Hoogsteen mode

PNA may be systematically modified to incorporate varied functionality. The two distinct portions of PNA, nucleobase and backbone, can both accommodate alterations. Nucleobase modifications affect a PNA s ability to bind DNA in a sequence-specific manner. A pseudoisocytosine nucleobase has been successfully incorporated in PNAs designed to bind DNA as a triple helix [31]. This nucleobase mimics a protonated cytosine and effectively binds DNA in the Hoogsteen mode. 

Figure 71. Ri t adenine-uracil, Hoogsteen left guanine-(protonated) cytosine, Hoogsteen. In order to pair in a Hoogsteen (or revose-Hoogsteen) mode, the p-RNA backbone would have to adjust by conformational deformation.

Changes in the free energy of hydration and its electrostatic and steric components (kcal/mol) for the dimerization of adenineilhymine (in Watson-Crick and Hoogsteen modes) and guaninercytosine (Watson Crick pairing)... 

We have modeled the interaction of adenine (198) with synthetic receptors 199 and 200 assuming Watson-Crick (WC) 201 and Hoogsteen 202 interactions [179], The receptors were replaced by simpler models, 203 and 204, for the B3LYP/6-31+G calculations. The different binding modes between pyridine 203 and 1,8-naphthyridine 204 derivatives with adenine were compared to those of the latter with uracil and cytosine. The dispositions of the calculated complexes indicate that the synthetic receptors with two pyridine moieties are able to interact simultaneously with two different parts of the adenine molecule. In contrast, those receptors... 

Rebek s second generation of self-replicating molecules [59] which restrain the preassociative bimolecular pathway is a diaminocarbazole-based diimide, a nearly ideal complement to the purine nucleus of adenine. Conformational complications from the switching bound adenine between Watson-Crick and Hoogsteen binding modes are eliminated. 

J5. In the allopyranosyl series thae is an intrinsic preference f( pairing mode which (vay probably) is revo se-Hoogsteen. 

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