B-form of DNA

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. 

Figure 35-2. A diagrammatic representation of the Watson and Crick modei of the doubie-heiicai structure of the B form of DNA.The horizontai arrow indicates the width of the doubie heiix (20 A), and the verticai arrow indicates the distance spanned by one compiete turn of the doubie heiix (34 A). One turn of B-DNA in-ciudes ten base pairs (bp), so the rise is 3.4 A per bp. The centrai axis of the doubie heiix is indicated by the verticai rod. The short arrows designate the poiarity of the antiparaiiei strands. The major and minor grooves are depicted. (A,adenine C, cytosine G, guanine ...

There are 16 possible pairs in one chain. These can be designated as in the following examples (AA/TT), (CG,CG), and (AG,CT). The first two letters within the parentheses represent the sequence (from 5 to 3 ) in one chain while the second pair of letters represent the sequence (again from 5 to 3 ) in the complementary chain. The rules state that (AA,TT) or (TT,AA) repeated in a sequence will stabilize die B form of DNA. Repetition of (CC,GG) or (GG,CC) will favor conversion to the A form. Repetitions of (CG,CG) favor the Z form, especially if an alternating sequence of purines and pyrimidines is present throughout the (G + C)-rich region. 

Suppose one double helical turn of a superhelical DNA molecule changes from a B conformation to the Z conformation. Calculate the approximate changes in (1) the linking AL/c, (2) the writhe AWr, and (3) the twist A Tw of the DNA as a result of this transition. Show your calculations and explain your answers. For this problem assume that the B form of DNA has 10.4 bp per turn. Why is the B—> Z transition favored in naturally occurring supercoiled DNA ... 

Figure 4-7 Comparison of the Raman spectra typical of DNA and RNA. The upper spectrum of a 2.5% aqueous solution of calf thymus DNA is representative of the B-form of DNA in aqueous solution. The lower spectrum of yeast RNA in a 2.5% aqueous solution at pH 7 is illustrative of the A-form structure adopted by RNA. (Reproduced with permission from Ref. 19. Copyright 1987 John Wiley Sons, Inc.)...

A dramatically different form of the double helix has been observed in DNA containing alternating purine-pyrimidine sequences, especially d(CG)n but also d(TG)n. It is a left-handed, rather than a right-handed helix and is known as the Z form of DNA. Helix parameters are contrasted in Table 7.2 and space-filling models of the Z form and B form of DNA are compared below (Fig. 7-4.). 

Figure 9.40. Distortion of the Recognition Site. The DNA is represented as a ball-and-stick model. The path of the DNA helical axis, shown in red, is substantially distorted on binding to the enzyme. For the B form of DNA, the axis is straight (not shown).

The B form of DNA, first described by Watson and Crick, is right-handed and contains 10 base pairs per turn, with 3.4A between base pairs. 

The sugar-phosphate backbones of the two strands, which are on the outside in all structures, are shown in red and blue the bases (lighter shades) are oriented inward, (a) The B form of DNA has =10.5 base pairs per helical turn. Adjacent stacked base pairs are 0.36 nm apart. (b)The more compact A form of DNA has 11 base pairs per turn and exhibits a large tilt of the base pairs with respect to the helix axis, (c) Z DNA is a left-handed double helix. 

The fiber diffraction technique has been used to determine the structures of a wide variety of synthetic and biological molecules including structural proteins such as collagen and keratin, a range of helical conformations of the nucleic acids, DNA and RNA, and polysaccharides. In the case of the B form of DNA, early fiber diffraction patterns, which were not fully crystalline, still provided sufficient information to show... 

Watson and Crick described the B form of DNA, a right-handed helix, containing 3.4 A between base pairs and 10.4 base pairs per turn. Although this form predominates in vivo, other forms also occur (Fig. 12.10). The A form, which predominates in DNA-RNA hybrids, is similar to the B form, but is more compact (2.3 A between base pairs and 11 base pairs per turn). In the Z form, the bases of the two DNA strands are positioned toward the periphery of a left-handed helix. There are 3.8 A between base pairs and 12 base pairs per turn in Z DNA. This form of the helix was designated Z because, in each strand, a line connecting the phosphates zigs and zags. ... 

The B form of DNA has long been considered the normal, physiological DNA form. It was predicted from the nature of the hydrogen bonds between purines and pyrimidines and later found experimentally. Although it is easy to focus completely on the base pairing and the order of bases in DNA, other features of DNA structure are just as important. The ring portions of the DNA bases are very hydrophobic and interact with each other via hydrophobic bond-... 

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