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Basic Molecular Cloning of DNA and RNA
Published in Jay L. Nadeau, Introduction to Experimental Biophysics, 2017
Polymerases make mistakes, inserting the wrong base pair (a transition if it substitutes a purine for a purine or a pyrimidine for a pyrimidine, a transversion if it substitutes a purine for a pyrimidine or vice versa); failing to insert one or more base pairs (a deletion); or inserting one or more extra base pairs (an insertion). All of these are called mutations, and the mutation rate varies among polymerases: from about 4 × 10−7 errors per base pair per cycle for high-fidelity polymerases, to 2 × 10−5 per base pair per cycle for typical commercial Taq polymerase, to 5 × 10−3 per base pair per cycle for error-prone polymerase. Because of the degeneracy of the amino acid code, a single nucleotide error, called a point mutation, may not change the resulting protein; this is a silent mutation. If a different amino acid is substituted, it is called a missense mutation. These may change the protein’s function very little or tremendously, depending upon the location and the degree of change. The insertion of a stop codon leads to a truncated protein and is called a nonsense mutation (Figure 2.16). The insertion or deletion of 1 or 2 base pairs leads to a frameshift mutation, changing the encoding of all of the amino acids downstream of the error.
Genetic toxicology
Published in Chris Winder, Neill Stacey, Occupational Toxicology, 2004
A gene is the simplest functional unit in a DNA molecule, and gene (or point) mutations are changes in the nucleotide sequence at one or a few coding segments. Base pair or base substitution mutations occur when one nucleotide base is replaced with another; frameshift mutations occur through the addition or deletion of one or more bases, which alters the sequences of bases in DNA, and, hence, the reading frame in RNA. These changes may occur at the site of the original mutation or at a second site on the chromosome. Missense mutations are gene mutations that specify the insertion of an ‘incorrect’ amino acid into a polypeptide and usually result in impaired function of the affected cell or organism. Nonsense mutations introduce terminator codons into the DNA, resulting in the premature cessation of polypeptide synthesis, which is usually associated with complete loss of function of the altered gene. Forward mutations lead to loss of normal function of a gene product; reverse, or back, mutations restore the normal function of the gene.
Glossary of scientific and technical terms in bioengineering and biological engineering
Published in Megh R. Goyal, Scientific and Technical Terms in Bioengineering and Biological Engineering, 2018
Nonsense mutation is a mutation which converts an amino-acid-specifying codon into a stop codon, e.g., a change from UAU (tyr) to UAG (amber) would lead to the premature termination of a polypeptide chain at the place where a tyrosine was inserted in the wild-type.
GASN: gamma distribution test for driver genes identification based on similarity networks
Published in Connection Science, 2023
Dazhi Jiang, Runguo Wei, Zhihui He, Senlin Lin, Cheng Liu, Yingqing Lin
Notice that most existing methods to evaluate the functional impact of mutations always focus on non-synonymous somatic mutations, such as mutation suppressors, polymers, and screening factors. Synonymous mutations and some mutations affect proteins. If nonsense mutations and small index fission deletion, the average FIS of mutations with silencing and ineffective effects cannot be calculated from the mutant synthon. In general, silent, non-coding, non-silent, and null mutations have a progressively more significant effect on proteins. Silent mutation does not affect the amino acids of protein sequence, and its FIS should be the smallest. Although non-coding mutation does not change amino acids, it will promote the development of cancer cells. For example, the non-coding mutation in the 3'-untranslated region (3'-UTR) can change the binding efficiency of microRNA (miRNA), resulting in the loss/increase of gene function (Akdeli et al., 2014). The non-silent mutation changes the amino acid sequence of the protein and has a significant functional impact on protein, accelerating tumour progression. For example, the R132 mutation in the IDH1 gene was found to be associated with early glioma formation (Cui et al., 2016). Null mutation, including “nonsense mutation”, “splice site”, “frameshift insertion”, and “frameshift deletion” will lead to continuous changes in amino acid sequences and have a more significant impact on organisms. For example, Waldenberg syndrome is caused by splicing mutation of PAX3 (Barber et al., 1999), and exon mutation is caused by nonsense/frameshift mutation of DMD gene, resulting in Becker muscular dystrophy (Al-Zaidy et al., 2015). Based on the above analysis, when the average FIS effect t cannot be calculated, the deletion FIS of mutation r with mutation effect t can be obtained as shown in Equation (4): The observed FIS of gene is obtained by accumulating the FIS of all mutation effects t of cumulative mutation r as follows: where is the total number of all mutation effects of mutation r.