Hydrogen bonding Hoogsteen type

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. 

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.)...

Authors of paper [48] studied the self-complementary duplexes A and B and compared them to their single strands, in order to compare helix or G-quadruplex. Clear differences in the UV spectra of the double heUx and G-quadruplex are observed, as compared to the corresponding single strands. The red shift upon higher-order structure formation is attributed to the absorption of clusters of bases interacting via hydrogen bonds (Watson-Crick type for the duplex and Hoogsteen... 

Two papers have dealt with relaxation-related measurements of exchange phenomena in nucleic adds. Nikolova et a/. described two methods for probing transient Hoogsteen type N H.N hydrogen bonds in cano-... 

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. 

Figure 8.2 (a) Mechanochemical reaction of 9-methyladenine and 1-methylthymine to form a co-crystal and (b) fragment of the (9-methyladenine) (1-methylthymine) co-crystal, displaying Hoogsteen-type dimers (a sin e dimer is highlighted in green and yellow) assembled into hydrogen-bonded... 

Certain guanine-rich DNA sequences readily fold into the four-stranded stmc-tures formed by stacked arrays of guanine quartets (or tetrads) - square planar arrangements of four guanine bases coimected by Hoogsteen-type hydrogen bonds (Fig. 6.1). 

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