Hoogsteen interactions

Figure 25 Structure of an individual G-tetrad showing the Hoogsteen interactions between the base pairs.

Three classes of nucleic acid triple helices have been described for oligonucleotides containing only natural units. They differ according to the base sequences and the relative orientation of the phosphate-deoxyribose backbone of the third strand. All the three classes involve Hoogsteen or reverse Hoogsteen-like hydrogen bonding interaction between the triple helix form-... 

Fig. 5. Possible base-pairing interactions for the quadruplex homodimer. Hoogsteen pairings of the parallel stranded PtDNA duplex requires protonation of the GC pair. Adapted from Ref. (28).

Fig. 38. Solid-state interactions of 37 involving Hoogsteen base-pairing of the coordinated adenine and the pendant thymine.

DNA structure. The hydrogen-bonding interaction of the AT base pair was previously described from XRD analysis by Hoogsteen on a single crystal grown from aqueous solution (Fig. 2a) [30]. Etter et al. reported that grinding A and... 

An alternative form of hydrogen bonding between base pairs is designated Hoogsteen. This type of bonding cannot readily occur in nature because the purine and pyrimidine bases are constrained to long chains that must interact at numerous points. 

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... 

Although Na+ and Li+ have been found stable in the center of G tetrad, the results of high level of theoretical studies indicate that K+ can only be stable when it is outside the tetrad plane, which explains the fact that potassium cations are usually located between the successive G tetrads. The interaction between a cation and G tetrad around the central area also changes the H-bonding pattern in the G tetrad. In the cation-G tetrad complex, bifurcated H-bonding pattern is replaced by the normal Hoogsteen H-bonding pattern [32]. 

J. Gu, J. Leszczynski, A remarkable alteration in the bonding pattern An HF and DFT study of the interactions between the metal cations and the hoogsteen hydrogen-bonded G-tetrad. J. Phys. Chem. A 104, 6308-6313 (2000)... 

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