Hoogsteen

Fig. 8. Non-Watson-Crick base pairs occurring in double-stranded RNA where — represents the site of attachment to the sugar (a) A—U reverse-Watson-Crick (b) G—C reverse-Watson-Crick (c) A—U Hoogsteen (d) A—U reverse-Hoogsteen (e) G—U wobble and (f) G—U reverse-wobble.

A large variety of nucleobases have also been used and developed in a PNA backbone context (Tab. A4). Several of these are routinely used in PNA applications. The pseudo isocytosine (Nl) is employed in the Hoogsteen strand of tri-... 

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-...

The formation of three-stranded nucleic acid complexes was first demonstrated over five decades ago [56] but the possible biological role of an extended triplex was expanded by the discovery of the H-DNA structure in natural DNA samples [57-59]. H-DNA is an intermolecular triplex that is generally of the pyrimidine-purine x pyrimidine type ( dot -Watson-Crick pairing and cross Hoogsteen base paring) and can be formed at mirror repeat sequences in supercoiled plasmids [59]. 

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.

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