Palindromic helix

A molecular helix is defined by an axis, by its screw sense and its pitch. If the radius is constant, there is a cylindrical helix, if it changes constantly, a conical helix exists. A palindromic helix is characterized by a constant pitch. 

Approximately 10 base pairs are required to make one turn in B-DNA. The centers of the palindromic sequences in the DNA-binding regions of the operator are also separated by about 10 base pairs (see Table 8.1). Thus if one of the recognition a helices binds to one of the palindromic DNA sequences, the second recognition a helix of the protein dimer is poised to bind to the second palindromic DNA sequence. 

Proteins with the helix-turn-helix or leucine zipper motifs form symmetric dimers, and their respective DNA binding sites are symmetric palindromes. In proteins with the zinc finger motif, the binding site is repeated two to nine times. These features allow for cooperative interactions between binding sites and enhance the degree and affinity of binding. 

The interaction between the receptor dimer and DNA is produced in an orderly manner. First, the dimer is placed in the main furrow of the double helix, and the first monomer interacts with the first pentamer of the HRE in the main furrow of the double helix. Later the second molecule of the receptor dimer binds to the second pentamer. The distance between both pentamers is minimum from zero to five nucleotides, depending on the type of receptor. This implies that the dimer assures a sufficiently compact and symmetrical structure among both receptor molecules, so that a similar intimacy can be produced in the association with the palindrome. 

A detailed oxidation study on an artificially designed palindromic peptide with a predicted high tendency to form antiparallel a-helices confirmed that stabilization of the a-helix by increasing amounts of TFE allowed the control of the product distribution in favor of the antiparallel dimer to a certain degree, although increasing amounts of cyclic trimers were formedi106 In the absence of or at low levels of TFE, formation of the cyclic monomer was predominant. 

Fig. 1.38. Formation of homo- and heterodimeric transcription factors and the specificy of DNA-binding. Shown are two different helrx-loop-helix proteins, which bind as homodimers (a, b) to the each of their cognate palindromic DNA elements (drawn as arrows). The two homodimers display different DNA-binding specificity. The heterodimerization (c) of the two proteins creates a complex that recognizes a hybrid DNA element.

Figure 5-35 Stereoscopic drawings illustrating the binding of a dimeric molecule of the Trp repressor protein to a palindromic sequence in DNA. (A) Schematic view showing structures of the aporepressor (partly shaded gray) and the holorepressor with bound tryptophan (unshaded) are superimposed. Cylinders represent the a helices in (B). From Zhang et al.wi (B) MolScript ribbon diagram with a few side chains that interact with the DNA shown. Two tandemly bound dimeric repressor molecules are shown. Two bound molecules of tryptophan are visible in each dimer. The DNA is drawn as a double helix with lines representing the base pairs. From Lawson and Carey.405...

Recently, a quite different model has been proposed that accounts for the appearance of many kinds of mutations, including base pair substitutions, additions and deletions, and small chromosomal mutations of the type that would usually be classified as gene mutations. The model accounts for frequent palindromic sequences (more exactly, imperfect palindromes or quasipalindromes) in DNA that can predispose to alternative DNA structures (e.g., clover leaves) that differ from the usual double helix. The alternative or "secondary" structures can then be acted on by any of a variety of DNA-processing enzymes in ways that may ultimately lead to mutations. The details of these processes are only now becoming manifest, but the general model clearly explains many hitherto mysterious mutational phenomena.371... 

A palindrome is a word or sentence that reads the same way backward and forward. An example is A man, a plan, a canal—Panama. When applied to DNA, palindrome means a sequence of nucleotides that reads the same in the 5 3 direction on both strands of the double helix. 

The DNA double helix is not necessarily the continuous smooth structure shown in Figure 10.20. There may be bulges of various sorts, loops, and palindromic hairpin turns. A palindrome is a section of DNA in which the two DNA strands have an identical base sequence running in opposite directions. Figure 10.23 shows a double-stranded DNA with some such features. Of most interest are the cruciform bulges and palindromic structures. Note that in the cruciform structure, there are two pairs of palindromic sequences on the vertical... 

FIGURE 9 A single turn of a right-handed (P) circular palindromic single-stranded helix. L is the pitch, z is the helical axis, and A is the area of the subtended circle in the plane xy (reproduced by permission from Piguet et al., 1997a,b, 1997 American Chemical Society). 

See Section 9.3.3 of the text [pp. 248-25 f] for an example of an enzyme, EcoRV, that recognizes a palindromic DNA sequence. Note, however, EcoRV does not use a helices to contact the DNA. See p. 874 for examples of helix-tum-helix-containing proteins that bind adjacent major grooves of B-DNA.)... 

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