Читать книгу Chemistry and Biology of Non-canonical Nucleic Acids - Naoki Sugimoto - Страница 24

Pyrimidine–pyrimidine mismatches can be categorized in unstable mismatches (Tables 2.1 and 2.2). When pyrimidine nucleotides base pair through hydrogen bonds, C1 atom of their sugar needs to be in close position. This distorts the duplex backbone and destabilize the structure. However, several hydrogen bonding patterns within the pyrimidine–pyrimidine mismatches have been observed. T·T mismatch adopts by interconverting two base pairing patterns, both of which form two hydrogen bonds with wobble-like configuration (Figure 2.4). C·T mismatch also forms two hydrogen bonds without wobble orientation. When N3 atom of the cytosine is protonated, C·T mismatch forms two hydrogen bonds with wobble-like configuration similar to the T·T mismatch. Protonation of cytosine also enables formation of two hydrogen bonds in C·C mismatch (Figure 2.4). If two cytosines, one of which is protonated, are placed on symmetric orientation, C·C mismatch can form three hydrogen bonds. This orientation is not adopted in duplex but observed in tetraplex structure, which is known as i-motif as described in Chapter 3.

Figure 2.4 Mismatched T-T, C-T, and C-C base pairs observed in nucleic acid structures. (a) Interconvertible T-T mismatched base pairs with wobble-like orientation. (b) C-T mismatched base pairs at neutral form (upper) and a form, in which cytosine nucleobase is protonated (lower). (c) C-C⁺ mismatched base pairs at wobble-like orientation (upper) and symmetric orientation (lower).