Synthesis and G-quadruplex binding studies of new 4-N-methylpyridinium porphyrins

TripDesign: A DNA Triplex Design Approach Based on Interaction Forces

A DNA triplex has the advantages of improved nanostructure stability and pH environment responsiveness compared with single-stranded and double-stranded nucleic acids. However, sequence stability and low design efficiency hinder the application of DNA triplexes. Therefore, a DNA triplex design approach (TripDesign) based on interaction forces is proposed. First, we present the stacking force constraint, torsional stress constraint, and G-quadruplex motif constraint and then use an improved memetic algorithm to design triplex sequences under combinatorial constraints. Finally, to quantify the process of triplex formation, we also explore the minimum length of the triplex-forming oligos (TFOs) required to form the triplex and the factors that produce depletion in cyclic pH-jump experiments. The experimental results show that the sequences produced by TripDesign have high stability and reversibility, and the proposed approach achieves efficient and automatic sequence design. In addition, this study characterizes multiple basic parameters of DNA triplex formation and promotes the wider application of DNA triplexes in nanotechnology.

Short LNA-modified oligonucleotide probes as efficient disruptors of DNA G-quadruplexes

G-quadruplexes (G4s) are well known non-canonical DNA secondary structures that can form in human cells. Most of the tools available to investigate G4-biology rely on small molecule ligands that stabilise these structures. However, the development of probes that disrupt G4s is equally important to study their biology. In this study, we investigated the disruption of G4s using Locked Nucleic Acids (LNA) as invader probes. We demonstrated that strategic positioning of LNA-modifications within short oligonucleotides (10 nts.) can significantly accelerate the rate of G4-disruption. Single-molecule experiments revealed that short LNA-probes can promote disruption of G4s with mechanical stability sufficient to stall polymerases. We corroborated this using a single-step extension assay, revealing that short LNA-probes can relieve replication dependent polymerase-stalling at G4 sites. We further demonstrated the potential of such LNA-based probes to study G4-biology in cells. By using a dual-luciferase assay, we found that short LNA probes can enhance the expression of c-KIT to levels similar to those observed when the c-KIT promoter is mutated to prevent the formation of the c-KIT1 G4. Collectively, our data suggest a potential use of rationally designed LNA-modified oligonucleotides as an accessible chemical-biology tool for disrupting individual G4s and interrogating their biological functions in cells.

Alkaline earth cations binding mode tailors excited-state charge transfer properties of guanine quadruplex: A TDDFT study

Quadruplexes formed by nucleic acids and their derivates tend to chelate different monovalent and bivalent cations, which simultaneously affect their excited electronic states properties. Cation binding to every and every other cavity of the central ion channel could be exploited for tuning exited-state charge transfer properties. In this work we utilize set of descriptors constructed on the basis of the one-electron transition density matrix obtained using linear-response TDDFT to study excited states properties of four crystallized tetramolecular quadruplexes that chelate alkaline earth cations (Ca²⁺, Sr²⁺ and Ba²⁺). Here, we show that alkaline earth cations situated at adjacent vacancies promote existence of the nucleobase-metal charge separation (CS) states, contrary to the structures with cations that occupy every second available vacancy. We argued that stabilization of these CS states is due to the strong electric field that stabilizes d orbitals of the cations which accept an excited-electron. Moreover, CS content is increased and redshifted below the first bright transition when number of the chelated cations is increased. Hydration effects stabilized CS states and increased their relative content. We also identified electron detachment states in the broad energy range for the Ca²⁺ containing system. These findings are valuable for understanding and development of the novel nanostructures based on the quadruplex scaffold with adjustable optical properties.

