DNA recognition sequences

Restriction enzyme Source DNA recognition sequence and cleavage sitea... 

Harrington, R.E. and Winicov, I. New concepts in protein-DNA recognition sequence directed DNA bending and flexibility (1994) Progr. Nucl. Add Res. Mol. Biol. 47,195-270... 

Table 17.2 DNA Recognition Sequences Utilized by Steroid, Estrogen, and Thyroid Receptor Family Members...

Figure 3 Structure of the Co(ll)-ldeR-DNA complex. (Top) Two IdeR dimers bind to the DNA recognition sequence, and each monomer (gray) binds two cobalt ions (spheres) (pdb 1U8 R). (Bottom) The two metal-binding sites in one monomer are connected by a hydrogen bond (not shown) between H79 and El 05.

An essential factor required for accurate RNA Pol I transcription is the selectivity factor SL1 (SL1 Clos et al., 1986a Learned et al., 1985). As mentioned earlier, SL1 is also a species-specific factor that directs promoter-specific transcription in the presence of its cognate template. SL1 does not bind specifically to the rRNA promoter however, in the presence of UBF, it forms a strong cooperative DNA-binding complex at the ribosomal DNA promoter that is critical for initiation of transcription (Bell et al., 1988, 1989 Learned et al., 1986). Mutations in the promoter sequences that affect either the binding of UBF to the DNA template or the interaction of UBF with SL1 result in drastic reduction of transcription activity (Bell et al., 1988). These findings indicate that the interactions between UBF and its DNA recognition sequence, and between UBF and SL1, play a major role in RNA Pol I transcription. For many years the molecular identification of SL1 has proven a difficult task. The... 

Tsai, R. Y. L., Reed, R. R. (1998). Identification of DNA recognition sequences and protein interaction domains of the multiple-Zn-finger protein Roaz. Mol Cell Biol 18, 6447-6456. 

---