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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...
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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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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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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...

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Related Experiment Video

Updated: Jun 20, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture (4C-seq)
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ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction

Chao Li1, Yuhua Li, Xiangmin Zhang

  • 1Department of Biomedical Informatics, Ira A Fulton School Engineering, Arizona State University, Phoenix, AZ 85004, USA. Charles.Li@asu.edu

BMC Bioinformatics
|September 15, 2009
PubMed
Summary
This summary is machine-generated.

ICRPfinder is a new algorithm that finds or creates specific DNA patterns, including restriction enzyme sites, without altering the protein sequence. This tool aids in gene engineering for recombinant applications by enabling custom DNA modifications.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Synthetic Biology

Background:

  • Restriction enzymes enable DNA segmentation via specific cut patterns.
  • Gene engineering requires tools to modify DNA for enhanced codons, specific cut sites, and other recombinant applications.
  • Existing software lacks comprehensive gene building capabilities for custom DNA sequence design.

Purpose of the Study:

  • To introduce a novel DNA pattern design algorithm, ICRPfinder.
  • To enable the identification and creation of specific DNA patterns, including restriction enzyme recognition sites, within target coding sequences.
  • To facilitate gene engineering by allowing modifications without altering the translated amino acid sequence.

Main Methods:

  • Development of a fast DNA pattern design algorithm named ICRPfinder.
  • Application of ICRPfinder to identify and generate restriction enzyme recognition sites using silent mutations.
  • Implementation as a browser-based JavaScript application for cross-platform compatibility.

Main Results:

  • ICRPfinder successfully maps existing restriction enzyme cut sites.
  • The algorithm generates novel, unique restriction enzyme recognition sites within specified DNA regions.
  • These newly generated sites are guaranteed not to exist elsewhere in the sequence.
  • Modifications are achieved through silent mutations, preserving the original protein sequence.

Conclusions:

  • ICRPfinder is a potent tool for designing specific DNA patterns, including restriction enzyme sites.
  • It enables precise gene engineering by creating custom DNA sequences without altering protein expression.
  • The browser-based, cross-platform nature of ICRPfinder enhances its accessibility for researchers.