《生物化学原理》（英文版）chapter 8 NUCLEOTIDES AND NUCLEIC ACIDS

278 Chapter 8 Nucleotide les and Nucleic Acids the sugar is always in its closed-ring B-furanose form in nucleic acids). The connecting lines between nucleotides (which pass through ( )are drawn diagonally from the middle(C-3) of the deoxyribose of one nucleotide to HON the bottom( c-5)of the next. Lactam Lactim Du bo ledi AC G T A Uracil 5 End 3 End FIGURE 8-9 Tautomeric forms of uracil. The lactam form predomi nates at pH 7.0; the other forms become more prominent as pH de- creases. The other free pyrimidines and the free purines also have tau- homeric forms, but they are more rarely encountered By convention, the structure of a single strand of nu- cleic acid is always written with the 5 end at the left and the 3 end at the right-that is, in the 5'-3' di rection. Some simpler representations of this pentade. planar, with a slight pucker. Free pyrimidine and purine oxyribonucleotide are pA-C-G-T-AoH, pApCpGp'TpA, bases may exist in two or more tautomeric forms de- and pACGTA pending on the pH Uracil, for example, occurs in a short nucleic acid is referred to as an oligonu tam, lactim, and double lactim forms(Fig.8-9).The leotide. The definition ofshort" is somewhat arbi- structures shown in Figure 8-2 are the tautomers that rary, but polymers containing 50 or fewer nucleotide predominate at pH 7.0. As a result of resonance, all nu- are generally called oligonucleotides. A longer nucleic cleotide bases absorb UV light, and nucleic acids are acid is called a polynucleotide characterized by a strong absorption at wavelengths 50m(Fg.8-10 The Properties of Nucleotide Bases Affect the three-Dimensional structure of nucleic acids ally he purine and pyrimidine bases are hydrophobic relatively insoluble in water at the near-neutral pH of the cell. At acidic or alkaline ph the bases become Free pyrimidines and purines are weakly basic com- charged and their solubility in water increases. Hy- pounds and are thus called bases. They have a variety drophobic stacking interactions in which two or more of chemical properties that affect the structure, and bases are positioned with the planes of their rings par ultimately the function, of nucleic acids. The purines (like a stack of coins) are one of two important and pyrimidines common in DNA and RNa are highly modes of interaction between bases in nucleic acids. The conjugated molecules(Fig. 8-2), a property with im- stacking also involves a combination of van der Waals portant consequences for the structure, electron distri- and dipole-dipole interactions between the bases. Base bution, and light absorption of nucleic acids. Resonance stacking helps to minimize contact of the bases with wa- among atoms in the ring gives most of the bonds par- ter, and base-stacking interactions are very important in tial double-bond character. One result is that pyrim- stabilizing the three-dimensional structure of nucleic dines are planar molecules; purines are very nearly acids, as described later. 14,000 10.000 Molar extinction FIGURE 8-10 Absorption spectra of the coefficient at 260 nm, common nucleotides. The spectra are 8.000 ∈2(Mcm-) shown as the variation in molar extinctio AMP15,400 coefficient with wavelength. The molar extinction coefficients at 260 nm and 型4000 pH 7.0 (eto) are listed in the table. The UMP 9900 spectra of corresponding ribonucleotides 2.000 dTMP 9 200 and deoxyribonucleotides, as well as the nucleosides, are essentially identical.For mixtures of nucleotides, a wavelength of 230240250260270280 260 nm(dashed vertical line) is used for

the sugar is always in its closed-ring
-furanose form in nucleic acids). The connecting lines between nucleotides (which pass through P
) are drawn diagonally from the middle (C-3
) of the deoxyribose of one nucleotide to the bottom (C-5
) of the next. By convention, the structure of a single strand of nu￾cleic acid is always written with the 5
end at the left and the 3
end at the right—that is, in the 5
n 3
