Sequence recognition

When mapping longer DNA species such as those on the order of a whole chromosome, other techniques are used. A few enzymes are known which have recognition sequences of 8 bp in length. These longer sequences occur relatively more rarely in a chromosome than do 6-bp sequences. In... 

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. 

Three residues. His 28, Glu 32 and Arg 36, form specific interactions with the edges of the bases in the major groove of DNA. Like MyoD, a Glu residue recognizes the first two bases, C and A, of the recognition sequence. 

Type II restriction enzymes have received widespread application in the cloning and sequencing of DNA molecules. Their hydrolytic activity is not ATP-depen-dent, and they do not modify DNA by methylation or other means. Most importantly, they cut DNA within or near particular nucleotide sequences that they specifically recognize. These recognition sequences are typically four or six nucleotides in length and have a twofold axis of symmetry. For example, E. coU has a restriction enzyme, coRI, that recognizes the hexanucleotide sequence GAATTC ... 

Enzyme Common Isoschizomers Recognition Sequence Compatible Cohesive Ends... 

Poly(A) tails are added to the S end of mRNA molecules in a posttranscriptional processing step. The mRNA is first cleaved about 20 nucleotides downstream from an AAUAA recognition sequence. Another enzyme, poly(A) polymerase, adds a poly(A) tail which is subsequently extended to as many as 200 A residues. The poly(A) tail appears to protect the S end of mRNA from S —> S exonuclease attack. The presence or absence of the poly(A) tail does not determine whether a precursor molecule in the nucleus appears in the cytoplasm, because all poly(A)-tailed hnRNA molecules do not contribute to cytoplasmic mRNA, nor do all cytoplasmic mRNA molecules contain poly(A) tails... 

Figure 48-3. Schematic representation of fibronectin. Seven functional domains of fibronectin are represented two different types of domain for heparin, cell-binding, and fibrin are shown. The domains are composed of various combinations of three structural motifs (I, II, and III), not depicted in the figure. Also not shown is the fact that fibronectin is a dimer joined by disulfide bridges near the carboxyl terminals of the monomers. The approximate location of the RGD sequence of fibronectin, which interacts with a variety of fibronectin integrin receptors on cell surfaces, is indicated by the arrow. (Redrawn after Yamada KM Adhesive recognition sequences.

Figure 48-4. Schematic representation of a cell interacting through various integrin receptors with collagen, fibronectin, and laminin present in the ECM. (Specific subunits are not indicated.) (Redrawn after Yamada KM Adhesive recognition sequences. J Biol Chem 1991 266 12809.)...

Pallitto MM, Ghanta J, Heizelman P, Kiessling LL, Murphy RM. Recognition sequence design for peptidyl modulators of beta-amyloid aggregation and toxicity. Biochemistry 1999 38 3570-3578. 

Table 4 Sequences of oligomer duplexes containing a BamYL I recognition sequence (GGATCC)... 

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. 

Protein farnesyl transferase also can be used to add a geranylazide derivative to a synthetic peptide by incorporating the enzyme recognition sequence CAAX at the C-terminal of any... 

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

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