Hoogsteen type pairing

The 2 -hydroxyl groups of the cytosine and of the guanosine in the anticodon are methylated. Moving far up the anticodon stem one can see two groups of base triplets which utilize both Watson-Crick and Hoogsteen types of base pairing. Drawing courtesy of Alexander Rich. 

The extra hydrogen-bonding sites can, however, also form further base pairs, as observed for poly(A) poly(U). In the Watson-Crick A-U pair, one of the adenine N(6)-H donors and the N(7) acceptor are still free and can form another A-U pair of the Hoogsteen type (Fig. 16.16). This is in fact observed if the Watson-Crick duplex poly(A) poly(U) is exposed to high salt conditions, it disproportionates to form a triplex poly(A)-2poly(U) and a single strand poly(A) [539] ... 

Fig. 12.3. Adenine-thymine hydrogen-bonded pairs (a) found by Hoogsteen in a 1 1 complex of 3-N-methyllhymine and 9-Af-methyladenine (b) postulated by Watson and Crick (current version refined by Arnott) for part of the structure of DNA. Guanine-cytosine pairs (c) Hoogsteen type (d) Watson-Crick type (Wilkins and Arnott, 1965). (From Mahler and Cordes, 1966.)...

Combining these evidences one of the probable mechanisms seems to be keto-enol equilibrium in the hydrogen-bonded dimers. If so, only the imino protons and the conjugated amino proton in the cyclic hydrogen bond can exchange. Watson-Crick type base pairs contribute to it, but Hoogsteen type does not, which would result in the lower rate of exchange than that expected from total dimer concentration. 

C11H14N4O3 250.257 Synthetic nucleoside showing Hoogsteen or reverse-Hoogsteen type base pairing. Incapable of Watson-Crick pairing. Cryst. (MeOH). Mp 217°. 

Nosenko Y, Menges F, Riehn C, Niedner-Schatteburg G (2013) Investigation by two-color IR dissociation spectroscopy of Hoogsteen-type binding in a metalated nucleobase pair mimic. Phys Chem Chem Phys 15 8171-8178... 

FIGURE 1.7 Base pairing schemes of Watson-Crick and non-Watson-Crick types. Among the non-Watson-Crick base pairs, wobble pairs are formed by H-bonds between tautomeric forms of hydroxyl (OH) and imino (NH) groups. Non-Watson-Crick base pairs also comprise Hoogsteen base pairs and reverse Watson-Crick base pairs which form the basal structural units in triplex DNA and In parallel-stranded DNA (psDNA), respectively. 

---