11.2 What Sorts of Secondary Structures Can Double-Stranded DNA Molecules Adopt? 323 The edges of the base pairs have a specific relationship to these grooves. The “top” edges of the base pairs (“top” as defined by placing the glycosidic bond at the bottom, as in Figure 11.7) are exposed along the interior surface or “floor” of the major groove; the base-pair edges nearest to the glycosidic bond form the interior surface of the minor groove. Some proteins that bind to DNA can actually recognize specific nu- cleotide sequences by “reading” the pattern of H-bonding possibilities presented by the edges of the bases in these grooves. Such DNA–protein interactions provide one step toward understanding how cells regulate the expression of genetic information encoded in DNA (see Chapter 29). Double Helical Structures Can Adopt a Number of Stable Conformations In solution, DNA ordinarily assumes the familar structure we have been discussing: B-DNA. However, nucleic acids also occur naturally in other double helical forms. The base-pairing arrangement remains the same, but the inherently flexible sugar– phosphate backbone can adopt different conformations. Base-pair rotations are an- other kind of conformational variation. Helical twist is the rotation (around the axis of the double helix) of one base pair relative to the next (Figure 11.8a). Successive base pairs in B-DNA show a mean rotation of 36° with respect to each other. Pro- pellor twist involves rotation around a different axis, namely, an axis perpendicular to the helix axis (Figure 11.8b). Propellor twist allows greater overlap between suc- cessive bases along a strand of DNA and diminishes the area of contact between bases and solvent water. A-Form DNA Is an Alternative Form of Right-Handed DNA An alternative form of the right-handed double helix is A-DNA. A-DNA molecules dif- fer from B-DNA molecules in a number of ways. 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 cen- tered on, the helix axis. Figure 11.9 and Table 11.1 show the relevant structural char- acteristics of the A- and B-forms of DNA. (Z-DNA, another form of DNA to be dis- cussed shortly, is also depicted in Figure 11.9 and Table 11.1.) A comparison of the structural properties of A-, B-, and Z-DNA is summarized in Table 11.1. Relatively dehydrated DNA fibers can adopt the A-conformation, and DNA may be in the A-form in dehydrated structures, such as bacterial and fungal spores. The pentose conformation in A-DNA is 3Ј-endo, as opposed to 2Ј-endo in B-DNA. Dou- ble helical DNAϺRNA hybrids have an A-like conformation. The 2Ј-OH in RNA sterically prevents double helical regions of RNA chains from adopting the B-form helical arrangement. Importantly, double-stranded regions in RNA chains often assume an A-like conformation, with their bases strongly tilted with respect to the helix axis. Z-DNA Is a Conformational Variation in the Form of a Left-Handed Double Helix Z-DNA was first discovered when X-ray analysis of crystals of the synthetic deoxynu- cleotide dCpGpCpGpCpG revealed an antiparallel double helix of unexpected con- formation. The alternating pyrimidine–purine (Py–Pu) sequence of this oligonu- cleotide is the key to its unusual properties. The N-glycosyl bonds of G residues in this alternating copolymer are rotated 180° with respect to their conformation in B-DNA, so now the purine ring is in the syn rather than the anti conformation (Fig- ure 11.10). The C residues remain in the anti form. Because the G ring is “flipped,” T = 32° (a) G C A T (b) (1) (c) base base H 2 O H 2 O (2) Two base pairs with 32° of right-handed helical twist: the minor-groove edges are drawn with heavy shading. Propellor twist, as in (2), allows greater overlap of successive bases along the same strand and reduces the area of contact between the bases and water. Propellor-twisted base pairs. Note how the hydrogen bonds between bases are distorted by this motion, yet remain intact. The minor-groove edges of the bases are shaded gray. base base A T G C FIGURE 11.8 Helical twist and propellor twist in DNA. (a) Successive base pairs in B-DNA show a rotation with respect to each other. (b) Rotation in a different dimension—propellor twist—allows the hydrophobic surfaces of bases to overlap better. Dots represent axes perpendicular to the helix axis.The view is from the sugar–P backbone. (c) Each of the bases in a base pair shows positive propellor twist (a clockwise rotation from the horizontal, as viewed along the N-glycosidic bond, from the pentose C1Ј to the base). (Adapted from Figure 3.4 in Callandine, C. R., and Drew, H. R., 1992. Understanding DNA: The Molecule and How It Works. London: Academic Press.) 