenous DNA repair system activity.

Purpose of the Study:

  • To review plant DNA repair pathways relevant to genome engineering applications.
  • To explore the potential of leveraging DNA repair mechanisms for enhancing genome engineering efficiency.
  • To discuss strategies for directing DNA repair processes towards desired sequence modification outcomes.

Main Methods:

  • Review of existing literature on plant DNA double-strand break repair pathways.
  • Analysis of the impact of different DNA repair mechanisms on genome editing outcomes.
  • Discussion of potential strategies for manipulating DNA repair pathways in plants.

Main Results:

  • Plant cells possess multiple DNA repair pathways that influence genome editing outcomes.
  • Unpredictable insertions and deletions frequently result from the repair of DNA double-strand breaks induced by site-directed nucleases.
  • Base editing efficiency is modulated by the specific base editor used and the plant's endogenous DNA repair activity.

Conclusions:

  • Understanding and manipulating plant DNA repair pathways are crucial for improving the predictability and efficiency of genome engineering.
  • Harnessing specific DNA repair mechanisms can lead to more controlled and desired sequence modifications in crop development.
  • Further research into plant DNA repair is essential for advancing precision agriculture and crop improvement strategies.