Base pair tilt

Structure type Pitch (A) Base-pair tilt (°) Number of nucleotides per pitch Axial rise h and turn angle t per nucleotide Groove widthb (A) Groove depthb (A) ... 

The principal structural difference between DNA and RNA is the 2 OH group of ribose in RNA molecules. In DNA, which lacks the 2 OH group in the deoxyribose sugar, hydrogen-bonded complementary strands can easily adopt the B-form double helix. In contrast, double-stranded regions of RNA molecules cannot adopt this conformation because of steric hindrance. Instead, they adopt the less compact A-helical form in which there are 11 bp per turn and the base pairs tilt 20° away from the horizontal. 

Figure 4.9 CD spectra of fixed concentration of plasmid DNA titrated with an increasing concentration of an adenoviral peptide, /x, known to template with DNA and induce condensation. Data illustrates that the peptide binding induces base-pair tilting and subsequent supercoiling (Chapters 1 and 7). Arrow shows direction of spectral increase with increasing /x peptide (Reproduced from Preuss et al., 2003, Fig. 4A).

Figure 4.2. Representation of the DNA double helix with some average structural parameters. The ribbons represent the sugar-phosphate backbone, and the lines represent the A-T or G-C base pairs. Adjacent base pairs are separated by 3.4 A ( axial rise ) one full twist of the double helix occurs over 10.5 base pairs, which is equal to 35.7 A ( helical pitch ). The base pair tilt angle (see text) is too small to be readily observable here, and thus the base pairs appear to stack parallel with each other. Shown in the inset is the 34.3° twist angle, not evident in the representation. [Adapted from Fig. 1.12 of Ref. 7, with permission.]...

Figure 7.17 Model of a 5 -d(ATGT)-3 section of A-DNA (with complementary strand) illustrating base pair tilt.

An alternative form of the right-handed double helix is A-DNA. A-DNA molecules differ in a number of ways from B-DNA. The pitch, or distance required to complete one helical turn, is different. In B-DNA, it is 3.4 nm, whereas in A-DNA it is 2.46 nm. One turn in A-DNA requires 11 bp to complete. Depending on local sequence, 10 to 10.6 bp define one helical turn in B-form DNA. In A-DNA, the base pairs are no longer nearly perpendicular to the helix axis but instead are tilted 19° with respect to this axis. Successive base pairs occur every 0.23 nm along the axis, as opposed to 0.332 nm in B-DNA. The B-form of DNA is thus longer and thinner than the short, squat A-form, which has its base pairs displaced around, rather than centered on, the helix axis. Figure 12.13 shows the relevant structural characteristics of the A- and B-forms of DNA. (Z-DNA, another form of DNA to be discussed shortly, is also depicted in Figure 12.13.) A comparison of the structural properties of A-, B-, and Z-DNA is summarized in Table 12.1. 

Fig. 12 (A) The d(CGCGAATTCGCG)2 duplex with a narrow groove and a sodium ion coordinated at the ApT step. (I) The DNA is shown in stick representation and the ion in space-filling size. Left view is directly into the central minor groove. Right view left view rotated 90° counterclockwise and tilted 30° to show the ion in the minor groove. (II) The base pair views are of the central ApT step. Top view is down the helix axis, bottom view is directly into the minor groove. (B) The DNA duplex with a phosphate-oxygen pair-sodium ion interaction and a water molecule coordinated at the ApT step. (II) Views as in Fig. 12A for the phosphate-ion-water-base complex at the AT site. Reproduced with permission from Ref. (42). Copyright 2000, American Chemical Society.

A -DNA The Watson-Crick model of DNA is based on the x-ray diffraction patterns of B-DNA. Most DNA is B-DNA however, DNA may take on two other conformations, A-DNA and Z-DNA. These conformations are greatly favored by the base sequence or by bound proteins. When B-DNA is slightly dehydrated in the laboratory, it takes on the A conformation. A-DNA is very similar to B-DNA except that the base pairs are not stacked perpendicular to the helix axis rather, they are tilted because the deoxyribose moiety puckers differently. An A-DNA helix is wider and shorter than the B-DNA helix. 

The exact nature of the lesion in DNA is unknown, and so is the type of DNA that is attacked. Recent X-ray crystallographic studies, as well as other physicochemical studies, have made it clear that DNA is not simply a polynucleotide, folded as Watson and Crick (106) proposed. There are three main conformational types of DNA they each keep the hydrogen-bonded bases in the center of the helix, but may tilt them by a "propellor twist," may slide them from the center of the helix in the plane of the base pairs, and may vary the amount of rotation from one base pair to the next up the helical axes. 

Efelixrise per base pair Base tilt normal to the 2.6 A 3.4 A 3.7 A... 

A form. A duplex DNA structure with right-handed twisting in which the planes of the base pairs are tilted about 70° with respect to the helix axis. 

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