DNA cruciform

One more interesting structure, also representing an unusual metal-binding center, is the DNA cruciform (or four-way junction) structure. This type of structure results from rearrangement of palindromes (inverted repeat sequences) and may be formed reversibly under certain conditions (e.g. to relax strain in supercoiled DNA). The relative efficiency of different divalent metal ions in promoting the formation of DNA cruciform structures is Mg + > Mn + > Co + >... 

Figure 17. Probing DNA cruciforms (88). Shown on the left is tris(diphenylphenanthroline)-rhodium(III), [Rh(DIP),] , which cleaves DNA cruciforms in a double-stranded fashion with photoactivation. On the right are shown the major cleavage sites for [Rh(DIP),] (delineated by the arrows) on a pBR322 cruciform.

DNA supercoiling provides conformational potential energy for DNA tertiary structure formation such as the development of DNA cruciform structures (Figure 1.77). Supercoiling also leads to the creation of DNA triple helix (DNA triplex) structures, which form when an oligodeoxynucleotide chain, with an appropriately complementary deoxynucleotide residue... 

AT- or GC-rich sequences, which are known to have propensities for assuming unusual conformations including kinks, Z-DNA, cruciforms, triple helices, or supercoils (see Section II, in Chapter 1). The inherent curvature, as well as protein-induced bending of DNA, is believe to be part of the driving force in the initiation of transcription. 

FIGURE 12.27 The formation of a cruciform structure from a paliudromic sequence within DNA. The self-complementary Inverted repeats can rearrange to form hydrogen-bonded cruciform loops. 

Bianchi, M.E. (1988) Interaction of a protein from rat liver nuclei with cruciform DNA. EMBO J. 7, 843-849. 

The Watson and Crick model for DNA as a double helix is only a generalized model to describe much more complex structures. Along with the typical double helix there exist structural elements such as supercoils, kinks, cruciforms, bends, loops, and triple strands as well as major and minor grooves. Each of these structural elements can vary in length, shape, location, and frequency. Even the simple DNA double helix can vary in pitch (number of bases per helical turn), sugar pucker conformation, and helical sense (whether the helix is left-or right-handed). 

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 backward 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 inverted repeat occurs within each individual strand of the DNA, the sequence is called a mirror repeat. Mrror 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 Fblindromic 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 either in the same strand or in the complementary strand. 

DNA can exist in several structural forms. Two variations of the Watson-Crick form, or B-DNA, are A- and Z-DNA. Some sequence-dependent structural variations cause bends in the DNA molecule. DNA strands with appropriate sequences can form hairpin/cruciform structures or triplex or tetraplex DNA... 

FIGURE 24-19 Promotion of cruciform structures by DNA under-winding. In principle, cruciforms can form at palindromic sequences (see Fig. 8-21), but they seldom occur in relaxed DNA because the linear DNA accommodates more paired bases than does the cruciform structure. Underwinding of the DNA facilitates the partial strand separation needed to promote cruciform formation at appropriate sequences. 

Until rather recently there had been little to indicate that DNA actually assumes cruciform conformations in cells. However, strong experimental evidence suggests that some cruciform structures do form naturally.380 Their formation from palindromic DNA [like the formation of Z-DNA from (G + C)-rich sequences] is a way of relieving torsional strain induced by super-coiling. Whether or not cruciform structures occur frequently within cells, there is no doubt that palindromic sequences are of great importance in the interaction of nucleic acids with symmetric dimeric and tetrameric protein molecules such as the gene repressor protein shown in Fig. 5-35.381-383... 

The Holliday junction is a cruciform structure composed of two unbound strands of DNA that have crossed over, that is, a single strand of one sequence is not paired with its complementary strand but with one from another sequence. Its existence has led to the use of DNA as a structural nanomaterial as will be seen in a later chapter. 

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 10.23 Section of double-stranded DNA showing a palindrome section, a cruciform hairpin loop structure, a bulge loop, and an interior loop. Palindromic sequences are boxed. A black dot between bases indicates hydrogen bonding. The interior loop is common in RNA and relatively uncommon in DNA.

Bonnefoy, E., Takahashi, M. Rouviere-Yaniv, J. (1994). DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA. J. Mol. Biol. 242,116-129. 

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