Artificial Intelligence in Aptamer-Target Binding Prediction

Aptamers are short single-stranded DNA, RNA, or synthetic Xeno nucleic acids (XNA) molecules that can interact with corresponding targets with high affinity. Owing to their unique features, including low cost of production, easy chemical modification, high thermal stability, reproducibility, as well as low levels of immunogenicity and toxicity, aptamers can be used as an alternative to antibodies in diagnostics and therapeutics. Systematic evolution of ligands by exponential enrichment (SELEX), an experimental approach for aptamer screening, allows the selection and identification of in vitro aptamers with high affinity and specificity. However, the SELEX process is time consuming and characterization of the representative aptamer candidates from SELEX is rather laborious. Artificial intelligence (AI) could help to rapidly identify the potential aptamer candidates from a vast number of sequences. This review discusses the advancements of AI pipelines/methods, including structure-based and machine/deep learning-based methods, for predicting the binding ability of aptamers to targets. Structure-based methods are the most used in computer-aided drug design. For this part, we review the secondary and tertiary structure prediction methods for aptamers, molecular docking, as well as molecular dynamic simulation methods for aptamer-target binding. We also performed analysis to compare the accuracy of different secondary and tertiary structure prediction methods for aptamers. On the other hand, advanced machine-/deep-learning models have witnessed successes in predicting the binding abilities between targets and ligands in drug discovery and thus potentially offer a robust and accurate approach to predict the binding between aptamers and targets. The research utilizing machine-/deep-learning techniques for prediction of aptamer-target binding is limited currently. Therefore, perspectives for models, algorithms, and implementation strategies of machine/deep learning-based methods are discussed. This review could facilitate the development and application of high-throughput and less laborious in silico methods in aptamer selection and characterization.

Theoretical insights into the effect of size and substitution patterns of azobenzene derivatives on the DNA G-quadruplex

Introducing photoswitches into the DNA G-quadruplex provides excellent opportunities to control folding and unfolding of these assemblies, demonstrating their potential in the development of novel nanodevices with medical and nanotechnology applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the effect of the size and substitution patterns of three azobenzene derivatives (AZ1, AZ2 and AZ3) on the excitation energies of the two lowest excited states of the smallest photoswitchable G-quadruplex reported to date. We demonstrated that the size and the substitution pattern do not affect the ultrafast cis-trans photoiomerization mechanism of the azobenzene derivatives significantly, in agreement with the experiment. However, molecular dynamics simulations revealed that while AZ2 and AZ3 G-quadruplexes are structurally stable during the simulations, the AZ1 G-quadruplex undergoes larger structural changes and shows two ground state populations that differ in the azobenzene backbone adopting two different conformations. AZ1, with para-para substitution pattern, provides more flexibility to the whole G-quadruplex structure compared to AZ2 and AZ3, and can thus facilitate the photoisomerization reaction between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after trans-cis isomerization occurring in a longer time dynamics, in agreement with the experimental findings. The QM/MM simulations of the absorption spectra indicated that the thermal fluctuation plays a more crucial role in the main absorption band of the azobenzene derivatives than the inclusion of the G-quadruplex, implying that the influence of the G-quadruplex environment is minimal. We propose that the latter is attributed to the position of the azobenzene linkers in the G-quadruplexes, i.e. the edgewise loops containing the azobenzene moieties that are located above the G-quartets, not being fully embedded inside or involved in the stacked structure. Our theoretical findings provide support to a recent study of the photoresponsive formation of photoswitchable G-quadruplex motifs.

Influence of the SPR Experimental Conditions on the G-Quadruplex DNA Recognition by Porphyrin Derivatives

Surface plasmon resonance (SPR) is a powerful technique to study the interactions of ligands with analytes and therefore a number of biosensor surfaces and injection methods have been developed so far. However, many experimental parameters can affect the interactions and consequently the affinity measurements. In particular, the interactions of positively charged analytes (often used for anionic nucleic acids targets) can be influenced by the sensing surfaces (e.g., negatively charged), leading to significant nonspecific interactions as well as regeneration problems. The aim of the present work is to investigate the effect of different parameters, including ionic strength, SPR biosensor (i.e., nature of the surfaces), and the injection method on the recognition of porphyrin G-quadruplex ligands. We demonstrate that the injection method does not influence the affinity whereas the ionic strength and the nature of the surface impact the recognition properties of the porphyrin for the G-quadruplex DNA. We also found that self-assembled monolayer coating surface presents many advantages in comparison with carboxymethylated dextran surface for SPR studies of G-quadruplex DNA/ligand interactions: (i) the electrostatic interaction with charged analytes is less important, (ii) its structure/composition is less sensitive to the ionic concentration and less prone to unspecific adsorption, (iii) it is easily homemade, and (iv) the cost is approximately 10 times cheaper.

