Stabilization and structure of telomeric and c-myc region intramolecular G-quadruplexes: the role of central cations and small planar ligands

Small molecules targeting c-Myc oncogene: promising anti-cancer therapeutics

The nuclear transcription factor c-Myc is a member of the Myc gene family with multiple functions and located on band q24.1 of chromosome 8. The c-Myc gene is activated by chromosomal translocation, rearrangement, and amplification. Its encoded protein transduces intracellular signals to the nucleus, resulting in the regulation of cell proliferation, differentiation, and apoptosis, and has the ability to transform cells and bind chromosomal DNA. c-Myc also plays a critical role in malignant transformation. The abnormal over-expression of c-Myc is frequently observed in some tumors, including carcinomas of the breast, colon, and cervix, as well as small-cell lung cancer, osteosarcomas, glioblastomas, and myeloid leukemias, therefore making it a possible target for anticancer therapy. In this minireview, we summarize unique characteristics of c-Myc and therapeutic strategies against cancer using small molecules targeting the oncogene, and discuss the prospects in the development of agents targeting c-Myc, in particular G-quadruplexes formed in c-Myc promoter and c-Myc/Max dimerization. Such information will be of importance for the research and development of c-Myc-targeted drugs.

Nucleic acid ion structures in the gas phase

Nucleic acids are diverse polymeric macromolecules that are essential for all life forms. These biomolecules possess a functional three-dimensional structure under aqueous physiological conditions. Mass spectrometry-based approaches have on the other hand opened the possibility to gain structural information on nucleic acids from gas-phase measurements. To correlate gas-phase structural probing results with solution structures, it is therefore important to grasp the extent to which nucleic acid structures are preserved, or altered, when transferred from the solution to a fully anhydrous environment. We will review here experimental and theoretical approaches available to characterize the structure of nucleic acids in the gas phase (with a focus on oligonucleotides and higher-order structures), and will summarize the structural features of nucleic acids that can be preserved in the gas phase on the experiment time scale.

Pyrrolobenzodiazepines (PBDs) do not bind to DNA G-quadruplexes

The pyrrolo[2,1-c][1,4] benzodiazepines (PBDs) are a family of sequence-selective, minor-groove binding DNA-interactive agents that covalently attach to guanine residues. A recent publication in this journal (Raju et al, PloS One, 2012, 7, 4, e35920) reported that two PBD molecules were observed to bind with high affinity to the telomeric quadruplex of Tetrahymena glaucoma based on Electrospray Ionisation Mass Spectrometry (ESI-MS), Circular Dichroism, UV-Visible and Fluorescence spectroscopy data. This was a surprising result given the close 3-dimensional shape match between the structure of all PBD molecules and the minor groove of duplex DNA, and the completely different 3-dimensional structure of quadruplex DNA. Therefore, we evaluated the interaction of eight PBD molecules of diverse structure with a range of parallel, antiparallel and mixed DNA quadruplexes using DNA Thermal Denaturation, Circular Dichroism and Molecular Dynamics Simulations. Those PBD molecules without large C8-substitutents had an insignificant affinity for the eight quadruplex types, although those with large π-system-containing C8-substituents (as with the compounds evaluated by Raju and co-workers) were found to interact to some extent. Our molecular dynamics simulations support the likelihood that molecules of this type, including those examined by Raju and co-workers, interact with quadruplex DNA through their C8-substituents rather than the PBD moiety itself. It is important for the literature to be clear on this matter, as the mechanism of action of these agents will be under close scrutiny in the near future due to the growing number of PBD-based agents entering the clinic as both single-agents and as components of antibody-drug conjugates (ADCs).

