G • U mismatches

Chow CS, Barton JK. Recognition of G-U mismatches by tris(4,7-diphenyl-l,10-phenanthroline)rhodium(III). Biochemistry 1992 31 5423-9. 

Chow CS, Cunningham PR, Lee KS, Meroueh M, SantaLucia J Jr, Varma S. Photoin-duced cleavage by rhodium complex at G U mismatches and exposed guanines in large and small RNAs. Biochimie 2002 84 859-68. 

Pol L also has the unprecedented ahility to misinsert dGMP opposite a template T at a rate that exceeds that of correct dAMP incorporation. Furthermore, on templates that contain two or more consecutive Ts, preferential dGMP incorporation opposite the first T is followed by preferential incorporation of A opposite the second template T. This remarkable specificity led us to speculate that Pol l may function in a specialized BER reaction, replacing dGs that are inadvertently removed by a DNA glycosylase from G—T or G—U mismatches that arise by deamination of 5-methyl-cytosine or cytosine (Bebenek et at, 2001). 

Bardwell, P. D., Martin, A., Wong, E., Li, Z., Edehnann, W., and Scharff, M. D. (2003). Cutting edge The G-U mismatch glycosylase methyl-CpG binding domain 4 is dispensable for somatic hypermutation and class switch recombination./. Immunol. 170, 1620-1624. 

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. 

This application exemplifies how theoretical methods were used to extend the MC-SYM database. The symmetrical tandem of G U mismatches is a motif that was identified in ribosomal RNAs. The secondary structure and a selected spanning tree of the motif are shown in Figure 11. The list of possible G U base pairing patterns that involve two hydrogen bonds are shown in Table 5. Two of these patterns, XXVII (reverse Wobble) and XXVIII (Wobble), were described in Saenger and both were found in RNA and DNA X-ray crystallography and NMR spectroscopy three-dimensional structures. 

Figure 11 Symmetrical tandem of G U mismatches, (a) Secondary structure. The arrows indicate the selected edges in the spanning tree, (b) MC-SYM script corresponding to the spanning tree in (a). The ANY-ANY list corresponds to combinations of C3 -, C2 -endo, anti, and syn nucleotide conformations. The XXVII relational list corresponds to the reverse Wobble G U base pairing pattern (see Table 5). The indicates that all examples of a given list are tested by MC-SYM...

Using the new database, MC-SYM produced consistent three-dimensional structures that contained the reverse Wobble, the Wobble, and the XXXI G U base pairing patterns. The three MC-SYM three-dimensional structures of symmetrical tandem of G U mismatches, refined using AMBER 4.1, are shown in Figure 12. In the case of class structures that include the reverse Wobble base pairing pattern, the guanosines were... 

Figure 12 Stereoviews of three three-dimensional structures of symmetrical tandem of G U mismatches generated by MC-SYM. (a) Class containing the reverse Wobble base pairing pattern, (b) Class containing the Wobble base pairing pattern, (c) Class containing the theoretical XXXI base pairing pattern, and the cross-strand stacking motif...

Barrett, T. E., Savva, R., Panayotou, G., Barlow, T., Brown, T.,Jiricny, J., and Pearl, L. H. (1998). Crystal structure of a G T/U mismatch-specific DNA glycosylase Mismatch recognition by complementary-strand interactions. Cell 92, 117-129. 

Grzella I, Muller BW, Oades RD, Bender S, Schall U, Zerbin D, Wolstein J, Sartory G. 2001. Novelty-elicited mismatch negativity in patients with schizophrenia on admission and discharge. J Psychiatry Neurosci 26 235-246. 

Methylation and Spontaneous Deamination Can Result in a C C A T Mutation Ccnnplete Repair of U C and T G Mismatches... 

Figyre 11. Activities of enzymes that remove inappropriate bases from DNA- The specific activities of uracil DMA glycosidase (black bars) and thymine ONA glycosidase (open bars) were measured in extracts of colon mucosa. Extracts were prepared from seven normal human subjects [subjects A to Q. To the extracts were added synthetic strands of double-stranded DNA that contained a mismatched U G pair or a mismatched T G pair. The unit of specific activity used was nmol/mg protein/min. The resuJts show, at least in tissue extracts, that the removal of U occurs at a dramatically greater rate than the removal ofT-... 

Schmuiie, C, Vang, A, S-, Beart, R. W., and Jones, R A. (1995). Base CKcision repair of U G mismatches at a mutational hotspot in the p53 gene is more efficient than base excision repair of T G mismatches in extracts of human colon tumors. Cancer Rei. 55,3742-3746. 

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