Hoogsteen base-pairing

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-...

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

Nair, D. T., Johnson, R. E., Prakash, S., Prakash, L. and Aggarwal, A. K. (2004). Rephcation by human DNA polymerase-iota occurs by Hoogsteen base-pairing. Nature 430,377-380. 

Ghosal G, Muniyappa K. Hoogsteen base-pairing revisited resolving a role in normal biological processes and human diseases. Biochem Biophys Res Commun 2006 343 1-7. 

Figure 5-7 Two base triplets that form in triple-stranded DNA and involve both Watson-Crick and Hoogsteen base pairing. (A) The triplet T A T, where the T (marked T ) of the third strand is hydrogen bonded as a Hoogsteen pair...

Hoogsteen pairs were first observed in nature in transfer RNA molecules (Fig. 5-31). These molecules contain mostly Watson-Crick base pairs but there are also two reversed Hoogsteen pairs. One of them, between U8 and A14, is invariant in all tRNAs studied. Hoogsteen pairing also occurs in four-stranded DNA, which has important biological functions. A G quartet from a DNA tetraplex held together by Hoogsteen base pairs is shown in Fig. 5-8. 

A reversed Hoogsteen base pair present in tRNA molecules... 

Figure 5-34 (A) Two conformations of a segment of the yeast phenylalanine tRNA gene. The segment shown codes for the 3 end of the tRNA molecule shown in Fig. 5-30, including the T /C loop. (B) Formation of H-DNA (Fig. 5-24) proposed for a sequence in plasmid pGG32. The major element of the structure is the triplex, which is formed from the Watson-Crick duplex ( ) associated with the homopyrimidine loop through Hoogsteen base pairing (o, +). One of the two possible "isomeric" forms is shown. See Mirkin et al.378...

Kawai K, Saito I (1998). Stabilization of Hoogsteen base pairing by introduction of NH2 group at the C8 position of adenine. Tetrahedron Lett 29 5221—5224. 

Combination AU62 is the Watson-Crick base pair, AUS2 is called reversed Watson-Crick (Fig. 16.10, left). AU32 is the base pair discovered by Hoogsteen, and AU22 is the reversed Hoogsteen base pair (Fig. 16.10, right). 

Fig. 16.16. The U-A-U base triple observed in poly(U) 2poly(A) is composed of a Watson-Crick AU62 and a Hoogsteen base pair AU32. A corresponding C-G-C triple is not observed. It would only be possible if the C of the Hoogsteen base pair were protonated...

The double helix formed by poly(G) poly(C) does not disproportionate. The reason is that it forms an extremely stable Watson-Crick duplex and that the Hoogsteen base pair could only form if poly(C) were protonated (legend to Fig. 16.16). 

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