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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.
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Riboswitches are RNA elements that regulate gene expression by altering their secondary structures in response to specific effector molecules. These elements, located in the leader regions of certain mRNAs, act as transcriptional regulators by toggling between alternative conformations to control downstream gene expression. Riboswitch-mediated regulation is a precise mechanism for modulating biosynthetic pathways, as exemplified by the riboflavin biosynthesis pathway in Bacillus...
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Cis-regulatory Sequences02:02

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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
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C.U.R.R.F. (Codon Usage regarding Restriction Finder): a free Java(®)-based tool to detect potential restriction

Michael Gatter1, Thomas Gatter, Falk Matthäus

  • 1Institut für Mikrobiologie, Technische Universität Dresden, 01062 Dresden, Germany. Michael.Gatter1@Mailbox.TU-Dresden.de

Molecular Biotechnology
|December 14, 2011
PubMed
Summary
This summary is machine-generated.

Gene synthesis offers advantages for heterologous expression, including codon optimization and restriction site insertion. The C.U.R.R.F. software aids in identifying restriction sites within DNA and mRNA sequences.

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Area of Science:

  • Molecular Biology
  • Bioinformatics

Background:

  • Gene synthesis is increasingly popular for heterologous gene expression due to cost reduction and enhanced control.
  • Key advantages include tailoring codon usage for specific hosts and introducing desired restriction enzyme sites.

Purpose of the Study:

  • To introduce a software tool, C.U.R.R.F. (Codon Usage regarding Restriction Finder), for identifying restriction sites in synthetic gene sequences.
  • To facilitate the design of genes with optimized codon usage and specific restriction sites.

Main Methods:

  • C.U.R.R.F. is a Java-based software that detects restriction sites in coding and non-coding DNA and mRNA sequences.
  • It considers silent or non-silent mutations to introduce restriction sites.
  • The software evaluates the deviation from optimal codon usage when searching for restriction sites.

Main Results:

  • C.U.R.R.F. can identify potential restriction sites within DNA and mRNA sequences.
  • The software accounts for codon usage optimization and sequence variations.

Conclusions:

  • C.U.R.R.F. provides a valuable tool for researchers designing synthetic genes.
  • It simplifies the process of incorporating specific restriction sites while maintaining optimal codon usage for heterologous expression.