di￾rection. Some simpler representations of this pentade￾oxyribonucleotide are pA-C-G-T-AOH, pApCpGpTpA, and pACGTA. A short nucleic acid is referred to as an oligonu￾cleotide. The definition of “short” is somewhat arbi￾trary, but polymers containing 50 or fewer nucleotides are generally called oligonucleotides. A longer nucleic acid is called a polynucleotide. The Properties of Nucleotide Bases Affect the Three-Dimensional Structure of Nucleic Acids Free pyrimidines and purines are weakly basic com￾pounds and are thus called bases. They have a variety of chemical properties that affect the structure, and ultimately the function, of nucleic acids. The purines and pyrimidines common in DNA and RNA are highly conjugated molecules (Fig. 8–2), a property with im￾portant consequences for the structure, electron distri￾bution, and light absorption of nucleic acids. Resonance among atoms in the ring gives most of the bonds par￾tial double-bond character. One result is that pyrim￾idines are planar molecules; purines are very nearly planar, with a slight pucker. Free pyrimidine and purine bases may exist in two or more tautomeric forms de￾pending on the pH. Uracil, for example, occurs in lac￾tam, lactim, and double lactim forms (Fig. 8–9). The structures shown in Figure 8–2 are the tautomers that predominate at pH 7.0. As a result of resonance, all nu￾cleotide bases absorb UV light, and nucleic acids are characterized by a strong absorption at wavelengths near 260 nm (Fig. 8–10). The purine and pyrimidine bases are hydrophobic and relatively insoluble in water at the near-neutral pH of the cell. At acidic or alkaline pH the bases become charged and their solubility in water increases. Hy￾drophobic stacking interactions in which two or more bases are positioned with the planes of their rings par￾allel (like a stack of coins) are one of two important modes of interaction between bases in nucleic acids. The stacking also involves a combination of van der Waals and dipole-dipole interactions between the bases. Base stacking helps to minimize contact of the bases with wa￾ter, and base-stacking interactions are very important in stabilizing the three-dimensional structure of nucleic acids, as described later. 278 Chapter 8 Nucleotides and Nucleic Acids Uracil FIGURE 8–9 Tautomeric forms of uracil. The lactam form predomi￾nates at pH 7.0; the other forms become more prominent as pH de￾creases. The other free pyrimidines and the free purines also have tau￾tomeric forms, but they are more rarely encountered. 14,000 12,000 10,000 8,000 6,000 4,000 2,000 280 Molar extinction coefficient,  Wavelength (nm) 230 240 250 260 270 Molar extinction coefficient at 260 nm, 260 (M1 cm1 ) AMP GMP UMP dTMP CMP 15,400 11,700 9,900 9,200 7,500 FIGURE 8–10 Absorption spectra of the common nucleotides. The spectra are shown as the variation in molar extinction coefficient with wavelength. The molar extinction coefficients at 260 nm and pH 7.0 (260) are listed in the table. The spectra of corresponding ribonucleotides and deoxyribonucleotides, as well as the nucleosides, are essentially identical. For mixtures of nucleotides, a wavelength of 260 nm (dashed vertical line) is used for absorption measurements.

8.2 Nucleic Acid Structure 27 H k-2.8A- CHe Adenine H H C HI FIGURE 8-11 Hydrogen-bonding patterns in the base pairs defined by Watson and Crick. Here as elsewhere, hydrogen bonds are represented by three blue lines and exocyclic amino groups. Hydrogen bonds involving I A nucleotide consists of a nitrogenous base the amino and carbonyl groups are the second impor- (purine or pyrimidine), a pentose sugar, and tant mode of interaction between bases in nucleic acid one or more phosphate groups. Nucleic acids molecules. Hydrogen bonds between bases permit a are polymers of nucleotides, joined together by complementary association of two(and occasionally phosphodiester linkages between the 5 three or four) strands of nucleic acid. The most imp hydroxyl group of one pentose and the 3 tant hydrogen-bonding patterns are those defined by James D. Watson and Francis Crick in 1953. in which A hydroxyl group of the next. bonds specifically to T (or U) and G bonds to C(Fi a There are two types of nucleic acid: RNA and 8-11). These two types of base pairs predominate in DNA The nucleotides in rna contain ribose double- stranded dna and rna. and the tautomers and the common pyrimidine bases are uracil shown in Figure 8-2 are responsible for these patterns and cytosine. In dnA, the nucleotides contain It is this specific pairing of bases that permits the du 2-deoxyribose, and the common pyrimidine plication of genetic information, as we shall discuss later bases are thymine and cytosine. The primary purines are adenine and guanine in both rNa and dna 8.2 Nucleic acid structure The discovery of the structure of dna by Watson and Crick in 1953 was a momentous event in science. an event that gave rise to entirely new disciplines and in- fluenced the course of many established ones. Our pres ent understanding of the storage and utilization of cell's genetic information is based on work made possi ble by this discovery, and an outline of how genetic in- formation is processed by the cell is now a prerequisite the discussion of any area of biochemistry. Here, James watson Francis Crick ern ourselves with dna structure itself the events