G-quadruplex vs. duplex-DNA binding of nickel(II) and zinc(II) Schiff base complexes

Novel nickel(II) (1) and zinc(II) (2) complexes of a Salen-like ligand, carrying a pyrimidine ring on the N,N' bridge, were synthesized and characterized. Their interaction with duplex and G-quadruplex DNA was investigated in aqueous solution through UV-visible absorption, circular dichroism and viscometry measurements. The results obtained point out that, while the zinc(II) complex does not interact with both duplex and G-quadruplex DNA, the nickel(II) complex 1 binds preferentially to G-quadruplex respect to duplex-DNA, with values of the DNA-binding constants, Kb, 2.6×10(5)M(-1) and 3.5×10(4)M(-1), respectively. Molecular dynamics simulations provided an atomic level model of the top-stacking binding occurring between 1 and hTelo (a 22-mer sequence oligonucleotide) in G-quadruplex conformation.

Photoresponsive Formation of an Intermolecular Minimal G-Quadruplex Motif

The ability of three different bifunctional azobenzene linkers to enable the photoreversible formation of a defined intermolecular two-tetrad G-quadruplex upon UV/Vis irradiation was investigated. Circular dichroism and NMR spectroscopic data showed the formation of G-quadruplexes with K(+)  ions at room temperature in all three cases with the corresponding azobenzene linker in an E conformation. However, only the para-para-substituted azobenzene derivative enables photoswitching between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after E-Z isomerization.

Binding modes of a core-extended metalloporphyrin to human telomeric DNA G-quadruplexes

A novel π-extended Ni^II-porphyrin shows a high selectivity towards human telomeric G-quadruplexes.

Selective G-quadruplex stabilizers: Schiff-base metal complexes with anticancer activity

Molecular dynamics simulations and quantum mechanics/molecular mechanics calculations provided a mechanism for G-quadruplex binding of three transition metal complexes.

Targeting telomeric G-quadruplexes with the ruthenium(II) complexes [Ru(bpy)(2)(ptpn)](2+) and [Ru(phen)(2)(ptpn)](2+)

Two ruthenium(II) polypyridyl complexes, [Ru(bpy)(2)(ptpn)](2+) (1) (bpy = 2,2'-bipyridine, ptpn = 3-(1,10-phenanthroline-2-yl)-as-triazino[5,6-f]1,10-phenanthroline) and [Ru(phen)(2)(ptpn)](2+) (2) (phen = 1,10-phenanthroline), were synthesized and characterized. Crystal structure analysis shows that complex 1 has a large planar aromatic area and possesses the potential to fit the geometric structure of G-quadruplex. The interaction of the G-quadruplex DNA with Ru(ii) complexes was explored by means of circular dichroism (CD), fluorescence resonance energy transfer (FRET) melting assay, competitive FRET assay and polymerase chain reaction (PCR) stop assay. The results indicated that complexes 1 and 2 both have the ability to promote the formation and stabilization of the human telomeric d[(TTAGGG)(n)] (HTG22) quadruplex and exhibit high G-quadruplex DNA selectivity over duplex DNA. The telomere repeat amplification protocol (TRAP) assay and long-term proliferation experiments further demonstrate that the Ru(II) complexes are potent telomerase inhibitors and HeLa cell proliferation inhibitors.

