Proteins Interact with Quadruplexes

A variety of natural proteins have been found to specifically bind quadruplexes. In addition, others have been designed artificially to bind quadruplexes, although these will not be discussed further here. 

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Structural model of the complex of the 3,6,9-trisubstituted acridine ligand (3) with the intramolecular basket quadruplex structure of the human telomeric sequence, (a) End-stacking with the terminal G-tetradpermits the substituent at the 9-position to interact with the flexible TTA loop structure in a specific manner, (b) X-ray structure of the complex of a di-substituted aninoalkylamido acridine (4) with the dimeric hairpin quadruplex structure derived from the Oxytricha nova sequence d(GGGGTTTTGGGG)2. The drug end-stacks and interacts extensively with the thymine loop ((a) Adapted from ref 25 and (b) from RCSB Protein Data Bank co-ordinates ILIH (ref 49)). 

In this chapter, I will first consider exactly how one defines a PQS, and then outline some of the specific quadruplex-forming sequences that have been identified. I will highlight the proteins that have been shown to interact specifically with quadruplexes. I will then discuss the physiological roles that PQS in general could play. Lastly, I will discuss the genome-wide studies that have been performed to date. The chapter then ends with some proposed future directions for this field. 

Inhibition of protein-protein interactions offers a potential target for medicinal chemists. Hamilton et al. have illustrated this approach through the synthesis of a range of calixarene derivatives that bind to and inhibit chy-motrypsin. The calixarene core in these molecules is appended with anionic peptide domains, which are spatially matched to positively charged domains on the chymotrypsin surface, resulting in strong electrostatic attraction. This approach has recently been extended to self-assembled systems that utilize a quadruplex DNA core. °... 

Redman JE (2007) Surface plasmon resonance for probing quadruplex folding and interactions with proteins and small molecules. Methods 43 302-312... 

Figure 5 Interactions of end-binding proteins with telomeric G-rich overhangs. (A) Human POTl binding disrupts G-quadruplexes to allow extension by telomer-ase at the 3 end of a telomeric overhang. (B) The ciliate end-binding complex TEBPajfi promotes G-quadruplex formation to prevent telomere extension...

In order to quantitate protein capture and binding capacity in the TBA coated capillary, eluate was collected after each step (load, wash, and elnte), and total amonnts of protein in each were determined using flnorescence spectroscopy. The experiment was also performed using a bare (unmodified) capillary and a capillary coated with an oligonucleotide that has the same base composition as the TBA bnt in a scrambled sequence that does not form a G-qnadrnplex strnctnre and does not bind with thrombin (Bock et ah, 1992). The resnlts (Table 11.1) showed that the aptamer-coated capillary captures approximately three times as much thrombin as the bare and scrambled oligonucleotide-coated capillaries. The scrambled oligonucleotide yielded no more captnre than the bare snrface, indicating that thrombin capture at the TBA surface is due to specific affinity interactions. Since thrombin capture occurs only if the TBA is in the G-qnadrnplex conformation, we conld further conclude that the immobilized TBA at the surface is able to form the G-quadruplex. 

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