Palindromic sequence

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. 

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. 

Since BamH I binds as a dimer to the palindromic sequence of 5 -GGATCC-3, two GG sites in the sequence should be equally insulated from one electron oxidation. In the absence of the protein, both G16G17 in ODN 35 (Fig. 8a, lane 2) and G8G9 in ODN 2 (Fig. 8b, lane 2) showed similar oxidization patterns under the irradiation conditions. In contrast, cleavage bands at both GG sites completely disappeared in the presence of BamH I (1.2 U/pL) (lane 3 in Fig. 8a,b). Simultaneous suppression of oxidation at both GG sites shows that insulation of both GG sites from one electron oxidation is due to the binding of BamH I to the recognition sequence. 

Characterization and analysis of biphalin an opioid peptide with a palindromic sequence. J Pept Res 57 151. 

In eukaryotes, DNA methylation is important in regulation of gene function. The predominant prodnct of methylation in the DNA of vertebrates is 5-methylcytosine. This methylated base is found largely in CG dinucleotides in palindromic sequences. These may occur in control regions upstream of transcribed DNA sequences. There is considerable evidence to strongly suggest that DNA methylation in vertebrates turns off gene expression. 

Fig. 3. DNA sequence used in Oak Ridge NCP structural studies. The DNA sequence of the human a-satellite sequence (A) and the a-satellite palindrome (B) for which it was a model. The palindrome is one of 24 potential phasing sequences taken from the human a-satellite DNA repeats. The center of the palindrome sequence is marked by a vertical bar. The a-satellite sequence continues to serve as the starting point for high-resolution NCP structures.

Double stranded DNA can be enzymatically cleaved by commercially available endonucleases (restriction enzymes). These enzymes recognise specific, usually palindromic, sequences and cut specifically at those positions. 

Distinction between DNA Structure and RNA Structure Hairpins may form at palindromic sequences in single strands of either RNA or DNA How is the helical structure of a long and fully base-paired (except at the end) hairpin in RNA different from that of a similar hairpin in 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. 

The timing of replication initiation is affected by DNA methylation and interactions with the bacterial plasma membrane. The oriC DNA is methylated by the Dam methylase (Table 25-3), which methylates the Na position of adenine within the palindromic sequence (5 )GATC. (Dam is not a biochemical expletive it stands for DNA adenine methylation.) The oriC region of E. coli is highly enriched in GATC sequences—it has 11 of them in its 245 bp, whereas the average frequency of GATC in the E. coli chromosome as a whole is 1 in 256 bp. 

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 5-35 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...

Notice the direct hydrogen bonds from amino acid side chains of lysine and threonine residues to bases in the specific palindromic sequence AGACGTCT. From Somers and Phillips.429 Drawings courtesy of S. E. V. Phillips. 

The most striking specificity in DNA hydrolysis is displayed by the restriction endonucleases which are discussed further in Chapter 26. These fussy catalysts cleave only at points within or close to a defined sequence of several nucleotides in double-stranded DNA. For example, the enzyme EcoR I cuts only at the following palindromic sequence ... 

The broad peaks B, D, and E are shifted far upfield by reaction with bisulfite (Eq. 5-11) suggesting that they are not hydrogen bonded and are present in the loop of the stem-loop structure. Peaks A, E, F, and G correspond to resonances 64, 7, 67, and 4, respectively, in (A) and represent fluorouracil in the stem structure. From Chu et al.69i Courtesy of Jack Horowitz. (C) A 31P NMR spectrum of a synthetic 14 base-pair DNA segment related to the E. coli lac operator. The palindromic sequence is TCTGAGCGCTCAGA. The numbers refer to the positions from the 5 end. From Schroeder et al.688... 

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 ... 

Another mechanism, which is utilized by some single-stranded parvoviruses,416,443 obviates the need for an RNA primer by use of a palindromic sequence to form a hairpin loop (Eq. 27-8). 

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...

Iho, S., Yamamoto, T., Takahashi, T. and Yamamoto, S. (1999) Oligodeoxynucleotides containing palindrome sequences with internal 5-CpG-i act directly on human NK and activated T cells to induce IFN-gamma production in vitro. J. Immunol., 163, 3642-3652. 

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