Structure of DNA

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Chapter: Biochemistry : DNA Structure, Replication, and Repair

DNA is a polymer of deoxyribonucleoside monophosphates (dNMPs) covalently linked by 3→5–phosphodiester bonds.


STRUCTURE OF DNA

DNA is a polymer of deoxyribonucleoside monophosphates (dNMPs) covalently linked by 3→5–phosphodiester bonds. With the exception of a few viruses that contain single-stranded (ss) DNA, DNA exists as a double-stranded (ds) molecule, in which the two strands wind around each other, forming a double helix. [Note: The sequence of the linked dNMPs is primary structure, whereas the double helix is secondary structure.] In eukaryotic cells, DNA is found associated with various types of proteins (known collectively as nucleoprotein) present in the nucleus, whereas in prokaryotes, the protein– DNA complex is present in a nonmembrane-bound region known as the nucleoid.

 

A. 3 →5 -Phosphodiester bonds

Phosphodiester bonds join the 3-hydroxyl group of the deoxypentose of one nucleotide to the 5-hydroxyl group of the deoxypentose of an adjacent nucleotide through a phosphoryl group (Figure 29.2). The resulting long, unbranched chain has polarity, with both a 5-end (the end with the free phosphate) and a 3-end (the end with the free hydroxyl) that are not attached to other nucleotides. The bases located along the resulting deoxyribose–phosphate backbone are, by convention, always written in sequence from the 5-end of the chain to the 3-end. For example, the sequence of bases in the DNA shown in Figure 29.2D (5I -TACG-3I) is read “thymine, adenine, cytosine, guanine.” Phosphodiester linkages between nucleotides can be hydrolyzed enzymatically by a family of nucleases: deoxyribonucleases for DNA and ribonucleases for RNA, or cleaved hydrolytically by chemicals. [Note: Only RNA is cleaved by alkali.]


Figure 29.2 A. DNA chain with the nucleotide sequence shown written in the 5I →3 I direction. A 3 I →5 I -phosphodiester bond is shown highlighted in the blue box, and the deoxyribose-phosphate backbone is shaded in yellow. B. The DNA chain written in a more stylized form, emphasizing the deoxyribose-phosphate backbone. C. A simpler representation of the nucleotide sequence. D. The simplest (and most common) representation, with the abbreviations for the bases written in the conventional 5 I →3 I  direction.

 

B. Double helix

In the double helix, the two chains are coiled around a common axis called the helical axis. The chains are paired in an antiparallel manner (that is, the 5 I -end of one strand is paired with the 3 I -end of the other strand) as shown in Figure 29.3. In the DNA helix, the hydrophilic deoxyribose–phosphate backbone of each chain is on the outside of the molecule, whereas the hydrophobic bases are stacked inside. The overall structure resembles a twisted ladder. The spatial relationship between the two strands in the helix creates a major (wide) groove and a minor (narrow) groove. These grooves provide access for the binding of regulatory proteins to their specific recognition sequences along the DNA chain. [Note: Certain anticancer drugs, such as dactinomycin (actinomycin D), exert their cytotoxic effect by intercalating into the narrow groove of the DNA double helix, thereby interfering with DNA (and RNA) synthesis.]


Figure 29.3 DNA double helix, illustrating some of its major structural features.

 

1. Base-pairing: The bases of one strand of DNA are paired with the bases of the second strand, so that an adenine (A) is always paired with a thymine (T) and a cytosine (C) is always paired with a guanine (G). [Note: The base pairs are perpendicular to the helical axis (see Figure 29.3).] Therefore, one polynucleotide chain of the DNA double helix is always the complement of the other. Given the sequence of bases on one chain, the sequence of bases on the complementary chain can be determined (Figure 29.4). [Note: The specific base-pairing in DNA leads to the Chargaff rule, which states that in any sample of dsDNA, the amount of A equals the amount of T, the amount of G equals the amount of C, and the total amount of purines equals the total amount of pyrimidines.] The base pairs are held together by hydrogen bonds: two between A and T and three between G and C (Figure 29.5). These hydrogen bonds, plus the hydrophobic interactions between the stacked bases, stabilize the structure of the double helix.


