Watson-Crick duplex strands

Figure 53. Model of a p-RNA Watson-Crick duplex. Strand (mentation is strictly expected to be antiparallel, due to the strong inclination of the backlxme and base pair axes.

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] ... 

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. 

G-rich sequences that fold into G-quadruplex structures can, of course, form Watson-Crick duplexes with their complementary C-rich strands. The formation of G-quadruplex or duplex structures within the cell will therefore depend... 

Thermodynamic and kinetic data snggest that quadruplex stability depends on a nnmber of factors, including the type of structure adopted by the DNA strand (or strands), strand sequence, the size of intervening loops, base and phosphate modifications, pH and the presence of cations [19]. Small molecules may stabilize quadraplex DNA (or facihtate DNA folding into quadruplex structures) due to shifting the competitive equilibrium between the single-stranded or Watson-Crick duplex and quadruplex DNA towards the latter form [19,20]. Inhibition activity of G4 ligands depends mainly on the stability of their complexes with telomeric DNA quadruplexes. 

ASON are sequences of usually 17-30 bases of single-stranded DNA that hybridize to specific genes or their mRNA products by Watson-Crick base pairing and disrupt their function. In the case of AS-ODN (antisense oligodeoxyribonucleotides) cellular RNAseH is able to bind to the DNA-RNA duplex and hydrolyze the RNA, resulting in increased transcript turnover. Modifications to the deoxy moiety at the 2 -sugar position prohibits RNAse H action. 

DNA is a helical polyanion built by the union of two linear polymeric strands that are composed of sugars (deoxyribose) finked by phosphates. Each sugar contains an aromatic base (G,C,A, or T) bound to C-l of the sugar. The two strands are normally complementary so that when they combine to form the duplex, each base on one strand forms Watson-Crick hydrogen bonds with its counterpart (G with C and A with T) on the opposite... 

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