Mutation base pairing

Mutation Escherichia coli WP2 tryptophan reversions Point mutations (base-pair substitutions) <3 wk L L M M... 

Salmonella typhimurium TA1535 his uvrB rfa — Reverse mutation base-pair substitution... 

Salmonella typhimurium TA100 his uvrB rfa pKMIOl Reverse mutation base-pair substitution and some... 

Salmonella typhimurium TA100, TA1535 TA98, TA1537, TA1538 Reverse mutations Base pair substitutions Frame shift mutations - - De Flora 1981 Petrilli and De Flora 1978b Chromium trichloride hexahydrate, chromium nitrite, monohydrate, chromium potassium sulfate, chromium acetate, neochromium, chromium alum, chromite... 

Perhaps the most widely used assay for mutagenic potential is the Ames test (Ames etal., 1973, 1975 Ames, 1979). In this test the compound under investigation is studied for its ability to bring about a reverse mutation in bacteria. The bacterial tester strains are selected to detect two types of mutation base-pair substitution (TA 1535, TA 100) and frameshift (TA 1537, TA 1538, TA 98). Generally, the assay is carried out in the presence and absence of an enzyme preparation (S-9) isolated from rodent liver in order to study the mutagenicity of potential metabolites. 

RUM H., Nielsen P.E., Egholm M., Berg R.H., Buchardt O., Stanley C. Single base pair mutation analysis by PNA directed PCR clamping. Nucleic Acids Res. 1993 21 5332-5336. 

Rephcation errors, even with a very efficient repair system, lead to the accumulation of mutations. A human has 10 nucleated cells each with 3 X 10 base pairs of DNA. If about 10 cell divisions occur in a lifetime and 10 mutations per base pair per cell generation escape repair, there may evenmaUy be as many as one mutation per 10 bp in the genome. Formnately, most of these will probably occur in DNA that does not encode proteins or will not affect the function of encoded proteins and so are of no consequence. In addition, spontaneous and chemically induced damage to DNA must be repaired. 

Figure 36-22. Mismatch repair of DNA. This mechanism corrects a single mismatch base pair (eg, C to A rather than T to A) or a short region of unpaired DNA. The defective region is recognized by an endonuclease that makes a single-strand cut at an adjacent methylated GATC sequence. The DNA strand is removed through the mutation, replaced, and religated.

Resistance to certain antibiotics can arise as a consequence of mutations to chromosomal genes because of changes in the DNA sequence. Mutations can occin due to single base pair changes. Transitions involve the substitution of one purine (A or G) for another and therefore one pyrimidine (C or T) for another. Transversions involve a change from a pyrimidine to a purine and vice versa. Frameshift mutations occin when one or... 

The extraordinary complexity of human genes and their products has encouraged the development of extremely high-resolution analytical methods.75 Capillary electrophoresis is competitive with slab gel methods, with resolution up to the order of about 1,000 base pairs for sequencing, sizing, and detection of mutation. Reversed phase HPLC is useful for restriction digest mapping and MALDI-MS up to about 1000 base pairs. 

DNA mismatch repair genes Genes that identify and correct errors in DNA base pairs during DNA replication. Mutations in the mismatch repair genes can lead to cancer by allowing abnormal cells to continue to grow. 

Finally, Santiago et al. (47) demonstrated that lymphocyte chemoattraction induced by rheumatoid arthritis synovial fluid is independent of CCR5. They showed that T cells from individuals with CCR5 delta 32 mutation (a 32-base-pair frameshift deletion resulting in absent CCR5 expression) migrate normally to chemokines present in the synovial fluids of RA patients (47). 

Eighty distinct mutations in type I AT deficiency, ranging from single nucleotide substitutions, to deletion or insertion of a small number of nucleotides of 22 base pairs or less, to major deletions of either a part of or the entire AT gene, have been recognized (83). 

More than 160 different mutations have been described for the protein C gene, which has nine exons ranging in size from 53 to 587 base pairs, separated by 8 in-trons ranging in size from 92 to 2668 base pairs (89). These mutations can result in a defective or even absent protein C molecule. Mutations that lead to reduced amounts of protein C molecule without accompanying evidence for an abonormal protein C molecule in the circulation are characterized as causing type I deficiency. Type II deficiency is represented by mutations that lead to the production of more or less normal amounts of defective protein C molecule (89). 

Figure 6. The c-mos negative regulatory element (NRE). Nucleotide positions of the NRE are shown relative to the spermatocyte transcription start site, taken as 280 base pairs upstream of the c-mos ATG (see Fig. 4). The endpoints of the NRE are defined by deletions that allow c-mos expression in NIH 3T3 and other somatic cells. Mutations of the sequences designated by boxes 1,2, and 3 also allow c-mos transcription in NIH 3T3 cells, indicating that these sequences represent functional elements within the NRE. Boxes 1 and 2 are similar to sequences upstream of the protamine (Prot) promoter that inhibit in vitro transcription in HeLa cell extracts. A sequence just upstream of box 2 is also similar to a putative repressor-binding site in the regulatory region of Pgk2.

The innate sensitivity of DNA-mediated CT to perturbations in the TT-stack has prompted us to employ this chemistry as a probe of stacking structure and dynamics. We have developed a new class of DNA-based diagnostic tools that diagnose DNA mutations such as single base-pair mismatches and lesions, analyze DNA-protein interactions, and probe the sequence-depen-dent dynamics and flexibility of DNA. These applications rely on electrochemical probing of CT in DNA films self-assembled on gold electrodes. 

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