324 Chapter 11 Structure of Nucleic Acids the C ring must also flip to maintain normal Watson–Crick base pairing. However, pyrimidine nucleosides do not readily adopt the syn conformation because it cre- ates steric interference between the pyrimidine C-2 oxy substituent and atoms of the pentose. Because the cytosine ring does not rotate relative to the pentose, the whole C nucleoside (base and sugar) must flip 180° (Figure 11.11). It is topologically pos- sible for the G to go syn and the C nucleoside to undergo rotation by 180° without breaking and re-forming the GϺC hydrogen bonds. In other words, the B-to-Z struc- tural transition can take place without disrupting the bonding relationships among the atoms involved. A-DNA B-DNA Z-DNA FIGURE 11.9 Comparison of the A-, B-, and Z-forms of the DNA double helix.The A- and B-structures show 12 bp of DNA; the Z-structures, 6 bp.The middle Z-structure shows just one strand of a Z-DNA double helix to illustrate better the left-handed zigzag path of the polynucleotide backbones in Z-DNA. (The light blue line was added to show the imaginary zigzag path.) A-DNA: pdb id ϭ 2D47, B-DNA: pdb id ϭ 355D, Z-DNA: pdb id ϭ 1DCG. 11.2 What Sorts of Secondary Structures Can Double-Stranded DNA Molecules Adopt? 325 Double Helix Type ABZ Overall proportions Short and broad Longer and thinner Elongated and slim Rise per base pair 2.3 Å 3.32 Å Ϯ 0.19 Å 3.8 Å Helix packing diameter 25.5 Å 23.7 Å 18.4 Å Helix rotation sense Right-handed Right-handed Left-handed Base pairs per helix repeat 1 1 2 Base pairs per turn of helix ϳ11 ϳ10 12 Mean rotation per base pair 33.6° 35.9° Ϯ 4.2° Ϫ60°/2 Pitch per turn of helix 24.6 Å 33.2 Å 45.6 Å Base-pair tilt from the perpendicular ϩ19° Ϫ1.2° Ϯ 4.1° Ϫ9° Base-pair mean propeller twist ϩ18° ϩ16° Ϯ 7° ϳ0° Helix axis location Major groove Through base pairs Minor groove Major groove proportions Extremely narrow but very Wide and with Flattened out on helix deep intermediate depth surface Minor groove proportions Very broad but shallow Narrow and with Extremely narrow but very intermediate depth deep Glycosyl bond conformation anti anti anti at C, syn at G Adapted from Dickerson, R. L., et al., 1983. Helix geometry and hydration in A-DNA, B-DNA, and Z-DNA. Cold Spring Harbor Symposium on Quantitative Biology 47:13–24. TABLE 11.1 Comparison of the Structural Properties of A-, B-, and Z-DNA Deoxyguanosine in B-DNA (anti position) Deoxyguanosine in Z-DNA (syn position) FIGURE 11.10 Comparison of the deoxyguanosine con- formation in B- and Z-DNA. B-DNA B-DNA Z-DNA B-DNA 1 2 FIGURE 11.11 The change in topological relationships of base pairs from B- to Z-DNA. A six-base-pair GCGCGC segment of B-DNA (1) is converted to Z-DNA (2) through rotation of the base pairs, as indi- cated by the curved arrows.The purine rings (green) of the deoxyguanosine nucleosides rotate via an anti to syn change in the conformation of the guanine– deoxyribose glycosidic bond; the pyrimidine rings (blue) are rotated by flipping the entire deoxycyto- sine nucleoside (base and deoxyribose). 326 Chapter 11 Structure of Nucleic Acids Because alternate nucleotides assume different conformations, the repeating unit on a given strand in the Z-helix is the dinucleotide. That is, for any number of bases, n, along one strand, n Ϫ 1 dinucleotides must be considered. For example, a GpCpGpC subset of sequence along one strand is composed of three successive dinu- cleotide units: GpC, CpG, and GpC. (In A- and B-DNA, the nucleotide conformations are essentially uniform and the repeating unit is the mononucleotide.) It follows that the CpG sequence is distinct conformationally from the GpC sequence along the al- ternating copolymer chains in the Z-double helix. The conformational alterations go- ing from B to Z realign the sugar–phosphate backbone along a zigzag course that has a left-handed orientation (Figure 11.9), thus the designation Z-DNA. Note that in any