Photoinduced antibacterial activity of two dicationic 5,15-diarylporphyrins

Antimicrobial photodynamic treatment combines the use of photosensitizers (PSs) and visible light to kill bacterial cells. Cationic porphyrins are PSs largely used against bacteria and, among them, those featuring one positive charge on each of the 5,10,15,20-tetraaryl substituent (tetracationic) are the most used. The aim of this study was to synthesize two dicationic 5,15-di(N-alkyl-4-pyridyl)porphyrins, bearing methyl (PS 3) and benzyl (PS 4) N-alkylating groups, and to compare the efficiency in antibacterial photodynamic treatment, upon irradiation with a halogen-tungsten white lamp. The killing efficiency of the PS 4 was constantly found higher than that of the PS 3 against both pure and mixed cultures of laboratory model microorganisms as well as against wild wastewater microflora. The two PSs are comparable as regards singlet oxygen generation, but show a different repartition coefficient; the more lipophilic benzylated PS 4 shows a better interaction with the bacterial cells than the methylated one (PS 3). The data support the hypothesis that an efficient PS-cell binding is required to obtain significant effects. A correlation among cell binding, photoinactivation and PS lipophilicity is suggested.

Thermodynamics-hydration relationships within loops that affect G-quadruplexes under molecular crowding conditions

We systematically investigated the effects of loop length on the conformation, thermodynamic stability, and hydration of DNA G-quadruplexes under dilute and molecular crowding conditions in the presence of Na(+). Structural analysis showed that molecular crowding induced conformational switches of oligonucleotides with the longer guanine stretch and the shorter thymine loop. Thermodynamic parameters further demonstrated that the thermodynamic stability of G-quadruplexes increased by increasing the loop length from two to four, whereas it decreased by increasing the loop length from four to six. Interestingly, we found by osmotic pressure analysis that the number of water molecules released from the G-quadruplex decreased with increasing thermodynamic stability. We assumed that base-stacking interactions within the loops not only stabilized the whole G-quadruplex structure but also created hydration sites by accumulating nucleotide functional groups. The molecular crowding effects on the stability of G-quadruplexes composed of abasic sites, which reduce the stacking interactions at the loops, further demonstrated that G-quadruplexes with fewer stacking interactions within the loops released a larger number of water molecules upon folding. These results showed that the stacking interactions within the loops determined the thermodynamic stability and hydration of the whole G-quadruplex.

Interaction of human telomeric DNA with N-methyl mesoporphyrin IX

The remarkable selectivity of N-methyl mesoporphyrin IX (NMM) for G-quadruplexes (GQs) is long known, however its ability to stabilize and bind GQs has not been investigated in detail. Through the use of circular dichroism, UV-visible spectroscopy and fluorescence resonance energy transfer (FRET) melting assay we have shown that NMM stabilizes human telomeric DNA dAG₃(TTAG₃)₃ (Tel22) and is selective for its parallel conformation to which it binds in 1:1 stoichiometry with a binding constant of ∼1.0 × 10⁵ M⁻¹. NMM does not interact with an antiparallel conformation of Tel22 in sodium buffer and is the second example in the literature, after TOxaPy, of a ligand with an excellent selectivity for a specific GQ structure. NMM's stabilizing ability toward predominantly parallel GQ conformation is universal: it stabilizes a variety of biologically relevant G-rich sequences including telomeres and oncogene promoters. The N-methyl group is integral for selectivity and stabilization, as the unmethylated analogue, mesoporphyrin IX, does not stabilize GQ DNA in FRET melting assays. Finally, NMM induces the isomerization of Tel22 into a structure with increased parallel component in K⁺ but not in Na⁺ buffer. The ability of NMM to cause structural rearrangement and efficient stabilization of Tel22 may bear biological significance.

A water soluble tri-cationic porphyrin-EDTA conjugate induces apoptosis in human neuroendocrine tumor cell lines

In this study, a completely water soluble tri-cationic porphyrin–EDTA conjugate was synthesized. We present data demonstrating the tumoristatic effects of the novel fully water soluble cationic porphyrin TMPy₃PhenEDTA-P-Cl₄ in the dark, in the medullary thyroid carcinoma cell lines MTC-SK and SHER-I and weaker effects in the small intestinal neuroendocrine tumor cell line KRJ-I. In addition, cytotoxic effects were also studied in normal human fibroblasts that represent normal tissue and the results are compared to the tumor cell lines.