Native electrospray mass spectrometry of DNA G-quadruplexes in potassium solution

A commonly used electrolyte in electrospray mass spectrometry (ESI-MS) of biomolecules is ammonium acetate (NH4OAc). Although some nucleic acid structures such as duplexes require only proper physiological ionic strength (whatever the monovalent ions) to be properly folded in ESI-MS conditions, the folding of some other nucleic acid structures such as DNA G-quadruplexes also depends on direct binding of specific cations. Here, we developed ESI-MS compatible conditions that allow one to observe DNA G-quaduplexes with K(+) ions specifically bound between G-quartets. NH4OAc was replaced with trimethylammonium acetate (TMAA), at concentrations up to 150 mM to provide physiological ionic strength, and the solution was doped with KCl at concentrations up to 1 mM. The trimethylammonium ion is too large to coordinate between G-quartets, where only K(+) ions bind. Compared with the equivalent NH4OAc/KCl mixtures, the TMAA/KCl mixtures provide cleaner spectra by suppressing the nonspecific adducts, and favor the formation of similar stacking arrangements as in 100 mM KCl (physiologically relevant cation) for the polymorphic human telomeric DNA G-quadruplexes. This new sample preparation method can be exploited to determine the number of potassium binding sites in new sequences, to screen ligand binding to the structures favored in potassium, and to transfer potassium-bound G-quadruplexes to the mass spectrometer for gas-phase structural probing, as illustrated herein with ion mobility spectrometry experiments.

Mass spectrometric studies on effects of counter ions of TMPyP4 on binding to human telomeric DNA and RNA G-quadruplexes

A comparative study on human telomeric DNA G-quadruplex binding of meso-5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin (TMPyP4) between its two salt forms, i.e., tetratosylate and tetrachloride, was conducted by using ESI-TOF-MS, UV-melting measurement, and molecular modeling methods. Besides cation TMPyP4, the tosyl anion was found to bind to human telomeric DNA G-quadruplex with multiple binding stoichiometries from 1:1 to 3:1 observed in ESI-TOF-MS spectra, indicating that the stabilization activity of TMPyP4 tetratosylate on G-quadruplex is derived from a synergetic effect of both TMPyP4 cation and tosyl anion. A molecular modeling study suggests that a tosyl anion fills up the vacant space between TMPyP4 cation and DNA G-quadruplex and thus stabilizes the complex by 3.8 kcal/mol. Therefore, it is estimated that TMPyP4 tetratosylate’s activity might not reflect the real effect of TMPyP4 cation in some bioassays related to G-quadruplex stabilization. This was verified by the results of less binding affinity of TMPyP4 tetrachloride with DNA G-quadruplex obtained from ESI-TOF-MS measurement, and of 2.27 °C less thermal stabilization of TMPyP4 tetrachloride for DNA G-quadruplex, compared to its tetratosylate under the same conditions. Our study demonstrated the influence of counter ions of TMPyP4 on G-quadruplex binding, which sheds light on the proper usage of TMPyP4 salt in the chemical and biological research associated with G-quadruplex binding. Subsequently, the binding of TMPyP4 tetrachloride to human telomeric RNA G-quadruplexes was studied with ESI-TOF-MS technique. The binding constants of TMPyP4 with human telomeric G-quadruplexes indicated that TMPyP4 binds to human telomeric RNA G-quadruplex one order of magnitude stronger than DNA counterpart. This is a comprehensive mass spectrometric report on binding study of TMPyP4 with human telomeric DNA/RNA G-quadruplexes.

Effects of pH and charge state on peptide assembly: the YVIFL model system

Peptide oligomerization is necessary but not sufficient for amyloid fibril formation. Here, we use a combination of experiments and simulations to understand how pH influences the aggregation properties of a small hydrophobic peptide, YVIFL, which is a mutant form of [Leu-5]-Enkephalin. Transmission electron microscopy and atomic force microscopy measurements reveal that this peptide forms small aggregates under acidic conditions (pH = 2), but that extensive fibrillization only occurs under basic conditions (pH = 9 and 11). Ion-mobility mass spectrometry identifies key oligomers in the oligomerization process, which are further characterized at an atomistic level by molecular dynamics simulations. These simulations suggest that terminal charges play a critical role in determining aggregation propensity and aggregate morphology. They also reveal the presence of steric zipper oligomers under basic conditions, a possible precursor to fibril formation. Our experiments suggest that multiple aggregation pathways can lead to YVIFL fibrils, and that cooperative and multibody interactions are key mechanistic elements in the early stages of aggregation.

