Site-specific recognition

D.B. Starr, B.C. Hoopes and D.K. Hawley. DNA bending is an important component of site-specific recognition by the TATA binding protein. J. Mol. Biol. 250 (1995) 434. 

Internal loops occur where two helices are separated by non-Watson-Crick base pairs. Bulges refer to cases where all bases on one strand can base pair while one or more bases on the opposite strand cannot (Fig. 1.1). Both bulges and internal loops are potential, and often used, targets for site-specific recognition of the RNA. 

One approach to site-specific recognition uses a synthetic strand of oligonucleotides. When a strand of oligonucleotides is added to natural double-stranded DNA, the strand wraps around the DNA, forming a triple helix (Figure 27.19). The hope is that if the DNA sequence of a particular gene is known, a deoxyribonucleotide can be synthesized that will bind to that gene. 

The principles guiding site-specific recognition in the DNA-protein interactions can be generalized as ... 

Site-specific recognition always involves a set of contacts with the bases and the DNA backbone. 

Multiple DNA-binding domains usually are required for site-specific recognition. The same motif may be used more than once. Different motifs may also be used in... 

CT-induced colorization of solutions of an aromatic peptide as a result of their encapsulation by coordination capsule 486 (Scheme 6.6) is reported in [9] to be applicable for the naked-eye recognition of three aromatic residues (Trp, Tyr, and Phe) the selectivity of this binding may be used for site-specific recognition of protein surfaces. 

Another class of promising new generation nucleases includes artificial and semiartificial nucleases. Chemical nucleases are typical artificial nucleases that make use of redox-active compounds (e.g., phenanthroline-copper and ferrous-EDTA) as the cutter and an attached oligonucleotide as the site-specific recognition module. Although the importance of chemical nucleases and the potential for their applications are bound to grow, this chapter focuses on some of the classical enzyme nucleases that are most widely used in recombinant DNA technology. 

Triplex formation, which involves site-specific recognition of duplex DNA by hydrogen bonding between oligonucleotide bases in the 3 end extension and purine bases in the major groove, can occur in two distinct patterns termed the pyrimidine motif and the purine motif [22,40]. In the former motif, pyrimidine... 

By analogy, a great many of other functionalized styrenes, including carboxyHc acids, amino acids, Schiff bases, or specific compounds, eg, l-DOPA, have successfully been appHed as print templates. Moreover, it has also been shown that siUca gel can be imprinted with similar templates, and that the resulting gel has specific recognition sites determined by the print molecule (162—164). 

Figure 7.8 Sequence-specific recognition sites in the major groove of DNA for three restriction enzymes—Eco RI, Bal I, and Sma I. The DNA sequences that are recognized by these enzymes ate represented by tbe color code defined in Figure 7.7.

A sequence stretch 300 base pairs upstream of the transcriptional start site suffices for most of the transcriptional regulation of the IL-6 gene (Fig. 1). Within this sequence stretch several transcription factors find their specific recognition sites. In 5 to 3 direction, AP-1, CREB, C/EBP 3/NF-IL6, SP-1 and NF-kB can bind to the promoter followed by TATA and its TATA binding protein TBP. Most enhancer factors become active in response to one or several different stimuli and the active factors can trigger transcription individually or in concert. For example, AP-1 is active upon cellular stress, or upon stimuli that tell cells to proliferate CREB becomes also active if cells experience growth signals, but also upon elevation of intracellular levels of cyclic adenosine monophosphate (cAMP), which occurs upon stimulation if so called hormone-activated G protein-coupled receptors. 

As will be demonstrated, surface branching has afforded a series of dendri-mers lacking site-specific [31-33] characteristics whereas, the use of branched monomers has the unique ability to instill tailored loci capable of site-specific molecular recognition and encapsulation. 

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