GpCpGp subset, the sugar–phosphates of GpC form the horizontal “zig” while the CpG backbone segment forms the vertical “zag.” The mean rotation angle circum- scribed around the helix axis is Ϫ15° for a CpG step and Ϫ45° for a GpC step (giving Ϫ60° for the dinucleotide repeat). The minus sign denotes a left-handed or counter- clockwise rotation about the helix axis. Z-DNA is more elongated and slimmer than B-DNA. Cytosine Methylation and Z-DNA The Z-form can arise in sequences that are not strictly alternating Py–Pu. For example, the hexanucleotide m5 CGAT m5 CG, a Py-Pu- Pu-Py-Py-Pu sequence containing two 5-methylcytosines ( m5 C), crystallizes as Z-DNA. Indeed, the in vivo methylation of C at the 5-position is believed to favor a B-to-Z switch because, in B-DNA, these hydrophobic methyl groups would protrude into the aqueous environment of the major groove, a destabilizing influence. In Z-DNA, the same methyl groups can form a stabilizing hydrophobic patch. It is likely that the Z-conformation naturally occurs in specific regions of cellular DNA, which oth- erwise is predominantly in the B-form. Furthermore, because methylation is impli- cated in gene regulation, the occurrence of Z-DNA may affect the expression of ge- netic information (see Part 4). The Double Helix Is a Very Dynamic Structure The long-range structure of B-DNA in solution is not a rigid, linear rod. Instead, DNA behaves as a dynamic, flexible molecule. Localized thermal fluctuations temporarily distort and deform DNA structure over short regions. Base and backbone ensembles of atoms undergo elastic motions on a time scale of nanoseconds. To some extent, these effects represent changes in rotational angles of the bonds comprising the polynucleotide backbone. These changes are also influenced by sequence-dependent variations in base-pair stacking. The consequence is that the helix bends gently. When these variations are summed over the great length of a DNA molecule, these bending influences give the double helix a roughly spherical shape, as might be expected for a long, semirigid rod undergoing apparently random coiling. It is also worth noting that, on close scrutiny, the surface of the double helix is not that of a totally feature- less, smooth, regular “barber pole” structure. Different base sequences impart their own special signatures to the molecule by subtle influences on such factors as the groove width, the angle between the helix axis and base planes, and the mechanical rigidity. Certain regulatory proteins bind to specific DNA sequences and participate in activating or suppressing expression of the information encoded therein. These proteins bind at unique sites by virtue of their ability to recognize novel structural characteristics imposed on the DNA by the local nucleotide sequence. Intercalating Agents Distort the Double Helix Aromatic macrocycles, flat hydro- phobic molecules composed of fused, heterocyclic rings, such as ethidium bromide, acridine orange, and actinomycin D (Figure 11.12), can slip between the stacked base pairs of DNA. The bases are forced apart to accommodate these so-called intercalating agents, causing an unwinding of the helix to a more ladderlike struc- ture. The deoxyribose–phosphate backbone is almost fully extended as successive base pairs are displaced 0.7 nm from one another, and the rotational angle about the helix axis between adjacent base pairs is reduced from 36° to 10°. 11.2 What Sorts of Secondary Structures Can Double-Stranded DNA Molecules Adopt? 327 Dynamic Nature of the DNA Double Helix in Solution Intercalating substances in- sert with ease into the double helix, indicating that the van der Waals stacking in- teractions that they share with the bases sandwiching them are more favorable than similar interactions between the bases themselves. Furthermore, the fact that these agents slip in suggests that the double helix must momentarily unwind and present gaps for these agents to occupy. That is, the DNA double helix in solution must be represented by a set of metastable alternatives to the standard B-conformation. These alternatives constitute a flickering repertoire of dynamic structures. Alternative Hydrogen-Bonding Interactions Give Rise to Novel DNA Structures: Cruciforms, Triplexes and Quadruplexes Cruciform