The most important functional groups of pyrim￾idines and purines are ring nitrogens, carbonyl groups, and exocyclic amino groups. Hydrogen bonds involving the amino and carbonyl groups are the second impor￾tant mode of interaction between bases in nucleic acid molecules. Hydrogen bonds between bases permit a complementary association of two (and occasionally three or four) strands of nucleic acid. The most impor￾tant hydrogen-bonding patterns are those defined by James D. Watson and Francis Crick in 1953, in which A bonds specifically to T (or U) and G bonds to C (Fig. 8–11). These two types of base pairs predominate in double-stranded DNA and RNA, and the tautomers shown in Figure 8–2 are responsible for these patterns. It is this specific pairing of bases that permits the du￾plication of genetic information, as we shall discuss later in this chapter. SUMMARY 8.1 Some Basics ■ A nucleotide consists of a nitrogenous base (purine or pyrimidine), a pentose sugar, and one or more phosphate groups. Nucleic acids are polymers of nucleotides, joined together by phosphodiester linkages between the 5
- hydroxyl group of one pentose and the 3
- hydroxyl group of the next. ■ There are two types of nucleic acid: RNA and DNA. The nucleotides in RNA contain ribose, and the common pyrimidine bases are uracil and cytosine. In DNA, the nucleotides contain 2
-deoxyribose, and the common pyrimidine bases are thymine and cytosine. The primary purines are adenine and guanine in both RNA and DNA. 8.2 Nucleic Acid Structure The discovery of the structure of DNA by Watson and Crick in 1953 was a momentous event in science, an event that gave rise to entirely new disciplines and in￾fluenced the course of many established ones. Our pres￾ent understanding of the storage and utilization of a cell’s genetic information is based on work made possi￾ble by this discovery, and an outline of how genetic in￾formation is processed by the cell is now a prerequisite for the discussion of any area of biochemistry. Here, we concern ourselves with DNA structure itself, the events 8.2 Nucleic Acid Structure 279 3
C C C G C G G G A A A A A T T T T T 5
5
3
10.8 Å N C O C N C H C C H C N C N C 11.1 Å 2.8 Å 3.0 Å H N C O CH3 C O N H N C H C H C N C C N C H N C N O N H H H H 2.9 Å 3.0 Å 2.9 Å Adenine Thymine Guanine Cytosine N H C-1
C-1
C-1
H H N C N C-1
FIGURE 8–11 Hydrogen-bonding patterns in the base pairs defined by Watson and Crick. Here as elsewhere, hydrogen bonds are represented by three blue lines. James Watson Francis Crick

that led to its discovery, and more recent refinements in our understanding. RNA structure is also introduced → As in the case of protein structure( Chapter 4),it is sometimes useful to describe nucleic acid structure in terms of hierarchical levels of complexity(primary Ltea capitated acid is its covalent structure and nucleotide regular, stable str cen up by some or all the nucleotides in a nucleic acid can be referred to as dary structure. All structures considered in th mainder of this chapter fall under the heading of sec- dary structure. The complex folding of large chro- 少 mosomes within eukaryotic chromatin and bacterial nucleoids is generally considered tertiary structure; this is discussed in Chapter 24 use fes DNA Stores genetic Information The biochemical investigation of dNa began with Friedrich Miescher, who carried out the first systematic chemical studies of cell nuclei. In 1868 Miescher isolated a phosphorus-containing substance, which he called 与 nuclein, "from the nuclei of pus cells (leukocytes)ob tained from discarded surgical bandages. He found → nuclein to consist of an acidic portion, which we know today as DNA, and a basic portion, protein. Miescher later found a similar acidic substance in the heads of sperm cells from salmon. Although he partially purified (c) bateria simulant hadan nuclein and studied its properties, the covalent(pri mary)structure of DNa (as shown in Fig. 8-7)was not known with certainty until the late 1940s Hout killed virulent bacteria Miescher and many others suspected that nuclein (nucleic acid) was associated in some way with cell in- heritance. but the first direct evidence that dna is the bearer of genetic information came in 1944 through discovery made by Oswald T Avery, Colin MacLeod, and Maclyn McCarty. These investigators found that DNA extracted from a virulent(disease-causing) strain of the L汉eDn bacterium Streptococcus pneumoniae, also known as pneumococcus, genetically transformed a nonvirulent nmvinaiat itur Mes strain of this organism into a virulent form(Fig. 8-12) nonvirulent had eria ee Lnenanvin int bateria FIGURE 8-12 The Avery-MacLeod-Mc Carty experiment. (a)When w INa isolated frmm heat killd vaunt bateria injected into mice, the encapsulated strain of pneumococcus is lethal (b)whereas the nonencapsulated strain, (c) like the heat-killed en- capsulated strain, is harmless.