Ammonium ion binding to DNA G-quadruplexes: do electrospray mass spectra faithfully reflect the solution-phase species?

G-quadruplex nucleic acids can bind ammonium ions in solution, and these complexes can be detected by electrospray mass spectrometry (ESI-MS). However, because ammonium ions are volatile, the extent to which ESI-MS quantitatively could provide an accurate reflection of such solution-phase equilibria is unclear. Here we studied five G-quadruplexes having known solution-phase structure and ammonium ion binding constants: the bimolecular G-quadruplexes (dG(4)T(4)G(4))(2), (dG(4)T(3)G(4))(2), and (dG(3)T(4)G(4))(2), and the intramolecular G-quadruplexes dG(4)(T(4)G(4))(3) and dG(2)T(2)G(2)TGTG(2)T(2)G(2) (thrombin binding aptamer). We found that not all mass spectrometers are equally suited to reflect the solution phase species. Ion activation can occur in the electrospray source, or in a high-pressure traveling wave ion mobility cell. When the softest instrumental conditions are used, ammonium ions bound between G-quartets, but also additional ammonium ions bound at specific sites outside the external G-quartets, can be observed. However, even specifically bound ammonium ions are in some instances too labile to be fully retained in the gas phase structures, and although the ammonium ion distribution observed by ESI-MS shows biases at specific stoichiometries, the relative abundances in solution are not always faithfully reflected. Ion mobility spectrometry results show that all inter-quartet ammonium ions are necessary to preserve the G-quadruplex fold in the gas phase. Ion mobility experiments, therefore, help assign the number of inner ammonium ions in the solution phase structure.

G-quadruplex DNA cleavage preference and identification of a perylene diimide G-quadruplex photocleavage agent using a rapid fluorescent assay

A rapid fluorescence assay for G-quadruplex DNA cleavage was used to investigate the preference of TMPyP4 photochemical and Mn·TMPyP4 oxidative cleavage. Both agents most efficiently cleave the c-Myc promoter G-quadruplex. Direct PAGE analysis of selected assay samples showed that for a given cleavage agent, different cleavage products are formed from different G-quadruplex structures. Cleavage assays carried out in the presence of excess competitor nucleic acid structures revealed the binding selectivity of cleavage agents, while comparisons with duplex cleavage efficiency employing a dual-labeled hairpin oligonucleotide revealed neither agent prefers G-quadruplex over duplex substrates. Finally, this assay was used to identify the perylene diimide Tel11 as a photocleavage agent for the c-Myc G-quadruplex.

Porphyrin binding mechanism is altered by protonation at the loops in G-quadruplex DNA formed near the transcriptional activation site of the human c-kit gene

BACKGROUND

G-quadruplex DNA structures are hypothesized to be involved in the regulation of gene expression and telomere homeostasis. The development of small molecules that modulate the stability of G-quadruplex structures has a potential therapeutic interest in cancer treatment and prevention of aging.

METHODS

Molecular absorption and circular dichroism spectra were used to monitor thermal denaturation, acid base titration and mole ratio experiments. The resulting data were analyzed by multivariate data analysis methods. Surface plasmon resonance was also used to probe the kinetics and affinity of the DNA-drug interactions.

RESULTS

We investigated the interaction between a G-quadruplex-forming sequence in the human c-kit proto-oncogene and the water soluble porphyrin TMPyP4. The role of cytosine and adenine residues at the loops of G-quadruplex was studied by substitution of these residues by thymidines.