Figure 29.4 Two complementary DNA sequences. T= thymine; A = adenine; C = cytosine; G = guanine.


Figure 29.5 Hydrogen bonds between complementary bases.

 

2. Separation of the two DNA strands in the double helix: The two strands of the double helix separate when hydrogen bonds between the paired bases are disrupted. Disruption can occur in the laboratory if the pH of the DNA solution is altered so that the nucleotide bases ionize, or if the solution is heated. [Note: Phosphodiester bonds are not broken by such treatment.] When DNA is heated, the temperature at which one half of the helical structure is lost is defined as the melting temperature (Tm). The loss of helical structure in DNA, called denaturation, can be monitored by measuring its absorbance at 260 nm. [Note: ssDNA has a higher relative absorbance at this wavelength than does dsDNA.] Because there are three hydrogen bonds between G and C but only two between A and T, DNA that contains high concentrations of A and T denatures at a lower temperature than G-and C-rich DNA (Figure 29.6). Under appropriate conditions, complementary DNA strands can reform the double helix by the process called renaturation (or reannealing). [Note: Separation of the two strands over short regions occurs during both DNA and RNA synthesis.]


Figure 29.6 Melting temperatures (Tm) of DNA molecules with different nucleotide compositions.

 

3. Structural forms of the double helix: There are three major structural forms of DNA: the B form (described by Watson and Crick in 1953), the A form, and the Z form. The B form is a right-handed helix with 10 base pairs per 360° turn (or twist) of the helix, and with the planes of the bases perpendicular to the helical axis. Chromosomal DNA is thought to consist primarily of B-DNA (Figure 29.7 shows a space-filling model of B-DNA). The A form is produced by moderately dehydrating the B form. It is also a right-handed helix, but there are 11 base pairs per turn, and the planes of the base pairs are tilted 20° away from the perpendicular to the helical axis. The conformation found in DNA-RNA hybrids or RNA-RNA double-stranded regions is probably very close to the A form. Z-DNA is a left-handed helix that contains 12 base pairs per turn (see Figure 29.7). [Note: The deoxyribose– phosphate backbone “zigzags,” hence, the name “Z”-DNA.] Stretches of Z-DNA can occur naturally in regions of DNA that have a sequence of alternating purines and pyrimidines (for example, poly GC). Transitions between the B and Z helical forms of DNA may play a role in regulating gene expression.


Figure 29.7 Structures of B-DNA and Z-DNA.

 

C. Linear and circular DNA molecules

Each chromosome in the nucleus of a eukaryote contains one long, linear molecule of dsDNA, which is bound to a complex mixture of proteins (histone and nonhistone) to form chromatin. Eukaryotes have closed, circular, dsDNA molecules in their mitochondria, as do plant chloroplasts. A prokaryotic organism typically contains a single, circular, dsDNA molecule. [Note: Circular DNA is “supercoiled”, that is, the double helix crosses over on itself one or more times. Supercoiling can result in overwinding (positive supercoiling) or underwinding (negative supercoiling) of DNA. Supercoiling, a type of tertiary structure, compacts DNA.] Each prokaryotic chromosome is associated with nonhistone proteins that help compact the DNA to form a nucleoid. In addition, most species of bacteria also contain small, circular, extrachromosomal DNA molecules called plasmids. Plasmid DNA carries genetic information, and undergoes replication that may or may not be synchronized to chromosomal division. [Note: The use of plasmids as vectors in recombinant DNA technology is described in Chapter 33.]

Plasmids may carry genes that convey antibiotic resistance to the host bacterium and may facilitate the transfer of genetic information from one bacterium to another.

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