(d) Earlier research by the bacteriol- ist Frederick Griffith had shown that adding heat-killed virulent bac- teria (harmless to mice)to a live nonvirulent strain permanently transformed the latter into lethal, virulent, encapsulated bacteria. (e) Avery and his colleagues extracted the DNA from heat-killed vir- ulent pneumococci, removing the protein as completely as possible, cneateulaled and added this DNA to nonvirulent bacteria. The DNA gained en- trance into the nonvirulent bacteria, which were permanently trans- bateria Iacapsuls ad &Ee vi kat bacteria formed into a virulent strain

that led to its discovery, and more recent refinements in our understanding. RNA structure is also introduced. As in the case of protein structure (Chapter 4), it is sometimes useful to describe nucleic acid structure in terms of hierarchical levels of complexity (primary, secondary, tertiary). The primary structure of a nucleic acid is its covalent structure and nucleotide sequence. Any regular, stable structure taken up by some or all of the nucleotides in a nucleic acid can be referred to as secondary structure. All structures considered in the re￾mainder of this chapter fall under the heading of sec￾ondary structure. The complex folding of large chro￾mosomes within eukaryotic chromatin and bacterial nucleoids is generally considered tertiary structure; this is discussed in Chapter 24. DNA Stores Genetic Information The biochemical investigation of DNA began with Friedrich Miescher, who carried out the first systematic chemical studies of cell nuclei. In 1868 Miescher isolated a phosphorus-containing substance, which he called “nuclein,” from the nuclei of pus cells (leukocytes) ob￾tained from discarded surgical bandages. He found nuclein to consist of an acidic portion, which we know today as DNA, and a basic portion, protein. Miescher later found a similar acidic substance in the heads of sperm cells from salmon. Although he partially purified nuclein and studied its properties, the covalent (pri￾mary) structure of DNA (as shown in Fig. 8–7) was not known with certainty until the late 1940s. Miescher and many others suspected that nuclein (nucleic acid) was associated in some way with cell in￾heritance, but the first direct evidence that DNA is the bearer of genetic information came in 1944 through a discovery made by Oswald T. Avery, Colin MacLeod, and Maclyn McCarty. These investigators found that DNA extracted from a virulent (disease-causing) strain of the bacterium Streptococcus pneumoniae, also known as pneumococcus, genetically transformed a nonvirulent strain of this organism into a virulent form (Fig. 8–12). 280 Chapter 8 Nucleotides and Nucleic Acids (a) (b) (c) (d) (e) FIGURE 8–12 The Avery-MacLeod-McCarty experiment. (a) When injected into mice, the encapsulated strain of pneumococcus is lethal, (b) whereas the nonencapsulated strain, (c) like the heat-killed en￾capsulated strain, is harmless. (d) Earlier research by the bacteriolo￾gist Frederick Griffith had shown that adding heat-killed virulent bac￾teria (harmless to mice) to a live nonvirulent strain permanently transformed the latter into lethal, virulent, encapsulated bacteria. (e) Avery and his colleagues extracted the DNA from heat-killed vir￾ulent pneumococci, removing the protein as completely as possible, and added this DNA to nonvirulent bacteria. The DNA gained en￾trance into the nonvirulent bacteria, which were permanently trans￾formed into a virulent strain

Avery and his colleagues concluded that the DNA ex- tracted from the virulent strain carried the inheritable ge- DNA netic message for virulence. Not everyone accepted these conclusions, because protein impurities present in the DNA could have been the carrier of the genetic informa- tion. This possibility was soon eliminated by the finding that treatment of the dNa with proteolytic enzymes did deoxyribonucleases(DNA-hydrolyzing enzymes) A second important experiment provided inde pendent evidence that DNA carries genetic information In 1952 Alfred D. Hershey and Martha Chase used ra dioactive phosphorus ('2P)and radioactive sulfur(S) tracers to show that when the bacterial virus(bacterio- phage)T2 infects its host cell, Escherichia coli, it is the phosphorus-containing DNA of the viral particle, not the sulfur-containing protein of the viral coat, that en- ters the host cell and furnishes the genetic