Nucleic Acid Structure:- Certain DNA Sequences Adopt Unusual Structures

A number of other sequence-dependent structural variations have been detected within larger chromosomes that may affect the function and metabolism of the DNA segments in their immediate vicinity. For example, bends occur in the DNA helix wherever four or more adenosine residues appear sequentially in one strand. Six adenosines in a row produce a bend of about 18.

FIGURE 8–20 Palindromes and mirror repeats. Palindromes are sequences of double-stranded nucleic acids with twofold symmetry. In order to superimpose one repeat (shaded sequence) on the other, it must be rotated 180 about the horizontal axis then 180 about the vertical axis, as shown by the colored arrows. A mirror repeat, on the other hand, has a symmetric sequence within each strand. Superimposing one repeat on the other requires only a single 180 rotation about the vertical axis.

The bending observed with this and other sequences may be important in the binding of some proteins to DNA. A rather common type of DNA sequence is a palindrome. A palindrome is a word, phrase, or sentence that is spelled identically read either forward or back ward; two examples are ROTATOR and NURSES RUN. The term is applied to regions of DNA with inverted repeats of base sequence having twofold symmetry over two strands of DNA (Fig. 8–20). Such sequences are self-complementary within each strand and therefore have the potential to form hairpin or cruciform (cross-shaped) structures (Fig. 8–21). When the in verted repeat occurs within each individual strand of the DNA, the sequence is called a mirror repeat. Mirror repeats do not have complementary sequences within the same strand and cannot form hairpin or cruciform structures. Sequences of these types are found

FIGURE 8–21 Hairpins and cruciforms. Palindromic DNA (or RNA) sequences can form alternative structures with intrastrand base pairing. (a) When only a single DNA (or RNA) strand is involved, the structure is called a hairpin. (b) When both strands of a duplex DNA are involved, it is called a cruciform. Blue shading highlights asymmetric sequences that can pair with the complementary sequence ei ther in the same strand or in the complementary strand.

in virtually every large DNA molecule and can encompass a few base pairs or thousands. The extent to which palindromes occur as cruciforms in cells is not known, although some cruciform structures have been demon strated in vivo in E.coli. Self-complementary sequences cause isolated single strands of DNA (or RNA) in solution to fold into complex structures containing multiple hairpins.

Several unusual DNA structures involve three or even four DNA strands. These structural variations merit investigation because there is a tendency for many of them to appear at sites where important events in DNA metabolism (replication, recombination, transcription) are initiated or regulated. Nucleotides participating in a Watson-Crick base pair (Fig. 8–11) can form a number of additional hydrogen bonds, particularly with functional groups arrayed in the major groove. For example, a cytidine residue (if protonated) can pair with the guanosine residue of a G≡C nucleotide pair, and a thymidine can pair with the adenosine of an AUT pair (Fig. 8–22). The N-7, O⁶, and N⁶ of purines, the atoms that participate in the hydrogen bonding of triplex DNA, are often referred to as Hoogsteen positions, and the non-Watson-Crick pairing is called Hoogsteen pairing, after Karst Hoogsteen, who in 1963 first recognized the potential for these unusual pairings. Hoogsteen pairing allows the formation of triplex DNAs. The triplexes shown in Figure 8–22 (a, b) are most stable at low pH

FIGURE 8–22 DNA structures containing three or four DNA strands. (a) Base-pairing patterns in one well-characterized form of triplex DNA. The Hoogsteen pair in each case is shown in red. (b) Triple helical DNA containing two pyrimidine strands (poly(T)) and one purine strand (poly(A)) (derived from PDB ID 1BCE). The dark blue and light blue strands are antiparallel and paired by normal Watson Crick base-pairing patterns. The third (all-pyrimidine) strand (purple) is parallel to the purine strand and paired through non-Watson-Crick hydrogen bonds. The triplex is viewed end-on, with five triplets shown. Only the triplet closest to the viewer is colored. (c) Base-pairing pat tern in the guanosine tetraplex structure. (d) Two successive tetraplets from a G tetraplex structure (derived from PDB ID 1QDG), viewed end-on with the one closest to the viewer in color. (e) Possible variants in the orientation of strands in a G tetraplex.

because the C≡G .C⁺ triplet requires a protonated cytosine. In the triplex, the pKa of this cytosine is >7.5, altered from its normal value of 4.2. The triplexes also form most readily within long sequences containing only pyrimidines or only purines in a given strand. Some triplex DNAs contain two pyrimidine strands and one purine strand; others contain two purine strands and one pyrimidine strand.

Four DNA strands can also pair to form a tetraplex (quadruplex), but this occurs readily only for DNA sequences with a very high proportion of guanosine residues (Fig. 8–22c, d). The guanosine tetraplex, or G tetraplex, is quite stable over a wide range of conditions. The orientation of strands in the tetraplex can vary as shown in Figure 8–22e.

A particularly exotic DNA structure, known as H-DNA, is found in polypyrimidine or polypurine tracts that also incorporate a mirror repeat. A simple example is a long stretch of alternating T and C residues (Fig. 8–23). The H-DNA structure features the triple-stranded form illustrated in Figure 8–22 (a, b). Two of the three strands in the H-DNA triple helix contain pyrimidines and the third contains purines.

In the DNA of living cells, sites recognized by many sequence-specific DNA-binding proteins (Chapter 28) are arranged as palindromes, and polypyrimidine or polypurine sequences that can form triple helices or even H-DNA are found within regions involved in the regulation of expression of some eukaryotic genes. In principle, synthetic DNA strands designed to pair with these sequences to form triplex DNA could disrupt gene expression. This approach to controlling cellular me tabolism is of growing commercial interest for its po tential application in medicine and agriculture.

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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:- DNA Can Occur in Different Three-Dimensional Forms

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