Half-palindrome

Tora L, Gaub MP, Mader S, Dierich A, Bellard M, Chambon P (1988) Cell-specific activity of a GGTCA half-palindromic oestrogen responsive element in the chicken ovoalbumin gene promoter. EMBO J 7 3771... 

After the a-satellite DNA palindrome was constructed and cloned, the task remained to produce it in large quantities. To do this multiple copies of the halfpalindrome fragment were cloned into a vector [26]. The half-palindrome fragment... 

The protein-DNA interactions have been analyzed in detail at high resolution in the complex between the 434 repressor fragment and the ORl containing 20mer DNA. A pseudo-twofold symmetry axis relates the halves of this complex. The symmetry is not exact since the nucleotide sequence of the DNA is slightly different in each half (see Table 8.2). However, the interactions between one protein subunit and one half of the DNA are very similar to those between the second subunit and the other half of the DNA since most of the bases that interact with the protein are identical in both halves. Details of the interaction are very similar to those in the complex with the palindromic synthetic 14mer of DNA shown in Figures 8.14 and 8.15. The base pairs at one end of the DNA, 1-14, 2-13, etc. are called base pairs 1, 2, etc. 

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. 

At Oak Ridge, the focus was to develop specific-sequence DNA to improve the diffraction quality of NCP crystals. The positioning of the DNA on the histone core has to be precise so that all the NCPs are identical. A project was undertaken to understand the DNA sequence effects on nucleosome phasing [25]. Second, a DNA palindrome was developed to extend the two-fold symmetry of the histone core to the DNA. The objective was to eliminate the two-fold disorder caused by the indeterminacy of packing of an asymmetric particle into the crystal lattice. A palindrome based on one-half of the primary candidate sequence was constructed and methods were developed to produce the palindrome fragment in large quantities for reconstitution of NCPs. 

Fig. 4.6. HRE structure of the RXR heterodimer. Shown is the consensus sequence of the HREs of the RXR heterodimers (see Fig. 4.7) and the different possible arrangements of the hexameric half-site sequences. The hexamers can be arranged palindromically as inverted repeats (a), as everted repeats (b), or as direct repeats (c). n indicates the number of base pairs that lie between the two hexamers. RXR receptor for 9-ds retinoic acid RAR receptor for all-trans retinoic acid T3R receptor for the T3 hormon PPAR peroxisome prohferator-activated receptor VDR receptor for vitamin D3.

The HREs of the steroid hormone receptors posses a palindromic structure, comparable to the DNA binding elements of procaryotic repressors (see fig. 4.7a). The glucocorticoid receptor, for example, binds as a homodimer to the two-fold symmetrical recognition sequence, whereby the receptor is already dimerized in solution. In complex with the DNA each subimit of the dimer contacts one half-site of the HRE. As a consequence of the two-fold repeat of the recognition sequence, a high affinity binding of the receptor dimer results (compare 1.2.4). 

Class I receptors are homodimers. Dimerization is ligand-induced and these receptors bind to DNA half-sites with inverted, palindromic repeats. 

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

Palindromic sequences with 2-fold symmetry are usually bound by dimeric proteins in which each subunit of the protein contacts one half-site of the DNA element. The use of twofold symmetry in the binding sequence and the protein dimers is an economical approach to achieving high-affinity binding. The DNA-binding motif of one subunit... 

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