Structures Arise from Inverted Repeats Inverted repeats (Figure 11.13) are duplex DNA sequences showing twofold symmetry (the 5Јn3Ј sequence is identical in both strands). Palindromes are words, phrases, or sentences that read the same backward or forward, such as “radar,” “sex at noon taxes,” “Madam, I’m Adam,” and “a man, a plan, a canal, Panama.” Inverted repeats are sometimes re- ferred to as palindromes (despite the inaccuracy of this description). Inverted re- peats have the potential to adopt cruciform (meaning “cross-shaped”) structures if the normal interstrand base pairing is replaced by intrastrand pairing. In effect, each strand forms a hairpin structure through alignment and pairing of the self- complementary sequences along the strand. Cruciforms are never as stable as nor- mal DNA duplexes because an unpaired segment must exist in the loop region. Cru- ciforms potentially create novel structures that can serve as distinctive recognition sites for specific DNA-binding proteins. + H 2 N NH 2 N + CH 2 CH 3 Ethidium bromide N(CH 3 ) 2 (CH 3 ) 2 N + N H Acridine orange C O CH 3 CH 3 O N C O NH 2 O Thr OD-Val L-MevalPro Sarcosine Thr OD-Val L-MevalPro Sarcosine Actinomycin D Intercalating agentsB-DNA before intercalation B-DNA after intercalation Br – or or Sar = Sarcosine = H 3 C N H CH 2 COOH (N-Methylglycine) Meval = Mevalonic acid = HOCH 2 CH 2 CH 3 OH CH 2 COOHC FIGURE 11.12 The structures of ethidium bromide, acri- dine orange, and actinomycin D, three intercalating agents, and their effects on DNA structure. 328 Chapter 11 Structure of Nucleic Acids Hoogsteen Base Pairs and DNA Multiplexes The AϺT and GϺC base pairs first seen by Watson (Figure 11.6) are the canonical building blocks for DNA structures. How- ever, Karst Hoogsteen found that adenine and thymine do not pair in this way when crystallized from aqueous solution. Instead, they form two H bonds in a different arrangement (Figure 11.14). Further, Hoogsteen observed that, in mildly acidic solu- tions, guanine and cytosine form base pairs different from Watson–Crick GϺC base pairs. These Hoogsteen base pairs depend upon protonation of cytosine N-3 (Figure 11.14) and have only two H bonds, not three. In both AϺT and GϺC Hoogsteen base pairs, the purine N-7 atom is an H-bond acceptor. The functional groups of adenine and guanine that participate in Watson–Crick H bonds remain accessible in Hoog- steen base pairs. Thus, base triplets can form, as shown in Figure 11.15, giving rise G C T A A T C G T A T A G C C G A T G C G C A T T A A T A T C G A T G C C G C G T A G C C G A T A T G C A T C G T A . . . . . . G C T A A T. . . . . . C G C G T A G C C G A T A T G C C G T A T A G C C G A T G C G C A T C G T A . . . . . . T A T T G T C A T A A C A G . . . . . . FIGURE 11.13 Self-complementary inverted repeats can rearrange to form hydrogen-bonded cruciform stem- loop structures. FIGURE 11.14 Hoogsteen base pairs: AϺT (left) and C ϩ ϺG (right). H H N N + N H H N N N N O O N N N N T:A C + :G N N N O O H H H CH 3 N H H T:A:T C + :G:C A T H N N N N N N N N N O O O O H H H CH 3 CH 3 T N + N N H H H N N N N O O G C C N N H H H N O H N H FIGURE 11.15 Base triplets formed when a purine interacts with one pyrimidine by Hoogsteen base pairing and another by Watson–Crick base pairing. 11.2 What Sorts of Secondary Structures Can Double-Stranded DNA Molecules Adopt? 329 to TAT and a C ϩ GC triplets, where each purine interacts with one of its pyrimidine partners through Hoogsteen base pairing and the other through Watson–Crick base pairing. H-DNA Is Triplex DNA Under certain conditions, triple-stranded DNA struc- tures can form. In H-DNA, two of the strands are pyrimidine-rich and the third is purine-rich. One pyrimidine-rich strand is hydrogen bonded to the purine-rich strand via Watson–Crick base pairing, and the other pyrimidine-rich strand is hydrogen bonded to the purine-rich strand by Hoogsteen base pairing. Such structures were originally referred to as H-DNA, because protonation of the cy- tosine N-3 atom was necessary, but the name also fits because a hinge is present between double- and triple-stranded DNA regions when H-DNA forms. Consider, for example, a long stretch of alternating CϺT sequence in one strand of a DNA duplex (Figure 11.16). If the CϺT bases in half of this stretch