Cruciform structure

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. 

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... 

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. 

Palindromes are often imperfect as is the one shown in Fig. 5-34. Here the two stems in the cruciform structure are related by an exact twofold rotational symmetry but the loops at the ends of the stems are not. 

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... 

Creutzfeldt-Jakob disease 248 Crick, Francis H. C. 84, 200 Cristae of mitochondria 14 Crossing-over 18 Crosslinking 79 Crotonase. See Enoyl hydratase Crowfoot Hodgkin, Dorothy M. 84 Cruciform structure in nucleic acids 229 Crustacea 24 Cruzain 619 Cryoenzymology 469 elastase 616 Cryoprotectants 191 Crystallins 169 Crystallography 131-137 electron 131 X-ray 132-137 Crystals, liquid 392-394 Crystal systems 133 Cubic symmetry... 

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... 

Palindromic double strands of this kind can potentially form cruciform structures through the individual single strands forming looped out structures. 

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 + >... 

A cruciform. A nucleic acid molecule is shown in a cruciform structure. Two strands with complementary base sequence are shown with the backbones highlighted in purple, the individual bases are the short lines perpendicular to the backbones. Base pairing occurs wherever a base is shown joined to its partner. Note that both interstrand and intrastrand base pairing occur. 

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