CONCLUSIONS

Here, we show the existence of two binding modes between TMPyP4 and the considered G-quadruplex. The stronger binding mode (formation constant around 107) involves end-stacking, while the weaker binding mode (formation constant around 106) is probably due to external loop binding. Evidence for the release of TMPyP4 upon protonation of bases at the loops has been observed.

GENERAL SIGNIFICANCE

The results may be used for the design of porphyrin-based anti-cancer molecules with a higher affinity to G-quadruplex structures which may have anticancer properties.

Isomer-selected photoelectron spectroscopy of isolated DNA oligonucleotides: phosphate and nucleobase deprotonation at high negative charge states

Fractionation according to ion mobility and mass-to-charge ratio has been used to select individual isomers of deprotonated DNA oligonucleotide multianions for subsequent isomer-resolved photoelectron spectroscopy (PES) in the gas phase. Isomer-resolved PE spectra have been recorded for tetranucleotides, pentanucleotides, and hexanucleotides. These were studied primarily in their highest accessible negative charge states (3-, 4-, and 5-, respectively), as provided by electrospraying from room temperature solutions. In particular, the PE spectra obtained for pentanucleotide tetraanions show evidence for two coexisting classes of gas-phase isomeric structures. We suggest that these two classes comprise: (i) species with excess electrons localized exclusively at deprotonated phosphate backbone sites and (ii) species with at least one deprotonated base (in addition to several deprotonated phosphates). By permuting the sequence of bases in various [A(5-x)T(x)](4-) and [GT(4)](4-) pentanucleotides, we have established that the second type of isomer is most likely to occur if the deprotonated base is located at the first or last position in the sequence. We have used a combination of molecular mechanics and semiempirical calculations together with a simple electrostatic model to explore the photodetachment mechanism underlying our photoelectron spectra. Comparison of predicted to measured photoelectron spectra suggests that a significant fraction of the detected electrons originates from the DNA bases (both deprotonated and neutral).

Telomere targeting with a new G4 ligand enhances radiation-induced killing of human glioblastoma cells

The aim of this study was to test in vitro the efficacy of TAC, an original G-quadruplex ligand, as a potential radiosensitizing agent for glioblastoma multiforme (GBM). Two human radioresistant telomerase-positive GBM cell lines (SF763 and SF767) were analyzed, with and without TAC treatment, for telomere length, cell proliferation, apoptosis, cell-cycle distribution, gene expression, cytogenetic aberrations, clonogenic survival assay, 53BP1 immunofluorescence staining, and γH2AX phosphorylation. We found that low concentrations of TAC (0.5 and 1 μmol/L) inhibited the proliferation of GBM cells in a concentration-dependent manner after only 1 week of treatment, with minimal effects on cell cycle and apoptosis. TAC treatment had no visible effect on average telomere length but modified expression levels of telomere-related genes (hTERT, TRF1, and TRF2) and induced concentration-dependent DNA damage response and dicentric chromosomes. Survival curves analysis showed that exposure to nontoxic, subapoptotic concentrations of TAC enhanced radiation-induced killing of GBM cells. Analysis of DNA repair after irradiation revealed delayed repair kinetics in GBM cells treated with TAC. Furthermore, the combined treatment (TAC and radiation) significantly increased the frequency of chromosomal aberrations as compared with radiation alone. These findings provide the first evidence that exposure to a G4 ligand radiosensitizes human glioblastoma cells and suggest the prospect of future therapeutic applications.