Induction of G-quadruplex DNA structure by Zn(II) 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin

G-quadruplexes (GQ) are formed by the association of guanine-rich stretches of DNA. Certain small molecules can influence kinetics and thermodynamics of this association. Understanding the mechanism of ligand-assisted GQ folding is necessary for the design of more efficient cancer therapeutics. The oligonucleotide d(TAGGG)(2) forms parallel bimolecular GQ in the presence of ≥66 mM K(+); GQs are not formed under Na(+), Li(+) or low K(+) conditions. The thermodynamic parameters for GQ folding at 60 μM oligonucleotide and 100 mM KCl are ΔH = -35 ± 2 kcal mol(-1) and ΔG(310) = -1.4 kcal mol(-1). Quadruplex [d(TAGGG)(2)](2) binds 2-3 K(+) ions with K(d) of 0.5 ± 0.2 mM. Our work addresses the question of whether metal free 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) and its Zn(II), Cu(II), and Pt(II) derivatives are capable of facilitating GQ folding of d(TAGGG)(2) from single stranded, or binding to preformed GQ, using UV-vis and circular dichroism (CD) spectroscopies. ZnTMPyP4 is unique among other porphyrins in its ability to induce GQ structure of d(TAGGG)(2), which also requires at least a low amount of potassium. ZnTMPyP4 binds with 2:1 stoichiometry possibly in an end-stacking mode with a ~10(6) M(-1) binding constant, determined through UV-vis and ITC titrations. This process is entropically driven and has ΔG(298) of -8.0 kcal mol(-1). TMPyP4 binds with 3:1 stoichiometry and K(a) of ~10(6) M(-1). ZnTMPyP4 and TMPyP4 are efficient stabilizers of [d(TAGGG)(2)](2) displaying ΔT(1/2) of 13.5 and 13.8 °C, respectively, at 1:2 GQ to porphyrin ratio; CuTMPyP4 shows a much weaker effect (ΔT(1/2) = 4.7 °C) and PtTMPyP4 is weakly destabilizing (ΔT(1/2) = -2.9 °C). The selectivity of ZnTMPyP4 for GQ versus dsDNA is comparable to that of TMPyP4. The ability of ZnTMPyP4 to bind and stabilize GQ, to induce GQ formation, and speed up its folding may suggest an important biological activity for this molecule.

Studies on synthesis, characterization, and G-quadruplex binding of Ru(II) complexes containing two dppz ligands

In this work, the interaction between the guanine-rich single-strand oligomer AG(3)(T(2)AG(3))(3) quadruplex and two Ru(II) complexes, [Ru(L(1))(dppz)(2)](PF(6))(4) (1) and [Ru(L(2))(dppz)(2)](PF(6))(4) (2) (L(1) = 5,5'-di(1-(trimethylammonio)methyl)-2,2'-dipyridyl cation, L(2) = 5,5'-di(1-(triethylammonio)methyl)-2,2'-dipyridyl cation, dppz = dipyrido[3,2-a:2',3'-c] phenazine), has been studied by UV-Visible, fluorescence, DNA melting, and circular dichroism in K(+) buffer. The two complexes after binding to G-quadruplex have shown different DNA stability and fluorescence enhancement. The results show that both complexes can induce the stabilization of quadruplex DNA. ΔT(m) values of complexes 1 and 2 at [Ru]/[DNA] ratio of 1:1 were 9.4 and 7.0, respectively. Binding stoichiometry along with the quadruplex was investigated through a luminescence-based Job plot. The major inflection points for complexes 1 and 2 were 0.49 and 0.46, respectively. The data were consistent with the binding mode at a [quadruplex]/[complex] ratio of 1:1. In addition, the conformation of G-quadruplex was not changed by the complexes at the high ionic strength of K(+) buffer.