separated from their GϺA partners and the unpaired CϺT segment folded back on the CϺT half still paired in the CϺT/GϺA duplex, triplex DNA could form through Hoogsteen base pairing. Triple-stranded DNA is implicated in the regulation of some eu- karyotic genes. DNA Quadruplex Structures Four-stranded DNA structures can form between polynucleotide strands rich in guanine. At the heart of such G-quadruplexes are cyclic arrays of four G residues united through Hoogsteen base pairing (Figure 11.17a). The presence of metal cations (K ϩ , Na ϩ , Ca 2ϩ ) favors their assembly. Free- electron pairs contributed by the closely spaced O6 carbonyl oxygens of the G-quartet coordinate the centrally located cation. A variety of different G-quadruplex structures have been reported, with different G-rich sequences leading to variations on a common quadruplex plan. Quadruplexes constructed from dG n strands usually form with all four strands in parallel orientation and all bases in the anti conforma- tion (Figure 11.17b). Polynucleotides with varying sequence repeats, such as (G 3 N) n or (G 2 N 2 ) n , form G-quadruplexes with variations on the dG n structural theme, such as the (dG 4 T 4 G 4 ) 2 structure in which two such strands pair in antiparallel fashion to form the G-quadruplex (Figure 11.17c and 11.17d). G-quadruplex structures have biological significance because they have been found in telomeres (structures that define the ends of chromosomes), in regulatory regions of genes, in immunoglobu- lin gene regions responsible for antibody diversity, and in sequences associated with human diseases. C G (a) (b) C40 • 3Ј 5Ј C G T A G G CG CG 3Ј 5Ј G50 C TA TA AT AT TA TA TA TA C T T A C G C G A AA T T G C A T G TC C A T G C A T G C A T G C A T G C A T G C A T 5 – 1 • 1 5 G • + • + • +• + • + • +• +• + C C TCTCTCTCTCTC T G G A T C • C AGAGAGAG 3 0 AGAGAGAG A A T T FIGURE 11.16 H-DNA.(a) The pyrimidine-rich strands of the duplex regions are blue, and the purine-rich strands are green.The Hoogsteen base-paired pyrimidine-rich strand in the triplex (H-DNA) structure is yellow. (b) Nucleotide sequence representation of H-DNA formation.TϺA Hoogsteen base pairing leading to triplex formation is shown by dots; C ϩ -G Hoogsteen base pair- ing leading to triplex formation is shown by ϩ signs. (Adapted from Htun, H., and Dahlberg, J. E., 1989.Topology and formation of triple-stranded H-DNA. Science 243:1571–1576.) 330 Chapter 11 Structure of Nucleic Acids 11.3 Can the Secondary Structure of DNA Be Denatured and Renatured? Thermal Denaturation of DNA Can Be Observed by Changes in UV Absorbance When duplex DNA molecules are subjected to conditions of pH, temperature, or ionic strength that disrupt base-pairing interactions, the strands are no longer held together. That is, the double helix is denatured, and the strands separate as indi- vidual random coils. If temperature is the denaturing agent, the double helix is said to melt. The course of this dissociation can be followed spectrophotometrically be- cause the relative absorbance of the DNA solution at 260 nm increases as much as 40% as the bases unstack. This absorbance increase, or hyperchromic shift, is due to the fact that the aromatic bases in DNA interact via their -electron clouds when stacked together in the double helix. Because the UV absorbance of the bases is a consequence of -electron transitions, and because the potential for these transi- tions is diminished when the bases stack, the bases in duplex DNA absorb less 260-nm radiation than expected for their numbers. Unstacking alleviates this sup- G4 G4 G1 G3 G2 G3 G4 (a) (c) (b) G2 G1 G1 G3 G2 G4 G1 G3 G2 G12 T8 T6 T5 G9 G10 G11 G2 G1 T7 G3 G4 G9 G11 G10 G4 G1 G3 G2 G12 N N N N O O H H H H H H N N NN NH H O NH N H H H N H N N N O H H H N N N NN (d) FIGURE 11.17 (a) G-quadruplex showing the cyclic array of guanines linked by Hoogsteen hydrogen bonding.(b) Four G-rich polynucleo- tide strands in parallel alignment with all bases in anti conformation. (c) Antiparallel dimeric hairpin quadruplex formed from d(G 4 T 4 G 4 ) 2 . (d) Structure of d(G 4 T 4 G 4 ) 2 K ϩ solved by X-ray crystal- lography.Two d(G 4 T 4 G 4 ) strands come together as hairpins to form a G-quadruplex .The back- bones of the two strands are traced in violet. (Adapted from Keniry, M. A., 2001. Quadruplex structures in nucleic acids. Biopolymers 56:123–146.) 