12-N-Methylated 5,6-dihydrobenzo[c]acridine derivatives: a new class of highly selective ligands for c-myc G-quadruplex DNA

12-N-Methylated and non-methylated 5,6-dihydrobenzo[c]acridine derivatives were designed and synthesized as new series of c-myc G-quadruplex binding ligands. Their interactions with c-myc G-quadruplex were evaluated using fluorescence resonance energy transfer (FRET) melting assay, circular dichroism (CD) spectroscopy, surface plasmon resonance (SPR), polymerase chain reaction (PCR) stop assay, and molecular modeling. Compared with the non-methylated derivatives, 12-N-methylated derivatives had stronger binding affinity and stabilizing ability to c-myc G-quadruplex structure, and could more effectively stack on the G-quartet surface. All these derivatives had high selectivity for c-myc G-quadruplex DNA over duplex DNA. The reverse transcription (RT) PCR assay showed that compound 21c could down-regulate transcription of c-myc gene in Ramos cell line containing NHE III(1) element, but had no effect in CA46 cell line with NHE III(1) element removed.

Polyamide recognition-mass spectrometry for distinguishing hairpin DNA from coil DNA

The discrimination between hairpin DNA and coil DNA has been well achieved through polyamides as probes by electrospray ionization (ESI) mass spectrometry. ESI mass spectra showed that polyamides bind to hairpin DNA with high selectivity, and almost no binding with coil DNA. In addition, the noncovalent interaction between polyamides and hairpin DNA was also studied; the results show that hairpin DNA with longer stem and polyamides with more heterocycles have higher binding affinity and stability in gas phase.

Charge and substituent effects on the stability of porphyrin/G-quadruplex adducts

The adduct ions of two tetramolecular G-quadruplexes formed from the d(TGGGGT) and d(TTGGGGGT) single strands with a group of cationic porphyrins, with different charges and substituents, and one neutral porphyrin, were investigated by ESI-MS and ESI-MS/MS in the negative ion mode. Formation of [Q + nNH(4)(+)+P(p+)-(z + n + p)H(+)](z-) adduct ions (where Q = quadruplex, n = number of quartets minus 1, P = porphyrin and p(+) = 0,1,2,3,4) indicates that the porphyrins are bound outside the quadruplexes providing an additional stabilization to those structures. The fragmentation pathways of the [Q + nNH(4)(+)+P(p+)-(z + n + p)H(+)](z-) adduct ions depend on the number of positive charges (p(+)) of the porphyrins and on the overall complex charge (z(-)), but do not show a significant dependence on the type of the substituent groups in the porphyrins. Formation of the 'unfilled' ions [Q + P(p+)-(z + p)H(+)](z-) predominates for porphyrins with a higher number of positive charges. Strand separation with the formation of [T + P(p+)-(z-2 + p)H(+)]((z-2)-) and (SS-2H(+))(2-) ions, where T = [d(TG(4)T)](3) and [d(T(2)G(5)T)](3) and SS = d(TG(4)T) and d(T(2)G(5)T) is only observed for the complexes with a higher overall negative charge. Porphyrin loss with the formation of [Q + nNH(4)(+)-(z + n)H(+)](z-) ions occurs predominantly for the neutral and monocharged porphyrins. The predominant formation of the 'unfilled' ions, [Q + P(p+)-(z + n)H(+)](z-), for porphyrins with a higher number of charges shows that these porphyrins can prevent strand separation and preserve, at least partially, the quadruplex structure.

Mass spectrometry of G-quadruplex DNA: formation, recognition, property, conversion, and conformation

G-quadruplexes are special secondary structures formed from G-rich sequences of DNA, and have proven to play important roles in a number of biological systems, including the regulation of gene transcription and translation. The highly distinctive nature of G-quadruplex structures and their functions suggest that G-quadruplexes can act as novel targets for drug development. As a highly sensitive analytical tool, mass spectrometry has been widely used for the analysis of G-quadruplex structures. Electrospray-ionization mass spectrometry, in particular, has found captivating applications to probe interactions between small molecules and G-quadruplex DNA. In this review, we will discuss: (1) mass spectrometry probing of the formation, binding affinity, and stoichiometry between G-quadruplexes and small molecules; (2) stabilization and collision-dissociation behavior of G-quadruplex DNA; (3) the exploration of the equilibrium transfer between a G-quadruplex and duplex DNA; and (4) the ESI-MS analysis of the conversion of intramolecular and intermolecular G-quadruplexes. Finally, we will also introduce the application of new techniques in the analysis of G-quadruplex conformation, such as ion-mobility and infrared multiphoton-dissociation mass spectrometry. We believe that, with the new technical developments, mass spectrometry will play an unparalleled role in the analysis of the G-quadruplex structures.

