Removing the redundancy from randomised gene libraries

Marcus D. Hughes*, David A. Nagel, Albert F. Santos, Andrew J. Sutherland, Anna V. Hine

*Corresponding author for this work

Research output: Contribution to journalArticle

Abstract

Amino acid substitution plays a vital role in both the molecular engineering of proteins and analysis of structure-activity relationships. High-throughput substitution is achieved by codon randomisation, which generates a library of mutants (a randomised gene library) in a single experiment. For full randomisation, key codons are typically replaced with NNN (64 sequences) or NNG CorT (32 sequences). This obligates cloning of redundant codons alongside those required to encode the 20 amino acids. As the number of randomised codons increases, there is therefore a progressive loss of randomisation efficiency; the number of genes required per protein rises exponentially. The redundant codons cause amino acids to be represented unevenly; for example, methionine is encoded just once within NNN, whilst arginine is encoded six times. Finally, the organisation of the genetic code makes it impossible to encode functional subsets of amino acids (e.g. polar residues only) in a single experiment. Here, we present a novel solution to randomisation where genetic redundancy is eliminated; the number of different genes equals the number of encoded proteins, regardless of codon number. There is no inherent amino acid bias and any required subset of amino acids may be encoded in one experiment. This generic approach should be widely applicable in studies involving randomisation of proteins. © 2003 Elsevier Ltd. All rights reserved.

Original languageEnglish
Pages (from-to)973-979
Number of pages7
JournalJournal of Molecular Biology
Volume331
Issue number5
DOIs
Publication statusPublished - Aug 2003

Fingerprint

Gene Library
Codon
Random Allocation
Amino Acids
Genetic Code
Protein Engineering
Proteins
Amino Acid Substitution
Structure-Activity Relationship
Methionine
Genes
Libraries
Arginine
Organism Cloning

Keywords

  • codon
  • library
  • randomisation
  • zinc finger

Cite this

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title = "Removing the redundancy from randomised gene libraries",
abstract = "Amino acid substitution plays a vital role in both the molecular engineering of proteins and analysis of structure-activity relationships. High-throughput substitution is achieved by codon randomisation, which generates a library of mutants (a randomised gene library) in a single experiment. For full randomisation, key codons are typically replaced with NNN (64 sequences) or NNG CorT (32 sequences). This obligates cloning of redundant codons alongside those required to encode the 20 amino acids. As the number of randomised codons increases, there is therefore a progressive loss of randomisation efficiency; the number of genes required per protein rises exponentially. The redundant codons cause amino acids to be represented unevenly; for example, methionine is encoded just once within NNN, whilst arginine is encoded six times. Finally, the organisation of the genetic code makes it impossible to encode functional subsets of amino acids (e.g. polar residues only) in a single experiment. Here, we present a novel solution to randomisation where genetic redundancy is eliminated; the number of different genes equals the number of encoded proteins, regardless of codon number. There is no inherent amino acid bias and any required subset of amino acids may be encoded in one experiment. This generic approach should be widely applicable in studies involving randomisation of proteins. {\circledC} 2003 Elsevier Ltd. All rights reserved.",
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Removing the redundancy from randomised gene libraries. / Hughes, Marcus D.; Nagel, David A.; Santos, Albert F.; Sutherland, Andrew J.; Hine, Anna V.

In: Journal of Molecular Biology , Vol. 331, No. 5, 08.2003, p. 973-979.

Research output: Contribution to journalArticle

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