Abstract
BackgroundRestriction enzymes can produce easily definable segments from DNA sequences by using a variety of cut patterns. There are, however, no software tools that can aid in gene building -- that is, modifying wild-type DNA sequences to express the same wild-type amino acid sequences but with enhanced codons, specific cut sites, unique post-translational modifications, and other engineered-in components for recombinant applications. A fast DNA pattern design algorithm, ICRPfinder, is provided in this paper and applied to find or create potential recognition sites in target coding sequences.ResultsICRPfinder is applied to find or create restriction enzyme recognition sites by introducing silent mutations. The algorithm is shown capable of mapping existing cut-sites but importantly it also can generate specified new unique cut-sites within a specified region that are guaranteed not to be present elsewhere in the DNA sequence.ConclusionICRPfinder is a powerful tool for finding or creating specific DNA patterns in a given target coding sequence. ICRPfinder finds or creates patterns, which can include restriction enzyme recognition sites, without changing the translated protein sequence. ICRPfinder is a browser-based JavaScript application and it can run on any platform, in on-line or off-line mode.
Highlights
Restriction enzymes can produce definable segments from DNA sequences by using a variety of cut patterns
Restriction enzymes in genetic engineering Restriction enzymes and methylase are components of a bacterial mechanism aimed at resisting attack from bacteriophages and removing foreign viral DNA sequences
We describe several key aspects of the ICRPfinder algorithm and provide sample results using ICRPfinder to find or create restriction enzyme recognition sites in target coding sequences
Summary
ICRPfinder is applied to find or create restriction enzyme recognition sites by introducing silent mutations. The algorithm is shown capable of mapping existing cut-sites but importantly it can generate specified new unique cut-sites within a specified region that are guaranteed not to be present elsewhere in the DNA sequence
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