Hoogsteen associations

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...

Because the glycosyl links and the associated sugar-phosphate backbone are related, in the Watson-Crick duplex, by a pseudodyad perpendicular to the helix axis, the two strands are oriented antiparallel. They are parallel in the Hoogsteen duplex because the glycosyl links are related by rotation about the helix axis. 

The flexible porphyrin-anthracene system of Sirish and Maiya assembles via complementary adenine-thymine base pairing [115]. Ensemble 30 associates with a binding constant of /Ca = 47 + 5 M. H NMR data suggest that both Hoogsteen and Watson-Crick adenine-thymine associations exist in solution. Time-resolved fluorescence data are consistent with the possibility of energy and electron transfer from the singlet excited state of the anthracene to the porphyrin. 

Hoogsteen and Watson-Crick faces of the guanine bases, including the central potassium cation, deoxyribose sugars removed for clarity (b) space filling model of a guanine tetrad with associated Kf metal ions located above and below plane, deoxyribose sugars removed for clarity... 

We and others have demonstrated that association of short strands containing a single guanine-repeat seems to obey a fourth-order kinetics model. Third or fourth-order reactions are not common in biochemistry, and the practical consequences of this reaction order are important. A fourth-order reaction does not imply that an elementary kinetic step involves a four-body collision. Such mechanism is extremely unlikely and other processes could lead to this fourth order. The structure of these elusive intermediates remains unknown Stefl et have recently demonstrated that a Hoogsteen G-G duplex is an improbable intermediate. Its identification will be experimentally difficult, as numerical simulations indicate that it may not be present at detectable levels. 

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