Watson-Crick base-pairing alteration

The tautomers of cytosine have also been examined with continuum solvation methods. Both Miertus-Scrocco-Tomasi (MST) and PCM computations predict that 13a is the lowest energy conformer in aqueous solution. This is consistent with the explicit water computations. Aqueous solvation, therefore, substantially alters the relative energies of the tautomers of cytosine. The canonical representation of cytosine 13a, the tautomer invoked in Watson-Crick base pairing, is in fact the most favorable tautomer in solution, but not in the gas phase. 

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]. 

The 3 terminal redundancy of the genetic code and its mechanistic basis were first appreciated by Francis Crick in 1966. He proposed that codons and anticodons interact in an antiparallel manner on the ribosome in such a way as to require strict Watson-Crick pairing (that is, A-U and G-C) in the first two positions of the codon but to allow other pairings in its 3 terminal position. Nonstandard base pairing between the 3 terminal position of the codon and the 5 terminal position of the anticodon alters the geometry between the paired bases Crick s proposal, labeled the wobble hypothesis, is now viewed as correctly describing the codon-anticodon interactions that underlie the translation of the genetic code. 

Figure 7.3 Analysis of the 4H four-way RNA junction of the human U1 snRNA by comparative gel electrophoresis (Duckett et al., 1995). The central sequence of the junction is shown. The A G pair at the center was retained in this analysis, although changing it to a Watson—Crick pair did not alter the global shape of the junction. The six long—short species can be considered to be derived from a junction with four arms of 40 bp. The central 20 bp comprises RNA, and the outer arms are DNA. The junction species were electrophoresed in an 8% polyacrylamide gel, in 90 mM Tris—borate (pH 8.3) and 1 mM Mg2+. The mobility pattern of the six species is slow, slow, fast, fast, slow, slow. The simplest interpretation (shown on the right-hand side) is that of a stacked structure based on A on D and B on C coaxial stacking, with the axes nearly perpendicular. The pattern would also be consistent with a rapid exchange between nearly equal populations of parallel and antiparallel forms. However, a recent crystal structure has found a perpendicular stacked structure for this RNA junction (Pomeranz-Krummel et al., 2009).

One problem for targeting RNA is that the A U and G U base pairs have similar stability, and G U wobble pairs account for almost half of known non-Watson-Crick pairs. 2-Thiouridine will increase the specificity for pairing with adenosine by a factor of 10. It has been reported that the complete substitution of pyrimidines by C5-propynyl pyrimidines enhances this specificity 100-fold without altering base pairing specificity. " ... 

Watson-Crick hydrogen bonding in natural base pairs is essential for most of the DNA functions. Initial effort was made largely to expand the genetic alphabet using altered hydrogen bonding. Benner and coworkers pioneered a way to enzymatic... 

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