information for viral replication(Fig. 8-13). These important early experiments and many other lines of evidence have shown that DNa is the exclusive chromosomal compo- nent bearing the genetic information of living cells DNA Molecules Have Distinctive Base Compositions A most important clue to the structure of DNA came from the work of Erwin Chargaff and his colleagues in the late 1940s. They found that the four nucleotide bases of dna occur in different ratios in the dnas of different organisms and that the amounts of certain radioactive Radioactive bases are closely related. These data, collected from DNAs of a great many different species, led Chargaff to the following conclusions 1. The base composition of dna generally varies from one species to another. 2. DNA specimens isolated from different tissues of the same species have the same base composition. 3. The base composition of DNA in a given species does not change with an organisms age, FIGURE 8-13 The Hershey-Chase experiment. Two batches of iso. nutritional state, or changing environment. topically labeled bacteriophage T2 particles were prepared. One wa labeled with"P in the phosphate groups of the DNA, the other with 4. In all cellular DNAS, regardless of the species, the 35s in the sulfur-containing amino acids of the protein coats (capsids) number of adenosine residues is equal to the (Note that DNA contains no sulfur and viral protein contains no phos- number of thymidine residues(that is, A phorus. )The two batches of labeled phage were then allowed to in. and the number of guanosine residues is equal to fect separate suspensions of unlabeled bacteria. Each suspension of the number of cytidine residues(G=C). From phage-infected cells was agitated in a blender to shear the viral these relationships it follows that the sum of the sids from the bacteria. The bacteria and empty viral coats (called purine residues equals the sum of the pyrimidine ghosts ")were then separated by centrifugation. The cells infected with residues that is a+g=T+c the3"p-labeled phage were found to containP, indicating that the labeled viral DNA had entered the cells; the viral ghosts contained These quantitative relationships, sometimes called radioactivity. The cells infected with 25s-labeled phage were found to Chargaffs rules, were confirmed by many subsequent have no radioactivity after blender treatment, but the viral ghosts con. researchers. They were a key to establishing the three- tained 35s. Progeny virus particles (not shown) were produced in both dimensional structure of DNa and yielded clues to how batches of bacteria some time after the viral coats were removed, in. genetic information is encoded in DNA and passed from dicating that the genetic message for their replication had been in. one generation to the next. troduced by viral DNA, not by viral protein

Avery and his colleagues concluded that the DNA ex￾tracted from the virulent strain carried the inheritable ge￾netic message for virulence. Not everyone accepted these conclusions, because protein impurities present in the DNA could have been the carrier of the genetic informa￾tion. This possibility was soon eliminated by the finding that treatment of the DNA with proteolytic enzymes did not destroy the transforming activity, but treatment with deoxyribonucleases (DNA-hydrolyzing enzymes) did. A second important experiment provided inde￾pendent evidence that DNA carries genetic information. In 1952 Alfred D. Hershey and Martha Chase used ra￾dioactive phosphorus (32P) and radioactive sulfur (35S) tracers to show that when the bacterial virus (bacterio￾phage) T2 infects its host cell, Escherichia coli, it is the phosphorus-containing DNA of the viral particle, not the sulfur-containing protein of the viral coat, that en￾ters the host cell and furnishes the genetic information for viral replication (Fig. 8–13). These important early experiments and many other lines of evidence have shown that DNA is the exclusive chromosomal compo￾nent bearing the genetic information of living cells. DNA Molecules Have Distinctive Base Compositions A most important clue to the structure of DNA came from the work of Erwin Chargaff and his colleagues in the late 1940s. They found that the four nucleotide bases of DNA occur in different ratios in the DNAs of different organisms and that the amounts of certain bases are closely related. These data, collected from DNAs of a great many different species, led Chargaff to the following conclusions: 1. The base composition of DNA generally varies from one species to another. 2. DNA specimens isolated from different tissues of the same species have the same base composition. 