1.9.2 Stability of Nucleic Acids

Unit 1 designation “Gro”). Unfolded proteins are bound within pockets in the GroEL complex, and the pockets are capped transiently by the GroES “lid” (Fig. 1.96). GroEL undergoes substantial conformational changes, coupled to ATP hydrolysis and the binding and release of GroES, which promote folding of the bound polypeptide. Although the structure of the GroEL/GroES chaperonin is known, many details of its mechanism of action remain unresolved.

Finally, the folding pathways of a number of proteins require two enzymes that catalyze isomerization reactions. Protein disulfide isomerase (PDI) is a widely distributed enzyme that catalyzes the interchange or shuffling of disulfide bonds until the bonds of the native conformation are formed. Among its functions, PDI catalyzes the elimination of folding intermediates with inappropriate disulfide cross-links. Peptide prolyl cistrans isomerase (PPI) catalyzes the interconversion of the cis and trans isomers of Pro peptide bonds, which can be a slow step in the folding of proteins that contain some Pro residue peptide bonds in the cis conformation. Protein folding is likely to be a more complex process in the densely packed cellular environment than in the test tube. More classes of proteins that facilitate protein folding may be discovered as the biochemical dissection of the folding process continues

1.9.2 Stability of Nucleic Acids

The role of DNA as a repository of genetic information depends in part on its inherent stability. The chemical transformations that do occur are generally very slow in the absence of an enzyme catalyst. The long-term storage of information without alteration is so important to a cell, however, that even very slow reactions that alter DNA structure can be physiologically significant.

Processes such as carcinogenesis and aging may be intimately linked to slowly accumulating, irreversible alterations of DNA. Other, non-destructive alterations also occur and are essential to function, such as the strand separation that must precede DNA replication or transcription. In addition to providing insights into physiological processes, our understanding of nucleic acid chemistry has given us a powerful array of technologies that have applications in molecular biology, medicine, and forensic science. We now examine the chemical properties of DNA and some of these technologies.

Denaturation and renaturation

Figure 1.9.7Heat denaturation of DNA. (a) The denaturation, or melting, curves of two DNA specimens. The temperature at the midpoint of the transition (tm) is the melting point; it depends on pH and ionic strength and on the size and base composition of the DNA.

Unit 1 decreases sharply, indicating that the DNA has undergone a physical change. Just as heat and extremes of pH denature globular proteins, they also cause denaturation, or melting, of double-helical DNA. Disruption of the hydrogen bonds between paired bases and of base stacking causes unwinding of the double helix to form two single strands, completely separate from each other along the entire length or part of the length (partial denaturation) of the molecule. No covalent bonds in the DNA are broken (Fig.1.9.7). Renaturation of a DNA molecule is a rapid one-step process, as long as a double-helical segment of a dozen or more residues still unites the two strands. When the temperature or pH is returned to the range in which most organisms live, the unwound segments of the two strands spontaneously rewind, or anneal, to yield the intact duplex (Fig. 1.9.7). However, if the two strands are completely separated, renaturation occurs in two steps. In the first, relatively slow step, the two strands “find” each other by random collisions and form a short segment of complementary double helix. The second step is much faster: the remaining unpaired bases successively come into register as base pairs, and the two strands “zipper” themselves together to form the double helix. The close interaction between stacked bases in a nucleic acid has the effect of decreasing its absorption of UV light relative to that of a solution with the same concentration of free nucleotides, and the absorption is decreased further when two complementary nucleic acids strands are paired. This is called the hypochromic effect. Denaturation of a double-stranded nucleic acid produces the opposite result: an Figure 1.9.8 Absorption spectra of the common nucleotides. The increase in absorption called the spectra are shown as the variation in molar extinction coefficient Hyperchromic effect. with wavelength. The molar extinction coefficients at 260 nm and pH

7.0 (260) are listed in the table. The spectra of corresponding

The transition from double-stranded ribonucleotides and deoxyribonucleotides, as well as the DNA to the single-stranded, nucleosides, are essentially identical. For mixtures of nucleotides, a denatured form can thus be wavelength of 260 nm (dashed vertical line) is used for absorption detected by monitoring the measurements. absorption of UV light. Viral or bacterial DNA molecules in solution denature when they are heated slowly (Fig. 1.9.7). Each species of DNA has a characteristic denaturation temperature, or melting point (tm): the higher its content of GqC base pairs, the higher the melting point of the DNA. This is because GqC base pairs, with three hydrogen bonds, require more heat energy to dissociate than AUT base pairs. Careful determination of the melting point of a DNA specimen, under fixed conditions of pH and ionic strength, can yield an estimate of its base composition. If denaturation conditions are carefully controlled, regions that are rich in AUT base pairs will specifically denature while most of the DNA remains double stranded. Strand separation of DNA must occur in vivo during processes such as DNA replication and transcription. As we shall see, the DNA sites where these processes are initiated are often rich in AUT base pairs. Duplexes of two RNA strands or of one RNA strand and one DNA strand (RNA-DNA hybrids) can also be denatured. Notably, RNA duplexes are more stable than DNA duplexes. At neutral pH, denaturation of a double helical RNA often requires temperatures 20oC or higher than those required for denaturation of a DNA molecule with a comparable sequence. The stability of an RNA-DNA hybrid is generally intermediate between that of RNA and that of DNA. The physical basis for these differences in thermal stability is not known.

 Bases are very nearly planar  Aromaticity => large absorbance at 260nm  Epsilon 260 ≈ 10,000 (M-1 cm-1 )  The A260 ≈ 50 μg /ml for DS DNA

Unit 1  The A260 ≈ 40 μg /ml for SS DNA or RNA  Flat surfaces are hydrophobic  Dipole-Dipole and Van Der Waals interactions also stabilize stacked structures  Bases have hydrogen bond donors and acceptors  H-bonding potential satisfied in paired structures Free pyrimidine and purines are weakly basic compounds 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, a property with important consequences for the structure, electron distribution, and light absorption of nucleic acids. Resonance among atoms in the ring gives most of the bonds partial double-bond character. One result is that pyrimidines 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 depending on the pH. As a result of resonance, all nucleotide bases absorb UV light, and nucleic acids are characterized by a strong absorption at wavelengths near 260 nm (Fig. 1.9.9). 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. Hydrophobic stacking interactions in which two or more bases are positioned with the planes of their rings parallel (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 water, and base-stacking interactions are very important in stabilizing the three-dimensional structure of nucleic acids.

Trans esterification reaction

RNA , bur not DNA can undergo the trans esterification reaction . This property is attributed to the presence of 2’OH group on the ribose sugar, which is absent in DNA. The following figure 1.9.9 shows the mechanism of the reaction.

Figure 1.9.9 Trans-esterification reaction. This is the first step in the splicing of group I introns. Here, the 3 OH of a guanosine molecule acts as nucleophile.

Critical thinking Questions 1. Suppose you want to radioactively label DNA but not RNA in dividing and growing bacterial cells. Which radioactive molecule would you add to the culture medium? 2. RNA is readily hydrolyzed by alkali whereas DNA is not. Why? 3. The amino acid coded by codon GGG could not be deciphered in the same way as UUU,

CCC or AAA. Why is polyG an ineffective template? 4. Griffith used heat-killed S. Pneumococci to transform R mutants. Studies years later showed that dsDNA is needed for efficient transformation and that high temperature melt the DNA double helix. Why were Griffith’s experiments nevertheless successful? 5. In designing of primers, the Tm of each primer should approximately be the same. What is the basis of this requirement?