Propeller twisting

The increase in fluorescence intensity of TO upon binding to dsDNA is due to the restriction of rotation around the monomethine bridge upon intercalation of the dye into the double helical structure as the benzothiazole and quinolinium rings adapt to the propeller twist of the base pairs [49]. The monomethine bridge has a low energy barrier to rotation and hence is free to rotate in solution, allowing for the electronically excited dye to relax by non-radiative decay [49]. The quantum yield of free TO in solution has been reported to be 2 x 10-4 at 25 °C [43]. The binding constant for TO is 106 M 1 while that of ethidium bromide is 1.5 x 105 M 1 [59]. 

The propeller twist bases in base pairs are rarely co-planar. When unsubstituted pyrimidine and purine bases crystallize in the form of homo or hetero base pairs (Part II, Chap. 16), these are generally planar due to symmetry requirements. If such symmetry constraints are absent, as in co-crystal of nucleosides or nucleotides or in crystals of oligonucleotides, the bases in the pairs are usually twisted... 

Three-center (bifurcated) hydrogen bonding between adjacent base pairs explains unusual properties of poly(dA) poly(dT). The stability of the B-form of this duplex (and of its ribo analog) formed by two homopolymers might be a consequence of the extreme propeller twist (Box 20.1) reported for the central portions (the A-tracts) of the double helical dodecamer d(CGCAAAAAAGCG) [702] and d(CGCAAATTTGCG) [703]. In both crystal structures the DNA molecules show the same unusual three-center bonds linking adjacent base pairs. 

Fig. 20.11. Stereo drawing of d(CGCAAAAAAGCG). The amino N(6)-H groups of the central A-tract form three-center (bifurcated) hydrogen bonds with adenine N(6)-H acting as double donors due to the strong propeller twist of the A-T base pairs. Only bases are shown, sugar-phosphate backbone omitted for clarity [702]...

Figure 27.9. Propeller Twist. The bases of a DNA base pair are often not precisely coplanar. They are twisted with respect to each other, like the blades of a propeller. 

A-tract DNA duplexes exhibit high propeller twist and rigidity, which makes A-tract DNA unfavourable for triplex formation. It has been demonstrated that the introduction of a single central GC pair into the duplex significantly enhances the stability of the resulting triplex, as does the introduction of dia-minopurine. In both cases, the stabilisation occurs due to the disruption of the intrinsic properties of A-tract DNA. 

Propeller twist (DNA) The dihedral angle between the planes of the pyrimidine and the purine in a base pair of a nucleic acid,... 

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