11.3 Can the Secondary Structure of DNA Be Denatured and Renatured? 331 pression of UV absorbance. The rise in absorbance coincides with strand separa- tion, and the midpoint of the absorbance increase is termed the melting tempera- ture, T m (Figure 11.18). DNAs differ in their T m values because they differ in rela- tive G ϩ C content. The higher the G ϩ C content of a DNA, the higher its melting temperature because GϺC pairs have higher base stacking energies than AϺT pairs. Also, T m is dependent on the ionic strength of the solution; the lower the ionic strength, the lower the melting temperature. Because cations suppress the electro- static repulsion between the negatively charged phosphate groups in the comple- mentary strands of the double helix, the double-stranded form of DNA is more sta- ble in dilute salt solutions. DNA in pure water melts even at room temperature. pH Extremes or Strong H-Bonding Solutes also Denature DNA Duplexes At pH values greater than 10, the bases of DNA become deprotonated, which de- stroys their base-pairing potential, thus denaturing the DNA duplex. Extensive pro- tonation of the bases below pH 2.3 also disrupts base pairing. Alkali is the preferred denaturant because, unlike acid, it does not hydrolyze the glycosidic bonds linking purine bases to the sugar–phosphate backbone. Small solutes that readily form H bonds can also denature duplex DNA at temperatures below T m. If present in suffi- ciently high concentrations, such small solutes will form H bonds with the bases, thereby disrupting H-bonding interactions between the base pairs. Examples in- clude formamide and urea. Single-Stranded DNA Can Renature to Form DNA Duplexes Denatured DNA will renature to re-form the duplex structure if the denaturing con- ditions are removed (that is, if the solution is cooled, the pH is returned to neutral- ity, or the denaturants are diluted out). Renaturation requires reassociation of the DNA strands into a double helix, a process termed reannealing. For this to occur, the strands must realign themselves so that their complementary bases are once again in register and the helix can be zippered up (Figure 11.19). Renaturation is dependent on both DNA concentration and time. Many of the realignments are imperfect, and thus the strands must dissociate again to allow for proper pairings to be formed. The process occurs more quickly if the temperature is warm enough to promote diffusion of the large DNA molecules but not so warm as to cause melting. The Rate of DNA Renaturation Is an Index of DNA Sequence Complexity The renaturation rate of DNA is an excellent indicator of the sequence complexity of DNA. For example, the DNA of bacteriophage T4 contains 2 ϫ 10 5 base pairs; an Escherichia coli cell contains more than ten times as much (4.64 ϫ 10 6 base pairs). 70 80 90 100 Temperature (ЊC) 1.0 1.2 1.4 Relative absorbance (260 nm) Pneumococcus (38% G + C) E. coli (52%) S. marcescens (58%) M. phlei (66%) FIGURE 11.18 Heat denaturation of DNA from various sources, so-called melting curves. (From Marmur, J., 1959. Heterogenity in deoxyribonucleic acids. Nature 183:1427–1429.) 332 Chapter 11 Structure of Nucleic Acids E. coli DNA is considerably more complex in that it encodes more information. Ex- pressed in another way, for any fixed amount of single-stranded DNA (in grams), the nucleotide sequences represented in an E. coli sample will show greater sequence variation than those in an equal weight of phage T4 DNA. Thus, it will take longer for the E. coli DNA strands to find their complementary partners and reanneal. Because the rate of DNA duplex formation depends on complementary DNA sequences en- countering one another and beginning the process of sequence alignment and rean- nealing, the time necessary for reconstituting double-stranded DNA molecules is an excellent index of the degree of sequence complementarity in a DNA sample. Nucleic Acid Hybridization: Different DNA Strands of Similar Sequence Can Form Hybrid Duplexes If DNA from two different species are mixed, denatured, and allowed to cool slowly so that reannealing can occur, hybrid duplexes may form, provided the DNA from one species is similar in nucleotide sequence to the DNA of the