Palindromic structure

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). 

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... 

Gierer (23) had proposed palindromic structures as recognition sites for DNA-protein interactions and, specifically for operon-repressor interactions. As will be seen below, certain nucleic acid sequences in such sites are, effectively, palindromes. 

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. 

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... 

We still need to clear up one or two points of nomenclature in normal replication of nucleic acids, the matrix (the + strand) and the newly formed daughter strand (- strand) are held together by Watson-Crick hydrogen bonding. This process is also referred to as cross-catalytic . Normal autocatalysis is different it leads to a product which corresponds in structure to the matrix, so that there is no difference between the + and - strands. Such self-complementary sequences are called palindromes. 

The structure in palindrome or in direct repetition and the size of the spacing sequence between the two pentamers are the critical variables in establishing the specificity of response to each one of the receptors that share the same pentamer. For example, the elements of estrogen and thyroid response can share the same palindrome and be differentiated only by the number of nucleotide spacers three for the first one, none for the second. 

The interaction between the receptor dimer and DNA is produced in an orderly manner. First, the dimer is placed in the main furrow of the double helix, and the first monomer interacts with the first pentamer of the HRE in the main furrow of the double helix. Later the second molecule of the receptor dimer binds to the second pentamer. The distance between both pentamers is minimum from zero to five nucleotides, depending on the type of receptor. This implies that the dimer assures a sufficiently compact and symmetrical structure among both receptor molecules, so that a similar intimacy can be produced in the association with the palindrome. 

Fig. 4. The molecular structure, determined by solution NMR (James et al., 1997), of Syrian hamster 90-231 (SHa90-231) prion with ball-and-stick representation of the HI domain (SHal09-122 MKHMAGAAAAGAW). Note that two short /(-chains (SI, S2) nearly stack in the hydrogen-bonding direction. If the palindromic polyalanine region was also in a /(-conformation, there would be a three-stranded /(-sheet. The structural difference between PrPc and PrPSc is in the 90-145 domain. [Model drawn using MOLSCRIPT (Kraulis, 1991)].

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.

The crystals of NCPs containing a-satellite DNA palindrome and chicken erythrocyte histones diffracted isotropically to 3.0 A using an in-house rotating anode X-ray source and to better than 2.5 A at a moderate intensity synchrotron beamline [30,31]. The crystals used for structure determination were grown in the microgravity environment using a counter-diffusion apparatus [32]. Ground-based... 

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.

The primary structure of DNA is a one-dimensional system similar to four-letter text and can be subjected to the simplest combinatory rules. The particular motifs can be combined with one or several other motifs in away similar to using building blocks. For instance, G-rich motif can be added to one or both ODN flanks. A certain sequence, e.g., a sequence containing unmethylated deoxyribodi-nucleotide CpG motifs that mimic prokaryotic DNA (I), can be placed between similar or different motifs, like GC-rich palindrome and/or G-rich motifs (Fig. I). Various motif combinations will yield a number of putative DNA sequence variants that can be used for further tests and selection of perspective ODN compounds (see Notes 1-4). 

The recognition sequences for specific DNA-binding proteins usually include only 3-8 base pairs, arranged either palindromically or in direct repeats (Fig. 1.18). The symmetry of the sequence in the DNA element is often reflected in the subunit structure of the binding protein. Less common is the occurrence of a singular recognition sequence. 

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.

---