Mismatch Watson-Crick base pairs

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. 

Mismatch repair. The replacement of a base in a heteroduplex structure by one that forms a Watson-Crick base pair. 

In nature, base pairs of the Watson-Crick type prevail [674] as described in the previous sections. However, there are some well-documented structures where other base pairs occur. In one type, illustrated in Fig. 20.4, the bases are in the canonical keto/amino forms but base pairs are in mismatch configurations called wobble base pairs [675]. They occur even systematically in interactions between messenger RNA (mRNA) and transfer RNA (tRNA), and appear to play a role in mutation processes during DNA replication. Another type of non-Watson-Crick base pairs is found if the bases occur in rare enol/imino forms. These are also believed to be involved in mutation processes, albeit by a mechanism other than wobble base pairs, vide infra. 

The simplest and most common stmctural motif formed is a stem-loop, created when two complementary sequences within a single strand come together to form double-helical structures (Figure 5.19). In many cases, these double helices are made up entirely of Watson-Crick base pairs. In other cases, however, the stmctures include mismatched or unmatched (bulged) bases. Such mismatches destabilize the local structure but introduce deviations from the standard double-helical stmcture that can be important for higher-order folding and for function (Figure 5.20). 

The replicative DNA polymerases themselves are able to correct many DNA mismatches produced in the course of replication. For example, the subunit of E. co/i DNA polymerase III functions as a 3 -to-5 exonuclease. This domain removes mismatched nucleotides from the 3 end of DNA by hydrolysis. How does the enzyme sense whether a newly added base is correct As a new strand of DNA is synthesized, it is proojread. If an incorrect base is inserted, then DNA synthesis slows down owing to the difficulty of threading a non-Watson-Crick base pair into the polymerase. In addition, the mismatched base is weakly bound and therefore able to fluctuate in position. The delay from the slowdown allows time for these fluctuations to take the newly synthesized strand out of the polymerase active site and into the exonuclease active site (Figure 28.41). There, the DNA is degraded, one nucleotide at a time, until it moves back into the polymerase active site and synthesis continues. 

The crystal structure of the duplex [r(guauaca)dC]2, which would be expected to form a self-complementary duplex with an AC mismatch, has been solved and instead shown to form only six Watson-Crick base pairs with two 3 -overhang-ing bases. There are two independent duplexes, each of which is bent, and which stack end to end to form a right-handed super-helix. The overhanging nucleotides are looped out of the structure, with the penultimate adenosine residues forming A-GC base triples. 

DNA duplex. Naegeli et al. have previously advanced a bipartite model of NER substrate discrimination that is initiated by the detection of disrupted Watson-Crick base-pairing followed by a lesion-sensing step that verifies the presence of a chemically altered nucleotide [29, 33]. The nature of the critically important verification step that leads to the dual incision is still not well understood [24]. The bipartite model is consistent with previous observatisons of Sugasawa et al. who found that XPC/HR23B binds to DNA that contains bubbles of several mismatched DNA bases in the absence of lesions or chemically modified nucleotides, but incisions occur only when a chemically modified base is also present [13, 35]. 

Figure 14.6 The shape of the syn-(+)-trans-anti-B[a]PDE-N2-dG dATP mismatch pair mimics that of a normal anti-T dATP Watson-Crick base pair (adapted with permission from [69], Figure 9, Copyright 2001, Elsevier). The B[o]P-modified guanine is shown in gray and the hypothetical thymine is shown in black. HB, hydrogen bond.

Mismatches, or non-Watson-Crick base pairs in a DNA duplex, can arise through the following... 

Mismatched bases (bases that do not form normal Watson-Crick base pairs) are recognized by enzymes of the mismatch repair system. Because neither of the bases in a mismatch is damaged, these repair enzymes must be able to determine which base of the mispair to correct. 

In addition to the standard Watson-Crick base pairing it has recently been discovered that thymine can selectively bind to mercuric ion (Hg ) via the formation of a thymine-Hg -thymine (T-Hg -T) complex (72). The presence of the Hg at the thymine-thymine mismatch leads to a significant increase ( 10°C) in the T . Mirkin and coworkers (40) incorporated this T-Hg "-T coordination chemistry in the DNA-AuNP system to design a novel colorimetric assay for detecting Hg " "(Fig. 12.15). In a typical assay, two batches of AuNPs were functionalized with two complementary sequences, respectively, and combined to form aggregates. 

Internal Loops in RNA Oligomer Crystals. The first crystal structure of an RNA internal loop was solved in 1991(8). The dodecamer rGGACUUCGGUCC (internal loop underlined) forms a duplex in the crystal with an internal loop of consecutive U-G, U-C, C-U and G-U mismatches as shown in Figure 2. The chains of the double helix show two-fold symmetry in the crystal, thus the U-G and U-C pairs are identical to the C-U and G-U pairs. As can be seen, the internal loop generally continues the double helices which surround it by formation of non-Watson-Crick base pairs. The major groove of the A-form helix is opened with respect to a canonical RNA helix. 

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