Effects of loops and nucleotides in G-quadruplexes on their interaction with an azacalixarene, methylazacalix[6]pyridine

A novel trend in G-quadruplex ligand design is to build a binder that is able to not only discriminate G-quadruplex from duplex-DNA, but also among various G-quadruplex structures. Methylazacalix[6]pyridine (MACP6), a new type of azacalixarene with flexible conformation, exhibits induced circular dichroism signals when interacted with most of G-quadruplexes. The intensities of the induced signals are strongly dependent on the topology of G-quadruplexes. Further evidence has shown that these signals can be ascribed to the preferred binding of MACP6 to the loops of G-quadruplexes, which rely on the nature of nucleotides in the loops.

The application of DNA and RNA G-quadruplexes to therapeutic medicines

The intriguing structural diversity in folded topologies available to guanine-rich nucleic acid repeat sequences have made four-stranded G-quadruplex structures the focus of both basic and applied research, from cancer biology and novel therapeutics through to nanoelectronics. Distributed widely in the human genome as targets for regulating gene expression and chromosomal maintenance, they offer unique avenues for future cancer drug development. In particular, the recent advances in chemical and structural biology have enabled the construction of bespoke selective DNA based aptamers to be used as novel therapeutic agents and access to detailed structural models for structure based drug discovery. In this critical review, we will explore the important underlying characteristics of G-quadruplexes that make them functional, stable, and predictable nanoscaffolds. We will review the current structural database of folding topologies, molecular interfaces and novel interaction surfaces, with a consideration to their future exploitation in drug discovery, molecular biology, supermolecular assembly and aptamer design. In recent years the number of potential applications for G-quadruplex motifs has rapidly grown, so in this review we aim to explore the many future challenges and highlight where possible successes may lie. We will highlight the similarities and differences between DNA and RNA folded G-quadruplexes in terms of stability, distribution, and exploitability as small molecule targets. Finally, we will provide a detailed review of basic G-quadruplex geometry, experimental tools used, and a critical evaluation of the application of high-resolution structural biology and its ability to provide meaningful and valid models for future applications (255 references).

Regulation of the equilibrium between G-quadruplex and duplex DNA in promoter of human c-myc oncogene by a pyrene derivative

It has been established that the equilibrium between duplex and G-quadruplex of the nuclease hypersensitivity element III1 (NHE III1) in human c-myc promoter is linked with this gene's transcription. Using NMR and ESI-MS, we have found a pyrene derivative, DMAPP, is able to modulate this equilibrium and, thus, might have the potential to regulate this oncogene's transcription. DMAPP has shown as a G-quadruplex binding agent and could induce c-myc G-quadruplex formation out of duplex. These results provide new clue for rational drug design to target transcription control of c-myc.

Targeting G-quadruplex structure in the human c-Kit promoter with short PNA sequences

The cKit87up sequence d((5')AGGGAGGGCGCTGGGAGGAGGG(3')) can form a unique G-quadruplex structure in the promoter region of the human c-kit protooncogene. It provides a peculiar platform for the design of selective quadruplex-binding agents, which could potentially repress the protooncogene transcription. In this study, we examined the binding of a small library of PNA probes (P1-P5) targeting cKit87up quadruplex in either K(+)- or NH(4)(+)-containing solutions by using a combination of UV, CD, PAGE, ITC, and ESI-MS methodologies. Our results showed that (1) P1-P4 interact with the cKit87up quadruplex, and (2) the binding mode depends on the quadruplex stability. In K(+) buffer, P1-P4 bind the ckit87up quadruplex structure as "quadruplex-binding agents". The same holds for P1 in NH(4)(+) solution. On the contrary, in NH(4)(+) solution, P2-P4 overcome the quadruplex structure by forming PNA/DNA hybrid complexes, thus acting as "quadruplex openers".

