Palindromes, DNA

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. 

The central 10 base pairs of the palindromic DNA molecule have a regular B-DNA structure. Between base pairs 5 and 6 in each half of the fragment (base pairs are counted from the center) there is a 40° kink which causes these base pairs to be unstacked (Figure 8.24a). After this localized kink the two end regions have an essentially B-DNA structure. The kink occurs at a TG step in the sequence GTG. These TG steps at positions 5 and 6 are highly conserved in both halves of different CAP-binding sites, presumably in part because they facilitate kinking. 

Like Thr 124 and Thr 215, the Asn 69 and Asn 159 residues occupy equivalent positions in the two homologous motifs of TBP. By analogy with the symmetric binding of a dimeric repressor molecule to a palindromic sequence described in Chapter 8, the two motifs of TBP form symmetric sequence-specific hydrogen bonds to the quasi-palindromic DNA sequence at the center of the TATA box. The consensus TATA-box sequence has an A-T base pair at position 4, but either a T-A or an A-T base pair at the symmetry-related position 5, and the sequence is, therefore, not strictly palindromic. However, the hydrogen bonds in the minor groove can be formed equally well to an A-T base pair or to a T-A base pair, because 02 of thymine and N3 of adenine occupy nearly stereochemically equivalent positions, and it is sufficient, therefore, for the consensus sequence of the TATA box to be quasi-palindromic. 

The individual domains of the two receptors both have structures similar to that of the glucocorticoid receptor, and they bind to DNA in a similar way, with their recognition helices in the major groove. The dimer contacts are, however, totally different. In the glucocorticoid receptor, which binds to a palindromic DNA sequence like the 434 repressor described in Chapter 8, the domains interact symmetrically in a head-to-head fashion equivalent... 

Akhmedov AT, Gross B, Jessberger R 1999 Mammalian SMC3 C-terminal and coiled-coil protein domains specifically bind palindromic DNA, do not block DNA ends, and prevent DNA bending. J Biol Chem 274 38216-38224... 

The center of the palindromic DNA was of necessity changed from the native a-satellite to provide for construction of the palindrome [30]. The deviation of the palindrome from perfect symmetry on the histone octamer may be a... 

Fig. 18. TLS analysis of the palindromic DNA on the NCP. (a) Composite motions of the DNA gyres looking at the ventral surface with the DNA colored by atom type. The two gyres reflect the structural asymmetry of the NCP with non-coincident axes of motion and different orientations for the primary axis of motion. The ventral gyre TLS axes more closely resemble the composite motions of the individual H3 H4 dimers (Fig. 17c), the dorsal TLS axes resemble the composite motion of the tetramer. (b) The composite motions of the DNA gyres are shown in a view down the dyad axis. The DNA is shown in a surface representation colored by atom type. Note that axes of motion appear parallel and in plane with the pitch of the DNA. In this view the ventral surface is on the bottom of the image.

In the nucleus, the hormone-receptor complex binds to nucleotide sequences known as hormone response elements (HREs). These are short palindromic DNA segments that usually promote transcription as enhancer elements (see p. 244). The illustration shows the HRE for glucocorticoids (GRE ... 

Recombinant 147bp palindromic DNA fragment 1.9 Davey etal., 2002 P2i2i2i 10-20 mM potassium... 

Other multinuclear protein-zinc interactions may be implicated for the GAL4 protein in vivo. For example, since the GAL4 dimer binds to palindromic DNA sequences (Giniger et al, 1985), one possibility is that the dimer interface of the intact protein could comprise three zinc ions tetrahedrally coordinated by the 12 cysteines of two GAL4 monomers... 

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.

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... 

Figure 5-36 Stereoscopic diagrams showing some of the interactions between an N-terminal helical domain of the yeast transcription factor GCN4-bZIP, a leucine zipper protein, and a specific palindromic DNA binding site ...

The response elements for glucocorticoids and estrogen receptors contain short palindromic sequences with various three-nucleotide "spacer" sequences in the center as follows.308,314,316-318 Two receptor proteins bind to the palindromic DNA forming a ho-modimeric receptor pair. For the 9-cis retinoic acid receptor RXR-a the response element contains a pair of direct repeats of a 6-base consensus sequence with a two-base pair spacer ... 

Figure 32-3 Hypothetical way of controlling stem cell replication by methylation or other marking system. Methyltransferases Ej and E2 methylate the cytosine in a 5 -CpG-3 or other palindromic sequence. In freely replicating cells these two enzymes keep the CG sequences methylated on both DNA strands. In stem cells another enzyme, perhaps a third methylase (E3), marks a location outside the palindromic DNA on one strand ( ). Replication leaves the...

Ripley, L. S. Model for the participation of quasi-palindromic DNA sequences in frameshift mutation. 

Fig. 13.1. Biological function of restriction/modification systems RM systems recognize and act on short palindromic DNA sequences. While the host genome is protected by the methyltransferase activity of the system, invading phage DNA is cleaved by the endonuclease activity.

Palindromic DNA-binding site a DNA sequence that contains one inverted repeat composed of two half-sites of nucleotides... 

Xu QS, Kucera RB, Roberts RJ, Guo H-C. An asymmetric complex of restrichon endonuclease MspI on Its palindromic DNA recogtuhon site. Structure 2004 12 1741-1747. 

Fig. 4.5 Oligomeric structure of nuclear receptors and structure ofthe HREs. The nuclear receptors can be subdivided into four groups based on strucutres ofthe receptors and HREs. Shown above are some representative examples, a) binding of a homodi-meric receptor to a two-fold symmetric palindromic DNA element, CR gluccocorticoid receptor, b) binding of a heterodimeric receptor to a DNA element with direct repeats ofthe recognition sequence, whereby the 5 side ofthe HRE is occupied by the...

Contiguous inverted repeats (i.e., inverted repeats with no spacer between the repeats) are examples of palindromes. A palindrome looks the same read from left to right or from right to left, as in the word "deed." A palindromic DNA or RNA sequence can fold back to form a "hairpin" double-stranded structure (Fig. 2.6). 

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