DNA minicircles connected via G-quadruplex interaction modules

G-quadruplexes are becoming reliable alternative interaction modules for the construction of DNA nanoarchitectures due to their prompt inducibility by salts. In this Full Paper, we report the design and synthesis of two different DNA minicircles equipped with G-rich appendixes that can self-hybridize into a G-quadruplex, which acts as a DNA recruiter and glue. Both minicircles, one containing a hairpin-like G-rich region and the other an open tuning-fork-like G-rich region, have the potential to form DNA G-nanoconstructs but only the tuning-fork minicircle does so. Incubation of the tuning-fork minicircle with Na(+) and Ni(2+) results in the formation of minicircle dimers, while K(+) and Sr(2+) unexpectedly induce the formation of multimers. Moreover, a catenated DNA nanoconstruct is obtained when the components of the hairpin minicircle are incubated with K(+) or Na(+) and assembled in a stepwise sequence. All nanoconstructs are visualized by atomic force microscopy.

Cationic porphyrin induced a telomeric DNA to g-quadruplex form in water

The formation of the DNA G-quadruplex is induced by the addition of a novel porphyrin carrying four cationic tethers. Circular dichroism spectroscopy reveals that the porphyrin binds to Tetrahymena telomeric repeat to form G-quadruplex under stabilizing-cation-deficient and no buffer conditions.

"One ring to bind them all"-part I: the efficiency of the macrocyclic scaffold for g-quadruplex DNA recognition

Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the “standard” B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. Stimulated by the pioneering studies on the cationic porphyrin TMPyP4 and the natural product telomestatin, follow-up studies have developed, rapidly leading to a large diversity of macrocyclic structures with remarkable-quadruplex binding properties and biological activities. In this review we summarize the current state of the art in detailing the three main categories of quadruplex-binding macrocycles described so far (telomestatin-like polyheteroarenes, porphyrins and derivatives, polyammonium cyclophanes), and in addressing both synthetic issues and biological aspects.

Synthesis, structural characterization, and quadruplex DNA binding studies of platinum(II)-terpyridine complexes

Three new substituted terpyridine ligands and their corresponding platinum(II) complexes have been prepared and fully characterized (including the X-ray crystal structures of two of the complexes). These compounds have shown to stack via pi-pi interactions both in the solid state and in solution. The interactions of these compounds with quadruplex DNA (both HTelo and c-myc sequences) have been studied by fluorescent indicator displacement (FID) assays, surface plasmon resonance (SPR), and in one case by circular dichroism (CD). The complexes have shown to interact strongly with quadruplex DNA (with binding constants of ca. 10(6) and DC(50) values between 2.24 and 0.26, as determined by SPR and FID, respectively). We have also investigated the interaction between the complexes and a sequence of duplex DNA to gain some insight into the selectivity of the compounds for quadruplex structures. FID and SPR studies have shown that the complexes have a modest selectivity (1 order of magnitude) for quadruplex, particularly c-myc, versus duplex DNA.

Steric effects direct the binding of porphyrins to tetramolecular quadruplex DNA

The binding motifs of copper(II) porphyrins with G quadruplex DNA structures vary markedly depending on the steric demands of the ligand and the host structure.

Stability and molecular recognition of quadruplexes with different loop length in the absence and presence of molecular crowding agents

G-quadruplexes are known to be potential targets for therapeutic intervention, thus resulting in development of various quadruplex interacting ligands. However, until now, no systemic study has been performed to understand molecular recognition of quadruplex in the presence of molecular crowding agents mimicking cellular conditions. The stability and molecular recognition of quadruplex can be influenced by loop length. Herein, we attempted to study the interaction of 5,10,15,20-tetrakis(1-methyl-4-pyridyl)-21H,23H-porphine (TMPyP4), a well-known G-quadruplex binding ligand with various DNA quadruplexes differing in total loop length and loop arrangement in both the absence and presence of molecular crowding agents. Results obtained from CD studies revealed that longer loops favor mixed and antiparallel conformation in both the absence and presence of 30% ethylene glycol. UV thermal melting studies revealed that the stability and formation of quadruplex increases in the presence of 30% ethylene glycol. Moreover, the binding of TMPyP4 molecule to both of the binding sites in different quadruplexes with total loop length varying from 3 to 9 remains unchanged in both the absence and presence of 30% ethylene glycol. The binding affinity (K(a)) of TMPyP4 was found to be decreased approximately by 1 order for the quadruplex sequences with total loop length varying from 11 to 15 in the presence of molecular crowding agents.