Developments in Electrospray Ionization Mass Spectrometry of Non-Covalent DNA–Ligand Complexes

Many anti-cancer drugs function by binding non-covalently to double-stranded (ds) DNA. Electrospray ionization mass spectrometry (ESI-MS) has emerged over the past decade as a sensitive technique for the determination of stoichiometries and relative binding affinities of DNA–ligand interactions. The chromosome contains nucleotide sequences, for example, guanosine-rich regions, that predispose them to the formation of higher order structures such as quadruplex DNA (qDNA). Sequences that form qDNA are found in the telomeres. The proposal that ligands that stabilize qDNA might interfere with the activity of telomerase in cancer cells has stimulated the search for ligands that are selective for qDNA over dsDNA. The insights gained from the development of ESI-MS methods for analysis of non-covalent dsDNA–ligand complexes are now being applied in the search for qDNA-selective ligands. ESI-MS is a useful first-pass screening technique for qDNA-binding ligands. This short review describes some experimental considerations for ESI-MS analysis of DNA–ligand complexes, briefly addresses the question of whether non-covalent DNA–ligand complexes are faithfully transferred from solution to the gas phase, discusses ion mobility mass spectrometry as a technique for probing this issue, and highlights some recent ESI-MS studies of qDNA-selective ligands.

The formation of thymidine-based T-tetramers with remarkable structural and metal ion size effects

We present direct ESI Q-TOF MS and X-ray evidence for remarkable structural and metal ion size effects on the formation of thymidine-based T-tetramers. The conventional H-bond acceptors on the ribose and deoxyribose may disfavor the formation of T-tetramers, and in the series of alkali metal ions, lithium did not induce T-tetramer due to its small ion size. Sodium, potassium, rubidium and caesium could produce thymidine-based T-tetramers. Furthermore, rubidium and caesium could induce T-pentamers and dimeric T-pentamers probably due to their larger ion sizes.

Fluorescence detection of lead(II) ions through their induced catalytic activity of DNAzymes

We have developed a fluorescence approach for the highly selective and sensitive detection of Pb(2+) ions using AGRO100, a G-quadruplex DNAzyme. The sensing strategy is based on Pb(2+) ions inducing increased DNAzyme activity of AGRO100 in the presence of hemin, which acts as a cofactor to catalyze H(2)O(2)-mediated oxidation of Amplex UltraRed (AUR). A test of eight aptamers of various sequences for the detection of Pb(2+) ions revealed that AGRO100 performed the best in terms of sensitivity. The AGRO100-AUR probe exhibited high selectivity (>100-fold) toward Pb(2+) ions over other tested metal ions. The fluorescence intensity (excitation/emission maxima, ca. 561/592 nm) of the AUR product was proportional to the concentration of Pb(2+) ions over the range 0-1000 nM, with a linear correlation (R(2) = 0.98). For 5 mM Tris-acetate (pH 7.4) solutions in the presence and absence of 100 mM NaCl, the AGRO100-AUR probe provided limits of detection (signal-to-noise ratio = 3) for Pb(2+) ions of 1.0 and 0.4 nM, respectively. We validated the practicality of the use of the AGRO100-AUR probe for the determination of the concentrations of Pb(2+) ions in soil samples. This approach allows the determination of the concentrations of Pb(2+) ions with simplicity, selectivity, and sensitivity.

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.

