Recognition of DNA Sequences

Recognition of DNA sequence and molecular design of artificial repressors, pyrrole-imidazole polyamides, and calicheamycin derivatives 97YGK384. 

Recognition of DNA sequence and DNA bending and molecular design for artificial repressors 97YGK384. 

In the following, the basic features of specific recognition of DNA sequences by DNA-binding proteins will be presented. 

Recognition of DNA sequences by pyrrole-imidazole polyamide 00YGK975. 

Figure 8.8 The DNA-binding heiix-turn-helix motif in lambda Cro. Ca positions of the amino acids in this motif have been projected onto a plane and the two helices outlined. The second helix (red) is called the recognition helix because it is involved in sequence-specific recognition of DNA.

Baird, P.B. Dervan, and D C. Rees. Structural effects of DNA sequence on T-A recognition by hydroxypyrrole/pyr-role pairs in the minor groove. J. Mol. Biol. 2000, 295, 557-567. 

SwALLEY, S.E., E.E. Baird, and P.B. Dervan. Effects of y-turn and j8-tail amino acids on sequence-specific recognition of DNA by hairpin polyamides. /. Am. 

Dervan. Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides. J. Mol. Biol. 2001,... 

Nielsen P.E., Egholm M., Berg R.H., Buchardt O. Sequence-selective recognition of DNA by strand displacement with a thymine-substituted polyamide. Science 1991, 254 1497-1500. 

The dimer of the hormone-receptor complex should scrutinize an infinity of sequences before finding its FIRE. The role of the hormone in the recognition of the HRE seems to be that of dramatically increasing the velocity of DNA sequence recognition, that is to say, it binds and disconnects more quickly to sequences of nonspecific DNA. When it finds the sequence of its HRE, a bond of affinity is formed that is similar to that of hormone-receptor interaction (Kd in the nM range). 

The recognition of positioning sequences has also made possible the construction of minichromosomes of regular defined structure (e.g., Ref. [44]), and reconstituted nucleosomes containing a defined DNA sequence. This latter advance was essential for the high-resolution X-ray diffraction studies of nucleosomes that have been accomplished (see Section 2.1). Defined minichromosomes have proved a powerful tool in many studies for a recent example, see Fan et al. [45]. 

Indirect recognition The DNA sequence can predetermine a particular conformation, which is a prerequisite for specific protein binding. Alternative DNA conformations will not be boimd and recognized. We speak here of an indirect recognition of a sequence ... 

Fig. 26. Nucleic acid structures. A The structure of the four bases in DNA, guanine (G), cytosine (C) adenine (A) and thymine (T). Uracil (U) replaces thymine (T) in RNA. B The spontaneous attraction of A for T and C for G allows the recognition of homologous sequences in aqueous solutions and the strong and specific hybridization of one sequence with its homologous sequence. C DNA forms a double helix at body temperature, which can be denatured to separate the strands by heating. D single stranded mRNA structure.

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