Nano-supramolecular assemblies constructed from water-soluble bis(calix[5]arenes) with porphyrins and their photoinduced electron transfer properties

Possessing 2D netlike and 1D linear morphologies, two nano-supramolecular architectures A1 and A2 are constructed by tetracationic porphyrin (G1) and dicationic porphyrin (G2), respectively, upon complexation with the novel water-soluble bis(p-sulfonatocalix[5]arenes) bridged at the lower rim (H2). Corresponding to the molecular design, the aggregation morphologies are well manipulated by the inherent binding sites of the building blocks through host-guest interactions as well as charge interactions. In comparison to the simple p-sulfonatocalix[5]arene H1 which can only form particle-type complexes C1 and C2 with porphyrin guests, H2 provides excellent pre-organized structure to construct highly complex nano-supramolecular assemblies. The exhibited electron-transfer process of the supramolecular systems is further investigated by steady-state and time-resolved fluorescence spectroscopy, electrochemical measurements, and transient absorption spectroscopy. The results obtained show that calixarenes are also effective electron donors in PET besides acting as significant building blocks, which gives them many advantages in constructing well-ordered nanomaterials with the capability of electron and energy transport.

Inhibition of dicing of guanosine-rich shRNAs by quadruplex-binding compounds

RNA interference is triggered by small hairpin precursors that are processed by the endonuclease dicer to yield active species such as siRNAs and miRNAs. To regulate the RNAi-mediated suppression of gene expression, we imagined a strategy that relies on the sequence-specific inhibition of shRNA precursor processing by immediate RNA-small molecule interactions. Here, we present a first step in this direction by augmenting shRNAs with guanosine-rich sequences that are prone to fold into four-stranded structures. The addition of small molecules that selectively bind to such quadruplex sequences should allow for the specific inhibition of dicing of shRNAs that contain suitable G-rich elements. In an attempt to find compounds that protect against dicer processing, we have examined the effects of quadruplex-binding compounds on the dicer processing of shRNAs containing G-quadruplexes. Although a variety of small molecules that are known to bind to quadruplexes inhibited in vitro dicing of shRNAs, only two substance classes, namely certain porphyrazines and bisquinolinium compounds, showed selective inhibition of G-rich shRNAs compared to control sequences lacking guanine-rich elements. The G-rich shRNAs displayed a potent knockdown of gene expression in mammalian cell culture, but the effect was not influenced by addition of the respective quadruplex-binding compounds.

Effect of loop orientation on quadruplex-TMPyP4 interaction

G-quadruplexes are believed to be potential targets for therapeutic intervention and this has resulted in designing of various quadruplex interacting ligands. Moreover, reports about existence of quadruplex forming sequences across the genome have propelled greater interest in understanding their interaction with small molecules. An intramolecular quadruplex sequence can adopt different conformations, owing to different orientation of loops in the structure. The differences in the loop orientation can affect their molecular recognition. Herein, we have studied the interaction of 5,10,15,20-tetrakis(1-methyl-4-pyridyl)-21H, 23H-porphine (TMPyP4), a well-known G quadruplex binding ligand with three DNA quadruplexes differing in loop orientations. Results obtained from UV, ITC, and SPR studies have coherently revealed that the TMPyP4 molecule shows preferential binding to parallel G-quadruplex ( c-myc and c-kit) over its antiparallel counterpart (human telomeric). The binding affinity for parallel quadruplex was (10(7)) 1 order of magnitude higher than that for antiparallel DNA quadruplex (10 ). The study shows two binding modes, stronger binding (10(7)) of TMPyP4 involving end stacking and a weaker external binding (10 ), while TMPyP4 shows only one binding mode with duplex with a binding affinity of the order of 10(6). Overall, the study emphasizes that differences in the loop orientation give rise to different conformations of quadruplex, which in turn govern its binding to small molecules, and thereby play a pivotal role in molecular recognition.

