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Saturation mutagenesis is commonly achieved by site-directed mutagenesis PCR with a randomised codon in the primers (e.g. SeSaM) [2] or by artificial gene synthesis, with a mixture of synthesis nucleotides used at the codons to be randomised. [3] Different degenerate codons can be used to encode sets of amino acids. [1]
Degeneracy or redundancy [1] of codons is the redundancy of the genetic code, exhibited as the multiplicity of three-base pair codon combinations that specify an amino acid. The degeneracy of the genetic code is what accounts for the existence of synonymous mutations . [ 2 ] :
Codon usage bias in Physcomitrella patens. Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA.A codon is a series of three nucleotides (a triplet) that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation (stop codons).
Early attempts at mutagenesis using radiation or chemical mutagens were non-site-specific, generating random mutations. [2] Analogs of nucleotides and other chemicals were later used to generate localized point mutations, [3] examples of such chemicals are aminopurine, [4] nitrosoguanidine, [5] and bisulfite. [6]
The Codon Adaptation Index (CAI) [1] is the most widespread technique for analyzing codon usage bias.As opposed to other measures of codon usage bias, such as the 'effective number of codons' (Nc), which measure deviation from a uniform bias (null hypothesis), CAI measures the deviation of a given protein coding gene sequence with respect to a reference set of genes.
LMNA missense mutation (c.1580G>T) introduced at LMNA gene – position 1580 (nt) in the DNA sequence (CGT) causing the guanine to be replaced with the thymine, yielding CTT in the DNA sequence. This results at the protein level in the replacement of the arginine by the leucine at the position 527. [ 6 ]
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The two other start codons listed by table 1 (GUG and UUG) are rare in eukaryotes. [3] Prokaryotes have less strigent start codon requirements; they are described by NCBI table 11 . B ^ ^ ^ The historical basis for designating the stop codons as amber, ochre and opal is described in an autobiography by Sydney Brenner [ 4 ] and in a historical ...