3. The base composition of DNA in a given species does not change with an organism’s age, nutritional state, or changing environment. 4. In all cellular DNAs, regardless of the species, the number of adenosine residues is equal to the number of thymidine residues (that is, A  T), and the number of guanosine residues is equal to the number of cytidine residues (G  C). From these relationships it follows that the sum of the purine residues equals the sum of the pyrimidine residues; that is, A G  T C. These quantitative relationships, sometimes called “Chargaff’s rules,” were confirmed by many subsequent researchers. They were a key to establishing the three￾dimensional structure of DNA and yielded clues to how genetic information is encoded in DNA and passed from one generation to the next. 32P experiment 35S experiment Radioactive DNA Nonradioactive coat Nonradioactive DNA Radioactive coat Injection Blender treatment shears off viral heads Separation by centrifugation Radioactive Not radioactive Phage Radioactive Not radioactive Bacterial cell FIGURE 8–13 The Hershey-Chase experiment. Two batches of iso￾topically labeled bacteriophage T2 particles were prepared. One was labeled with 32P in the phosphate groups of the DNA, the other with 35S in the sulfur-containing amino acids of the protein coats (capsids). (Note that DNA contains no sulfur and viral protein contains no phos￾phorus.) The two batches of labeled phage were then allowed to in￾fect separate suspensions of unlabeled bacteria. Each suspension of phage-infected cells was agitated in a blender to shear the viral cap￾sids from the bacteria. The bacteria and empty viral coats (called “ghosts”) were then separated by centrifugation. The cells infected with the 32P-labeled phage were found to contain 32P, indicating that the labeled viral DNA had entered the cells; the viral ghosts contained no radioactivity. The cells infected with 35S-labeled phage were found to have no radioactivity after blender treatment, but the viral ghosts con￾tained 35S. Progeny virus particles (not shown) were produced in both batches of bacteria some time after the viral coats were removed, in￾dicating that the genetic message for their replication had been in￾troduced by viral DNA, not by viral protein.

282 Chapter 8 Nucleotides and Nucleic Acids DNA Is a double helix To shed more light on the structure of DNA, Rosalind Franklin and Maurice Wilkins used the powerful method of x-ray diffraction(see Box 4-4)to analyze DNA fibers They showed in the early 1950s that DNA produces a haracteristic x-ray diffraction pattern(Fig. 8-14) From this pattern it was deduced that DNA molecules are helical with two periodicities along their long axis, a primary one of 3. 4 A and a secondary one of 34 A.The problem then was to formulate a three-dimensional model of the DNa molecule that could account not only Rosalind Franklin Maurice wilkins for the x-ray diffraction data but also for the spe- ific a=T and g=c base equivalences discovered by Chargaff and for the other chemical properties of DNa finding that separation of paired DNA strands is more In 1953 Watson and Crick postulated a three- difficult the higher the ratio of G=C to A-T base pairs dimensional model of DNA structure that accounted for Other pairings of bases tend(to varying degrees)to all the available data. It consists of two helical dna destabilize the double-helical structure. chains wound around the same axis to form a right- When Watson and Crick constructed their model handed double helix (see Box 4-1 for an explanation of they had to decide at the outset whether the strands the right- or left-handed sense of a helical structure) of DNA should be parallel or antiparallel--whether The hydrophilic backbones of alternating deoxyribose their 5 3"phosphodiester bonds should run in the same and phosphate groups are on the outside of the double or opposite directions. An antiparallel orientation pro helix, facing the surrounding water. The furanose ring duced the most convincing model, and later work with of each deoxyribose is in the C-2 endo conformation. DNA polymerases( Chapter 25)provided experimental The purine and pyrimidine bases of both strands are evidence that the strands are indeed antiparallel, a find stacked inside the double helix, with their hydrophobic ing ultimately confirmed by x-ray analysis. and nearly planar ring structures very close together To account for the periodicities observed in the x and perpendicular to the long axis. The offset pairing of ray diffraction patterns of DNA fibers, Watson and Crick the two strands creates a major groove and minor groove on the surface of the