Propeller twist base pairs

Restrained refngment of the monodinic form of ueast phenulalanlna transfer RNA. Temperature factors and dvnamica. coordinated waters, and base-pair propeller twist armlaa. 

Base Pair Propeller Twist Base Pair Propeller Twist... 

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 examination of crystallized DNA fragments of varying base composition show sequence-dependent variations in the double helix while emphasizing the A, B and Z forms as structurally distinct families. Variation occurs in the orientation of each base pair to the next by rotation about the X axis or tilt, the Y axis or roll or the Z axis or twist of the helix. Bases in a pair may also rotate in opposition producing variations in buckle, propeller and opening (Fig. 7-5). 

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. 

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

Fig. 18.4. a Schematic representations of selected helical parameters, characterizing the relative positions and orientations of bases within base pairs. From top Shear, buckle and propeller twist, b Schematic representations of selected helical parameters, characterizing the relative positions and orientations of base pairs. From top Displacement, roll and helical twist... 

The series of crystal structures of the B-DNA dodecamer with sequence d(CGCGAATTCGCG) as well as of a 5-bromocytosine analogue with sequence d(CGCGAATT CGCG) revealed that the central six base pairs show relatively high propeller twists with values between -)-17° and +28°, and that they are bracketed... 

The occurrence of structural/dynamic deviations from the ideal base pair in real base pairs of DNA is not random. Certain sequences of the DNA bases and base pairs are more predisposed than others to adopt certain propeller twist angles, are more fluctional in base-pair opening, and so forth. This is the fundamental basis for the sequence-directed structure and dynamics that are the subject of this chapter. 

Figure 4.4. Schematic representations of base-pair structural deviations from the ideal coordinate frame of the upper and middle left. The most important rotations for the purposes of this chapter are propeller twist, twist, and roll. [Adapted from Figs. 7 and 8 (erroneously listed as Fig. 9 in its caption) of Ref. 13, with permission].

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