Mismatched base pairs

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.

Modulation of DNA structure and dynamics is also possible using base-pair mismatches. Mismatches exert little influence on the global structure of B-DNA duplexes. Locally, the extent of base stacking perturbation depends sensitively on the nature of the mismatch [139-141]. Therefore, while a CA mismatch introduces a significant distortion in local stacking, the well-stacked GA mismatch is, by many criteria, barely perceptible. The dynamics of mismatched base-pairs may also be significantly distinct from matched Watson-Crick base pairs [9]. We exploit these features of DNA mismatches to probe the sensitivity of DNA-mediated CT to base structure and dynamics. 

Fluorescence probes possessing the PyU base 46 selectively emit fluorescence only when the complementary base is adenine. In this case, the chromophore of is extruded to the outside of the duplex because of Watson-Crick base pair formation, and exposed to a highly polar aqueous phase. On the contrary, the duplex containing a PyU/N (N = G, C and T) mismatched base pair shows a structure in which the glycosyl bond of uridine is rotated to the syn conformation. In this conformation, the fluorophore is located at a hydrophobic site of the duplex. The control of base-specific fluorescence emission is based on the polarity change in the microenvironment where the fluorophore locates are dependent on the l>yU/A base-pair formation. 

Hereditary nonpolyposis colorectal cancer results from a deficiency in the ability to repair mismatched base pairs in DNA that are accidentally introduced during replication. 

This multiprobe RPA offers the advantages of its sensitivity and capacity to simultaneously quantitate several mRNA species in a single sample of total RNA. This allows comparative analysis of different mRNA species within samples, moreover, by incorporating probes for housekeeping gene transcripts, the levels of individual mRNA species can be compared between samples. Furthermore, the assay is highly specific and quantitative owing to the RNase sensitivity of mismatched base pairs and the use of solution-phase hybridization driven toward completion by excess probe. Finally, the multiprobe RPA can be performed on total RNA preparations derived by standard methods from either frozen tissues or cultured cells. 

The fluorescence of 2AP is strongly quenched by nucleic acid bases [17, 18, 24-29]. Time-correlated single-photon counting studies have shown that the interactions of 2AP with different nucleic acid bases significantly decrease the 2AP fluorescence hfetime [17, 24-29]. While the fluorescence lifetime of free 2AP in aqueous solution is about 10 ns, in double-stranded DNA the 2AP hfetimes are reduced to 30-50 ps. This effect has been used extensively to study the dynamics of mismatched base pairs [19, 21, 25, 30], local changes in dynamics of DNA molecules produced by their binding to the active sites of polymerases [26, 31-33], stacking interactions at abasic... 

When base selection and proofreading are combined, DNA polymerase leaves behind one net error for every 106 to 108 bases added. Yet the measured accuracy of replication in E. coli is higher still. The additional accuracy is provided by a separate enzyme system that repairs the mismatched base pairs remaining after replication. We describe this mismatch repair, along with other DNA repair processes, in Section 25.2. 

A final check of the fidelity of replication is made after a new strand has been formed. Mismatched base pairs are identified, and the incorrect nucleotides are cut out and replaced by correct ones.655 670 681 683 Some of the thymine dimers created by the action of light are also repaired photochemically by photolyases (see Chapter 23). Photoreactivation was the first DNA repair process recognized.684 However, most thymine... 

The combination of Raman spectroscopy and Raman optical activity provides spectral signatures to assess valuable information on RNA structural motifs in the encephalomyocarditis virus (EMCV). Raman and ROA spectra were collected for RNA oligonucleotides to investigate contributions of helix, tetraloop, mismatch base pairs, and asymmetric bulge structures of the RNA... 

The discovery of sequence alterations can be accomplished by the creation of mismatched base pairs, which occur when a test sample containing a sequence alteration is denatured and re-annealed with an otherwise complementary normal control sequence. The routine and specific discovery of these mismatches and their localization to within an easily sequenced region is the goal of several techniques. There are two general methods for identification of mismatched sequences ... 

This set of methods makes use of specific enzymes to recognize mismatched base pairs in heteroduplexed DNA strands. In general a test sample is amplified and heat denatured in the presence of a normal control sample. This combination of test and normal control samples is allowed to slowly reanneal forming a mixture of homo and heteroduplexes. The mixture is then exposed to any one of a number of enzymes, which recognize mismatched base pairs at various efficiencies and the sample is then analyzed for these recognized mismatches. There are several types of enzymes and assays available which purport to recognize mismatched base pairs in a heteroduplex or secondary structures formed by mismatches. A short selection of these enzymes and assays are listed below ... 

A.K. Singh et al., Mismatch base pairing of the mutagen 8-oxoguanine and its derivatives with adenine A theoretical search for possible antimutagenic agents. Int. J. Quantum Chem. 102, 343-351 (2005)... 

Fig. 4.2.6. A fluorophore that serves as fluorescent base surrogate is forced to intercalate adjacent to the expected mutation site. This forced intercalation enables detection of mismatched base pairs even within a formed duplex.

Finally, the Tm of a DNA depends on how well its bases match up. A synthetic DNA double strand made with some mismatched base-pairs has a lower Tm compared to a completely double-stranded DNA. This last property is important in using DNA from one species to detect similar DNA sequences of another species. For example, the DNA coding for an enzyme from human cells can form double helices with mouse DNA sequences coding for the same enzyme however, the mouse-mouse and human-human double strands will both melt at a higher temperature than will the human-mouse hybrid DNA double helices. 

Spontaneous DNA Damage Hydrolysis of the A-glycosyl bond between deoxyribose and a purine in DNA creates an AP site. An AP site generates a thermodynamic destabilization greater than that created by any DNA mismatched base pair. This effect is not completely understood. Examine the structure of an AP site (see Fig. 8-33b) and describe some chemical consequences of base loss. 

Tautomeric enol and imino forms of bases occur only rarely, and can lead to mutations. It should be emphasized that in none of the above described mismatch base pairs is there any evidence for the existence of rare tautomeric forms. For the A-C pair, protonation at (adenine)N(l) appears more probable than the imino form (Fig. 20.6). However, conclusive evidence is still lacking because hydrogen atoms cannot be located at the attainable resolution of about 2 A. Moreover, in none of the crystal structures of the nucleosides and nucleotides or of the bases themselves is there any evidence of the enol-imino tautomers (Part II, Chaps. 15, 16, 17). 

Fig. 20.7. Some mismatch base pairs with rare imino and enol tautomeric bases (marked ) likely to be involved in transition and transversion mechanism. For more possibilities, see [522, 678] atomic designation as Fig. 20.4...

Brown T, Kennard O, Kneale G, Rabinovich D (1985) High resolution structure of a DNA helix containing mismatched base pairs. Nature (Lond) 315 604- 606... 

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