Quadruplex ligands may act as molecular chaperones for tetramolecular quadruplex formation

Abstract

G-quadruplexes are a family of four-stranded DNA structures, stabilized by G-quartets, that form in the presence of monovalent cations. Efforts are currently being made to identify ligands that selectively bind to G-quadruplex motifs as these compounds may interfere with the telomere structure, telomere elongation/replication and proliferation of cancer cells. The kinetics of quadruplex–ligands interactions are poorly understood: it is not clear whether quadruplex ligands lock into the preformed structure (i.e. increase the lifetime of the structure by lowering the dissociation constant, koff) or whether ligands actively promote the formation of the complex and act as quadruplex chaperones by increasing the association constant, kon. We studied the effect of a selective quadruplex ligand, a bisquinolinium pyridine dicarboxamide compound called 360A, to distinguish these two possibilities. We demonstrated that, in addition to binding to and locking into preformed quadruplexes, this molecule acted as a chaperone for tetramolecular complexes by acting on kon. This observation has implications for in vitro and in vivo applications of quadruplexes and should be taken into account when evaluating the cellular responses to these agents.

Differential Effects of the G-Quadruplex Ligand 360A in Human Normal and Cancer Cells

“…The effectiveness of the G-quadruplex ligand depends more on its specificity for the Gquadruplex structure. In vitro studies have found that 360A more actively induces the G-quadruplex structure compared with other G-quadruplex ligands tested (telomestatin, TMPyP4 and BRACO19) (de Cian & Mergny, 2007). G-quadruplex ligands lock into the Gquadruplex structure but this situation is complicated by the existence of a number of different G-quadruplex structures (dimeric, tetrameric, intra-or inter-molecular).…”

Targeting G-Quadruplex DNA with Small Molecules

“…3. The equilibrium between duplex and G-quadruplex/i-motif structures can be influenced by DNA binding proteins, [7] small-molecule binding, [10][11][12] negative supercoiling, [12][13][14][15][16] changes in pH and temperature, [29] and molecular crowding. [30] plex-specific antibodies.…”

“…Single-stranded DNA viral genomes and telomeric DNA circles are known exceptions to this rule. [6] The thermodynamic and kinetic barriers of duplex dissociation, a prerequisite for singlestranded DNA folding, might be off-set in part or in whole by single-stranded DNA binding proteins, [7] chaperones, [8,9] smallmolecule binding, [10][11][12] and/or negative supercoiling. [12][13][14][15][16] Polypurine-polypyrimidine tracts and other repetitive sequences can form nonduplex and/or higher-order chromatin structures possibly related to a wide variety of biological activities.…”

“…[22] But much faster rates of folding have been observed when G-quadruplex DNA was imbedded in a molecular matrix at temperatures slightly below the T m (k f ~1.0 s -1 ). [43] Molecular crowding, [44] synthetic and endogenous chaperones, [8][9][10][11][12] and dehydrating conditions inside the nucleus might also accelerate the rates of G-quadruplex formation in vivo. [22] Due to the self-complementary nature of duplex DNA, approximately 370'000 Crich motifs (C 3+ N 1-7 ) 4+ (where C = cytosine and N = any base) are present in the human genome.…”

Inhibition of Dicing of Guanosine‐Rich shRNAs by Quadruplex‐Binding Compounds

“…[45,46] With respect to the mechanism of action of such compounds, several possibilities such as stabilization of a quadruplex, induction, as well as chaperoning of the quadruplex fold need to be considered. [47] Results and Discussion…”