other. The degree A DEEPER LOOK The Buoyant Density of DNA Density gradient ultracentrifugation is a variant of the basic tech- nique of ultracentrifugation (discussed in the Appendix to Chap- ter 5). The densities of DNAs are about the same as those of con- centrated solutions of cesium chloride, CsCl (1.6 to 1.8 g/mL). Centrifugation of CsCl solutions at very high rotational speeds, where the centrifugal force becomes 10 5 times stronger than the force of gravity, causes the formation of a density gradient within the solution. This gradient is the result of a balance that is estab- lished between the sedimentation of the salt ions toward the bot- tom of the tube and their diffusion upward toward regions of lower concentration. If DNA is present in the centrifuged CsCl solution, it moves to a position of equilibrium in the gradient equivalent to its buoyant density (as shown in the figure). For this reason, this technique is also called isopycnic centrifugation. Cesium chloride centrifugation is an excellent means of re- moving RNA and proteins in the purification of DNA. The density of DNA is typically slightly greater than 1.7 g/cm 3 , whereas the density of RNA is more than 1.8 g/cm 3 . Proteins have densities less than 1.3 g/cm 3 . In CsCl solutions of appropriate density, the DNA bands near the center of the tube, RNA pellets to the bottom, and the proteins float near the top. Single-stranded DNA is denser than double helical DNA. The irregular structure of randomly coiled ssDNA allows the atoms to pack together through van der Waals interactions. These interactions compact the molecule into a smaller volume than that occupied by a hydrogen-bonded dou- ble helix. The net movement of solute particles in an ultracentrifuge is the result of two processes: diffusion (from regions of higher con- centration to regions of lower concentration) and sedimentation due to centrifugal force (in the direction away from the axis of ro- tation). In general, diffusion rates for molecules are inversely pro- portional to their molecular weight—larger molecules diffuse more slowly than smaller ones. On the other hand, sedimentation rates increase with increasing molecular weight. A macromolecu- lar species that has reached its position of equilibrium in isopycnic centrifugation has formed a concentrated band of material. Essentially three effects are influencing the movement of the molecules in creating this concentration zone: (1) diffusion away to regions of lower concentration, (2) sedimentation of molecules situated at positions of slightly lower solution density in the den- sity gradient, and (3) flotation (buoyancy or “reverse sedimenta- tion”) of molecules that have reached positions of slightly greater solution density in the gradient. The consequence of the physics of these effects is that, at equilibrium, the width of the concentration band established by the macromolecular species is inversely proportional to the square root of its molecular weight. That is, a population of large molecules will form a concentration band that is narrower than the band formed by a population of small molecules. For example, the bandwidth formed by dsDNA will be less than the bandwidth formed by the same DNA when dissociated into ssDNA. CsCl solution [6 M; density ()~1.7] Cell extract Mix CsCl solution and cell extract and place in centrifuge. Centrifuge at high speed for ~48 hours. Proteins and nucleic acids absorb UV light. The positions of these molecules within the centrifuge can be determined by ultraviolet optics. =1.65 =1.80 CsCl density DNA RNA Protein 1.80 1.65 Molecules move to positions where their density equals that of the CsCl solution. Density () in g/mL RNA DNA Protein . re- ferred to as palindromes (despite the inaccuracy of this description). Inverted re- peats have the potential to adopt cruciform (meaning “cross-shaped”) structures if the normal interstrand base. as nor- mal DNA duplexes because an unpaired segment must exist in the loop region. Cru- ciforms potentially create novel structures that can serve as distinctive recognition sites for specific. Because the UV absorbance of the bases is a consequence of -electron transitions, and because the potential for these transi- tions is diminished when the bases stack, the bases in duplex DNA absorb