Recognition sequence Palindromic

Many proteins that switch off or on gene expression in bacteria are dimeric molecules, and the DNA sequences that they specifically recognize are palindromic at their ends. The twofold symmetry of the protein is therefore matched by twofold symmetry at the ends of the recognition sequence. 

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. 

The BamHI site Is palindromic—rotate It In the plane of the paper by 180° and the recognition sequence doesn t change. 

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. 

An example for such an arrangement is the Met repressor of E. coli. The palindromic recognition sequence of the MeO repressor occurs in 2-5 copies on the DNA. The repressor itself binds as a dimer on one copy of the recognition sequence. Protein-protein interactions mediate cooperative binding of the repressor dimers to the adjacent copies of the recognition sequence. 

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). 

Thousands of restriction endonucleases have been discovered in different bacterial species, and more than 100 different DNA sequences are recognized by one or more of these enzymes. The recognition sequences are usually 4 to 6 bp long and palindromic (see Fig. 8-20). Table 9-2 lists sequences recognized by a few type II restriction endonucleases. In some cases, the interaction between a restriction endonuclease and its target sequence has been elucidated in exquisite molecular detail for example, Figure 9-2 shows the complex of the type II restriction endonuclease EcoRV and its target sequence. 

The cuts in the two strands are made at the points indicated by the arrows. This one endonuclease will cut almost any DNA into long pieces averaging about 5000 base pairs each. These pieces can in turn be cleaved by other restriction endonucleases to form smaller fragments. Since there are about 2400 of these enzymes known, with 188 different specificities,536 it is possible to cut any piece of DNA down to a size of 100-500 base pairs, ideal for sequencing.537 539 Each fragment has known sequences at the two ends. Some restriction enzymes cleave outside their specific recognition sequence (see Table 26-2). Some recognize 16-nucleotide palindromes and cut at rare sites. 

Two enzymes (Kpnl and Pst in the list in Table 26-2) form 3 -cohesive ends rather than 5 -cohesive ends. In addition, there are three (Alul, EcoRV, and HaellT) that cut at the local twofold axis they form no cohesive ends but leave blunt ends (flush ends). Blunt end fragments are also much used in genetic engineering. "Linkers" that provide cohesive ends can be added.119 The Sfil endonuclease cuts between two 4-bp palindromes in a 13-bp recognition sequence (Table 26-2).120... 

New England Biolabs, Inc. catalogue 1982-83 contains up to date restriction endonuclease maps of pBR322, M13mp8, phage A and SV40 DNA updated lists of restriction endonucleases, M13 primers, linkers and adapters as well as cross indexes of palindromic recognition sequences and much other useful data. A valuable up to date compendium obtainable from ... 

The distance between and nature of the bases in both the palindromic and the direct repeats of the recognition sequence plays an important role. It is evident that a dimeric protein would bind optimally to a twofold symmetric sequence only if the distance between the recognition elements matches the distance as determined by the protein structure. If one increases the distance by a few base pairs, a loss in cooperative binding capacity of the dimerization motifs of the protein to the rigid intervening DNA may... 

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...

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