A Metal-Mediated Conformational Switch Controls G-Quadruplex Binding Affinity

Small-molecule selectively recognizes human telomeric G-quadruplex DNA and regulates its conformational switch

Structural complexity is an inherent feature of the human telomeric sequence, and it presents a major challenge for developing ligands of pharmaceutical interest. Recent studies have pointed out that the induction of a quadruplex or change of a quadruplex conformation on binding may be the most powerful method to exert the desired biological effect. In this study, we demonstrate a quadruplex ligand that binds selectively to different forms of the human telomeric G-quadruplex structure and regulates its conformational switch. The results show that not only can oxazine750 selectively induce parallel quadruplex formation from a random coil telomeric oligonucleotide in the absence of added cations, it also can easily surpass the energy barrier between two structures and change the G-quadruplex conformation in Na(+) or K(+) solution. The combination of its unique properties, including the size and shape of the G-quadruplex and the small molecule, is proposed as the predominant force for regulating the special structural formation and transitions. These results may stimulate the design of new quadruplex binders that would be capable of discriminating different G-quadruplex structures as well as controlling biological phenomena, functional molecules, and nanomaterials.

Synthesis and evaluation of fused bispyrimidinoacridines as novel pentacyclic analogues of quadruplex-binder BRACO-19

The present article reports on the design and the synthesis of a series of mono- and bis-pyrimidinoacridines and their evaluation as a novel family of quadruplex-binders. It is shown that bispyrimidinoacridines represent an interesting compromise between easy synthetic access and efficiency in terms of quadruplex interaction (both affinic and selective), as judged by G4-FID assay and molecular modelling. The present study also highlights that control of the pi-stacking interactions taking place between the ligand and the accessible G-tetrad of a quadruplex-DNA is indeed essential for good recognition but not exclusively (key role of direct and water-mediated H-bonds). The introduction of additional amino side chains, valuable in the acridine series, results here in steric perturbations of the ligand/quadruplex recognition and lowers the quadruplex/duplex selectivity.

Crystal violet-G-quadruplex complexes as fluorescent sensors for homogeneous detection of potassium ion

A novel K(+) detection method was reported using a label-free G-quadruplex-forming oligonucleotide and a triphenylmethane fluorescent dye crystal violet (CV). This method is based on the fluorescence difference of some CV/G-quadruplex complexes in the presence of K(+) or Na(+), and the fluorescence change with the variation of K(+) concentration. According to the nature of the fluorescence change of CV as a function of ionic conditions, two K(+) detection modes can be developed. One is a fluorescence-decreasing mode, in which T(3)TT(3) (5'-GGGTTTGGGTGGGTTTGGG) is used, and the fluorescence of CV decreases with an increased concentration of K(+). The other is a fluorescence-increasing mode, in which Hum21 (5'-GGGTTAGGGTTAGGGTTAGGG) is used, and the fluorescence of CV increases with an increased concentration of K(+). Compared with some published K(+) detection methods, this method has some important characteristics, such as lower cost of the test, higher concentrations of Na(+) that can be tolerated, adjustable linear detection range and longer excitation and emission wavelengths. Preliminary results demonstrated that the method might be used in biological systems, for example in urine.

Fluorescent sensor for monitoring structural changes of G-quadruplexes and detection of potassium ion

G-rich sequences with the potential for quadruplex formation are common in genomic DNA. Considering that the biological functions of G-quadruplexes may well depend on their structures, the development of a sensitive structural probe for distinguishing different types of quadruplexes has received great attention. Crystal violet (CV) is a triphenylmethane dye, which can stack onto the two external G-quartets of a G-quadruplex. The ability of CV to discriminate G-quadruplexes from duplex and single-stranded DNAs has been reported by us. Herein, the ability of CV to discriminate parallel from antiparallel structures of a G-quadruplex was studied. The binding of CV to an antiparallel G-quadruplex can make its fluorescence intensity increase to a high level because of the protection of bound CV from the solvent by quadruplex end loops. The presence of side loops in parallel G-quadruplexes cannot provide bound CV such protection, causing the fluorescence intensity of CV/G-quadruplex mixture to be obviously weaker when the G-quadruplex adopts a parallel structure than that when the G-quadruplex adopts an antiparallel structure. Therefore, CV can be developed as a sensitive fluorescent biosensor for the discrimination of antiparallel G-quadruplexes from parallel G-quadruplexes and for monitoring the structural interconversion of G-quadruplexes. In addition, considering that some G-rich DNA sequences can adopt different G-quadruplex structures under Na(+) or K(+) ion conditions, a novel, cheap and simple K(+) ion detection method was developed. This method displays a high K(+) ion selectivity against Na(+) ion, the change of 200 mM in Na(+) ion concentration only causes a similar fluorescent signal change to 0.3 mM K(+) ion.

The poly dA helix: a new structural motif for high performance DNA-based molecular switches

We report a pH-dependent conformational transition in short, defined homopolymeric deoxyadenosines (dA₁₅) from a single helical structure with stacked nucleobases at neutral pH to a double-helical, parallel-stranded duplex held together by AH⁺-H⁺A base pairs at acidic pH. Using native PAGE, 2D NMR, circular dichroism (CD) and fluorescence spectroscopy, we have characterized the two different pH dependent forms of dA₁₅. The pH-triggered transition between the two defined helical forms of dA₁₅ is characterized by CD and fluorescence. The kinetics of this conformational switch is found to occur on a millisecond time scale. This robust, highly reversible, pH-induced transition between the two well-defined structured states of dA₁₅ represents a new molecular building block for the construction of quick-response, pH-switchable architectures in structural DNA nanotechnology.

Controlled self-assembly of nucleotide-lanthanide complexes: specific formation of nanofibers from dimeric guanine nucleotides

Monomeric and dimeric guanine nucleotides monophosphate spontaneously self-assemble into nanoparticles and nanofibers in the presence of lanthanide ions, which reflects differences in the unit coordination structures and their hierarchical assembly.

Recognition and discrimination of DNA quadruplexes by acridine-peptide conjugates

We have explored a series of trisubstituted acridine-peptide conjugates for their ability to recognize and discriminate between DNA quadruplexes derived from the human telomere, and the c-kit and N-ras proto-oncogenes. Quadruplex affinity was measured as the peptide sequences were varied, together with their substitution position on the acridine, and the identity of the C-terminus (acid or amide). Surface plasmon resonance measurements revealed that all compounds bound to the human telomeric quadruplex with sub-micromolar affinity. Docking calculations from molecular modelling studies were used to model the effects of substituent orientation and peptide sequence. Modelling and experiment were in agreement that placement of the peptide over the face of the acridine is detrimental to binding affinity. The highest degrees of selectivity were observed towards the N-ras quadruplex by compounds capable of forming simultaneous contacts with their acridine and peptide moieties. The ligands that bound best displayed quadruplex affinities in the 1-5 nM range and at least 10-fold discrimination between the quadruplexes studied.