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Related Concept Videos

Restriction Enzymes01:11

Restriction Enzymes

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.
The host bacteria protect their own genomic DNA from these enzymes by methylating these sites. Some...
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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...
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
Homologous Recombination02:31

Homologous Recombination

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...
Base Excision Repair01:54

Base Excision Repair

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...
Base Excision Repair01:54

Base Excision Repair

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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Related Experiment Video

Updated: Jul 18, 2026

Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage
06:51

Parallel High Throughput Single Molecule Kinetic Assay for Site-Specific DNA Cleavage

Published on: May 6, 2020

Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases.

Yi-Ting Wang1, Wei-Jen Yang, Chia-Lung Li

  • 1Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, Republic of China.

Nucleic Acids Research
|December 19, 2006
PubMed
Summary

Nonspecific endonucleases show sequence preference in DNA cleavage. Structural analysis reveals DNA backbone distortion near thymine bases enhances cleavage by ColE7, explaining sequence-dependent nuclease activity.

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Last Updated: Jul 18, 2026

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Background:

  • Nonspecific endonucleases cleave DNA but exhibit sequence preferences.
  • The structural basis for this sequence preference is not well understood.

Purpose of the Study:

  • To investigate the structural mechanisms underlying sequence-dependent DNA cleavage by nonspecific endonucleases.
  • To compare the cleavage preferences and structural interactions of ColE7 and Vvn endonucleases with DNA.

Main Methods:

  • X-ray crystallography was used to determine the structures of ColE7 and Vvn in complex with DNA.
  • Analysis of DNA phosphate backbone distortion and proximity of the scissile phosphate to the active site.

Main Results:

  • ColE7 showed a preference for nicking DNA after thymine bases, associated with a distorted DNA phosphate backbone.
  • Vvn exhibited less sequence preference, with its DNA-bound structures showing minimal backbone distortion.
  • The distorted backbone in ColE7-DNA complexes brought the scissile phosphate closer to the active site, enhancing cleavage efficiency.

Conclusions:

  • DNA sequence influences endonuclease cleavage rates through sequence-dependent DNA backbone deformation.
  • Nonspecific endonucleases can induce distinct DNA structural changes based on local sequence, leading to varied cleavage efficiencies.