Nucleic Acid Structure:- DNA Can Occur in Different Three-Dimensional Forms

DNA is a remarkably flexible molecule. Considerable rotation is possible around a number of bonds in the sugar–phosphate (phosphodeoxyribose) backbone, and thermal fluctuation can produce bending, stretching, and unpairing (melting) of the strands. Many significant deviations from the Watson-Crick DNA structure are found in cellular DNA, some or all of which may play important roles in DNA metabolism. These structural varia tions generally do not affect the key properties of DNA defined by Watson and Crick: strand complementarity, antiparallel strands, and the requirement for APT and G≡C base pairs.

Structural variation in DNA reflects three things: the different possible conformations of the deoxyribose, rotation about the contiguous bonds that make up the phosphodeoxyribose backbone (Fig. 8–18a), and free rotation about the C-1–N-glycosyl bond (Fig. 8–18b). Because of steric constraints, purines in purine nucleotides are restricted to two stable conformations with respect to deoxyribose, called syn and anti (Fig. 8–18b). Pyrimidines are generally restricted to the anti-conformation because of steric interference between the sugar and the carbonyl oxygen at C-2 of the pyrimidine.

FIGURE 8–18 Structural variation in DNA. (a) The conformation of a nucleotide in DNA is affected by rotation about seven different bonds. Six of the bonds rotate freely. The limited rotation about bond 4 gives rise to ring pucker, in which one of the atoms in the five-membered furanose ring is out of the plane described by the other four. This conformation is endo or exo, depending on whether the atom is displaced to the same side of the plane as C-5 or to the opposite side (see Fig. 8–3b). (b) For purine bases in nucleotides, only two conformations with respect to the attached ribose units are sterically permitted, anti or syn. Pyrimidines generally occur in the anti-conformation.

The Watson-Crick structure is also referred to as B form DNA, or B-DNA. The B form is the most stable structure for a random-sequence DNA molecule under physiological conditions and is therefore the standard point of reference in any study of the properties of DNA. Two structural variants that have been well characterized in crystal structures are the A and Z forms. These three DNA conformations are shown in Figure 8–19, with a summary of their properties. The A form is favored in many solutions that are relatively devoid of water. The DNA is still arranged in a right-handed double helix, but the helix is wider and the number of base pairs per helical turn is 11, rather than 10.5 as in B-DNA. The plane of the base pairs in A-DNA is tilted about 20with respect to the helix axis. These structural changes deepen the major groove while making the minor groove shallower. The reagents used to promote crystallization of DNA tend to dehydrate it, and thus most short DNA molecules tend to crystallize in the A form. Z-form DNA is a more radical departure from the B structure; the most obvious distinction is the left-handed helical rotation. There are 12 base pairs per helical turn, and the structure appears slenderer and more elongated. The DNA backbone takes on a zigzag appearance. Certain nucleotide sequences fold into left-handed Z helices much more readily than others. Promi nent examples are sequences in which pyrimidines alternate with purines, especially alternating C and G or 5-methyl-C and G residues. To form the left-handed helix in Z-DNA, the purine residues flip to the syn conformation, alternating with pyrimidines in the anti-conformation. The major groove is barely apparent in Z-DNA, and the minor groove is narrow and deep. Whether A-DNA occurs in cells is uncertain, but there is evidence for some short stretches (tracts) of Z-DNA in both prokaryotes and eukaryotes. These Z-DNA tracts may play a role (as yet undefined) in regulating the ex pression of some genes or in genetic recombination.

FIGURE 8–19 Comparison of A, B, and Z forms of DNA. Each structure shown here has 36 base pairs. The bases are shown in gray, the phosphate atoms in yellow, and the riboses and phosphate oxygens in blue. Blue is the color used to represent DNA strands in later chapters. The table summarizes some properties of the three forms of DNA.

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مواضيع ذات صلة

Nucleic Acid Structure:- Many RNAs Have More Complex Three-Dimensional Structures

Nucleic Acid Structure:- Messenger RNAs Code for Polypeptide Chains

Nucleic Acid Structure:- Certain DNA Sequences Adopt Unusual Structures

Nucleic Acid Structure:- DNA Is a Double Helix

Nucleic Acid Structure:- DNA Molecules Have Distinctive Base Compositions

Nucleic Acid Structure:- DNA Stores Genetic Information

Carbohydrates as Informational Molecules: The Sugar Code:- Lectin-Carbohydrate Interactions Are Very Strong and Highly Specific

Carbohydrates as Informational Molecules: The Sugar Code:- Lectins Are Proteins That Read the Sugar Code and Mediate Many Biological Processes

Polysaccharides:- Glycolipids and Lipopolysaccharides Are Membrane Components

Polysaccharides: - Glycoproteins Have Covalently Attached Oligosaccharides

Polysaccharides:- Proteoglycans Are Glycosaminoglycan-Containing Macromolecules of the Cell Surface and Extracellular Matrix

Polysaccharides:- Glycosaminoglycans Are Heteropolysaccharides of the Extracellular Matrix