duplex(Fig. 8-15). Each manipulated molecular models to arrive at a structure nucleotide base of one strand is paired in the same plane with a base of the other strand Watson and Crick found that the hydrogen-bonded base pairs illustrated in Fig ure 8-11.G with C and a with T are those that fit best rule that in any DNA, G=C and A=T. It is important gimel to note that three hydrogen bonds can form between G and C, symbolized G=C, but only two can form between A and T, symbolized A-T. This is one reason for the M FIGURE 8-15 Watson-Crick model for the structure of dNA. The original model proposed by Watson and Crick had 10 base pairs,or A(3.4 nm), per turn of the helix subsequent measurements revealed FIGURE 8-14 X-ray diffraction pattern of DNA. The spots forming a 10.5 base pairs, or 36 A(3.6 nm), per turn. (a)Schematic represen- cross in the center denote a helical structure. The heavy bands at the tation, showing dimensions of the helix. (b) Stick representation show left and right arise from the recurring bases ing the backbone and stacking of the bases. (c)Space-filling model

DNA Is a Double Helix To shed more light on the structure of DNA, Rosalind Franklin and Maurice Wilkins used the powerful method of x-ray diffraction (see Box 4–4) to analyze DNA fibers. They showed in the early 1950s that DNA produces a characteristic x-ray diffraction pattern (Fig. 8–14). From this pattern it was deduced that DNA molecules are helical with two periodicities along their long axis, a primary one of 3.4 Å and a secondary one of 34 Å. The problem then was to formulate a three-dimensional model of the DNA molecule that could account not only for the x-ray diffraction data but also for the spe￾cific A  T and G  C base equivalences discovered by Chargaff and for the other chemical properties of DNA. In 1953 Watson and Crick postulated a three￾dimensional model of DNA structure that accounted for all the available data. It consists of two helical DNA chains wound around the same axis to form a right￾handed double helix (see Box 4–1 for an explanation of the right- or left-handed sense of a helical structure). The hydrophilic backbones of alternating deoxyribose and phosphate groups are on the outside of the double helix, facing the surrounding water. The furanose ring of each deoxyribose is in the C-2
endo conformation. The purine and pyrimidine bases of both strands are stacked inside the double helix, with their hydrophobic and nearly planar ring structures very close together and perpendicular to the long axis. The offset pairing of the two strands creates a major groove and minor groove on the surface of the duplex (Fig. 8–15). Each nucleotide base of one strand is paired in the same plane with a base of the other strand. Watson and Crick found that the hydrogen-bonded base pairs illustrated in Fig￾ure 8–11, G with C and A with T, are those that fit best within the structure, providing a rationale for Chargaff’s rule that in any DNA, G  C and A  T. It is important to note that three hydrogen bonds can form between G and C, symbolized GqC, but only two can form between A and T, symbolized AUT. This is one reason for the finding that separation of paired DNA strands is more difficult the higher the ratio of GqC to AUT base pairs. Other pairings of bases tend (to varying degrees) to destabilize the double-helical structure. When Watson and Crick constructed their model, they had to decide at the outset whether the strands of DNA should be parallel or antiparallel—whether their 5
,3
-phosphodiester bonds should run in the same or opposite directions. An antiparallel orientation pro￾duced the most convincing model, and later work with DNA polymerases (Chapter 25) provided experimental evidence that the strands are indeed antiparallel, a find￾ing ultimately confirmed by x-ray analysis. To account for the periodicities observed in the x￾ray diffraction patterns of DNA fibers, Watson and Crick manipulated molecular models to arrive at a structure 282 Chapter 8 Nucleotides and Nucleic Acids FIGURE 8–14 X-ray diffraction pattern of DNA. The spots forming a cross in the center denote a helical structure. The heavy bands at the left and right arise from the recurring bases. FIGURE 8–15 Watson-Crick model for the structure of DNA. The original model proposed by Watson and Crick had 10 base pairs, or 34 Å (3.4 nm), per turn of the helix; subsequent measurements revealed 10.5 base pairs, or 36 Å (3.6 nm), per turn. (a) Schematic represen￾tation, showing dimensions of the helix. (b) Stick representation show￾ing the backbone and stacking of the bases. (c) Space-filling model. Rosalind Franklin, 1920–1958 Maurice Wilkins