Hoogsteen binding

Castellano, R.K., Gramlich, V. and Diederich, F. (2002) Rebekimides and their adenine complexes Preferences for Hoogsteen binding in the solid state and in solution. Chemistry - A European Journal, 8, 118-129 and references therein. 

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. 

Fig. 4.3 Triplex invasion by homopyrimidine PNA oligomers. One PNA strand binds via Watson-Crick base pairing (preferably in the antiparallel orientation), while the other binds via Hoogsteen base pairing (preferably in the parallel orientation). It is usually advanta-...

Figure 11.6. A TAT triplet showing the positioning of the three grooves and the neomycin binds to the larger triplex Watson-Hoogsteen (W-H) groove.

Triplex formation with cytosine containing PNAs (or oligonucleotides) requires N3 protonation of cytosine (Scheme 2) and is therefore only efficient at acidic pH (pH <6). However, substituting pseudoisocytosine for cytosine in the Hoogsteen strand of bis-PNAs in triplex recognition gives pH independent binding, because pseudoisocytosine mimics the proto-nated cytosine. The synthesis of pseudoisocytosine is shown in Scheme 5.[25]... 

Hoogsteen face The Hoogsteen face refers to a part of nucleo-bases that is exposed along the major groove of DNA. The Hoogsteen face is a potential site of interaction with other molecules and especially useful for binding of a third oligonucleotide strand to form a triple helix. 

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... 

---