Study of the interaction between the G-quadruplex-forming thrombin-binding aptamer and the porphyrin 5,10,15,20-tetrakis-(N-methyl-4-pyridyl)-21,23H-porphyrin tetratosylate

The G-quadruplex DNA structure has been suggested to be a potential target for anticancer therapies. Therefore, there is increasing interest in the development of drugs that could modulate the stability of G-quadruplex structures. In the current work, the interaction between the thrombin-binding aptamer (TBA, 5'-GGT TGG TGT GGT TGG-3'), which can form an intramolecular G-quadruplex structure, and the porphyrin 5,10,15,20-tetrakis-(N-methyl-4-pyridyl)-21,23H-porphyrin tetratosylate (TmPyP4) was studied. The application of a high-performance liquid chromatography-photodiode array (HPLC-PDA) detector-based method to study this kind of interaction was tested. Molecular absorption data recorded along the chromatographic runs were analyzed by means of multivariate data analysis methods. Moreover, biospecific interaction analysis (BIA) by surface plasmon resonance (SPR) and melting and mole ratio experiments monitored by UV-visible molecular absorption and circular dichroism spectroscopies, were applied to confirm and expand the chromatographic studies. The results showed the formation of an interaction complex with a stoichiometry 1:1 (TmPyP4/TBA) and logarithm of the equilibrium constant equal to 5.7+/-0.2. Melting and circular dichroism data reflected that the initial G-quadruplex structure of TBA is stabilized in the interaction complex, being slightly distorted by the presence of the ligand.

A hitchhiker's guide to G-quadruplex ligands

Over the past decade, nucleic acid chemists have seen the spectacular emergence of molecules designed to interact efficiently and selectively with a peculiar DNA structure named G-quadruplex. Initially derived from classical DNA intercalators, these G-quadruplex ligands progressively became the focal point of new excitement since they appear to inhibit selectively the growth of cancer cells thereby opening interesting perspectives towards the development of novel anti-cancer drugs. The present article aims to help researchers enter this exciting research field, and to highlight recent advances in the design of G-quadruplex ligands.

A platinum–quinacridine hybrid as a G-quadruplex ligand

A novel platinum-quinacridine hybrid, comprising a monofunctional Pt moiety and a G-quadruplex ligand (mono-para-quinacridine or MPQ), has been synthesized and shown to interact with quadruplex DNA via a dual noncovalent/covalent binding mode. Denaturing gel electrophoresis was used to separate the various platination products of 22AG (an oligonucleotide that mimics the human telomeric repeat) by Pt-MPQ, and it was shown that two platinated adducts are highly stable quadruplex structures. Dimethylsulfate/piperidine treatment and 3'-exonuclease digestion of the isolated adducts allowed us to precisely determine the platination pattern of 22AG by Pt-MPQ, which displays three main sites G2, G10 and G22. Data presented herein support the hypothesis that Pt-MPQ traps preferentially the antiparallel structure of the 22AG quadruplex. Finally, the kinetics of Pt-MPQ platination using a construct containing both quadruplex DNA and a duplex DNA parts provide the first insights into the Pt-MPQ preference for quadruplex DNA over duplex DNA.

Cationic corrole derivatives: a new family of G-quadruplex inducing and stabilizing ligands

Water-soluble cationic corrole derivatives were designed and synthesized, and the first observation of their interactions with the telomeric G-quadruplex was made.

Tetramethylpyridiniumporphyrazines--a new class of G-quadruplex inducing and stabilising ligands

3,4-Tetramethylpyridiniumporphyrazines bind strongly and selectively to human telomeric G-quadruplex DNA, inducing the formation of an antiparallel quadruplex in a process that mimics molecular chaperones.