Conformational stability of Syrian hamster prion protein PrP(90-231)

Many transmissible spongiform encephalopathies (TSEs) are believed to be caused by a misfolded form of the normal cellular prion protein (PrP(C)) known as PrP(Sc). While PrP(Sc) is known to be exceptionally stable and resistant to protease degradation, PrP(C) has not shown these same unusual characteristics. However, using ion mobility spectrometry mass spectrometry (IMS-MS), we found evidence for at least one very stable conformation of a truncated form of recombinant PrP(C) consisting of residues 90-231, which resists unfolding in the absence of solvent at high injection energies and at temperatures in excess of 600 K. We also report the first absolute collision cross sections measured for recombinant Syrian hamster prion protein PrP(90-231).

A rigid dinuclear ruthenium(II) complex as an efficient photoactive agent for bridging two guanine bases of a duplex or quadruplex oligonucleotide

The rigid dinuclear [(tap)(2)Ru(tpac)Ru(tap)(2)](4+) complex (1) (TAP=1,4,5,8-tetraazaphenanthrene, TPAC=tetrapyridoacridine) is shown to be much more efficient than the mononuclear bis-TAP complexes at photodamaging oligodeoxyribonucleotides (ODNs) containing guanine (G). This is particularly striking with the G-rich telomeric sequence d(T(2)AG(3))(4). Complex 1, which interacts strongly with the ODNs as determined by surface plasmon resonance (SPR) and emission anisotropy experiments, gives rise under illumination to the formation of covalent adducts with the G units of the ODNs. The yield of photocrosslinking of the two strands of duplexes by 1 is the highest when the G bases of each strand are separated by three to four base pairs. This corresponds with each Ru(tap)(2) moiety of complex 1 forming an adduct with the G base. This separation distance of the G units of a duplex could be determined thanks to the rigidity of complex 1. On the basis of results of gel electrophoresis, mass spectrometry, and molecular modelling, it is suggested that such photocrosslinking can also occur intramolecularly in the human telomeric quadruplex d(T(2)AG(3))(4).

Cation involvement in telomestatin binding to g-quadruplex DNA

The binding mode of telomestatin to G-quadruplex DNA has been investigated using electrospray mass spectrometry, by detecting the intact complexes formed in ammonium acetate. The mass measurements show the incorporation of one extra ammonium ion in the telomestatin complexes. Experiments on telomestatin alone also show that the telomestatin alone is able to coordinate cations in a similar way as a crown ether. Finally, density functional theory calculations suggest that in the G-quadruplex-telomestatin complex, potassium or ammonium cations are located between the telomestatin and a G-quartet. This study underlines that monovalent cation coordination capabilities should be integrated in the rational design of G-quadruplex binding ligands.

Chemical standards in ion mobility spectrometry

In ion mobility spectrometry (IMS), reduced mobility values (K(0)) are used as a qualitative measure of gas phase ions, and are reported in the literature as absolute values. Unfortunately, these values do not always match with those collected in the field. One reason for this discrepancy is that the buffer gas may be contaminated with moisture or other volatile compounds. In this study, the effect of moisture and organic contaminants in the buffer gas on the mobility of IMS standards and analytes was investigated for the first time using IMS directly coupled to mass spectrometry. 2,4-Dimethylpyridine, 2,6-di-tert-butylpyridine (DTBP), and tetrabutylammonium, tetrapropylammonium, tetraethylammonium, and tetramethylammonium chlorides were used as chemical standards. In general, the mobility of IMS standard product ions was not affected by small amounts of contamination while the mobilities of many analytes were affected. In the presence of contaminants in the buffer gas, the mobility of analyte ions is often decreased by forming ion-molecule clusters with the contaminant. To ensure the measurement of accurate reduced mobility values, two IMS standards are required: an instrument and a mobility standard. An instrument standard is not affected by contaminants in the buffer gas, and provides an accurate measurement of the instrumental parameters, such as voltage, drift length, pressure, and temperature. The mobility standard behaves like an analyte ion in that the compound's mobility is affected by low levels of contamination in the buffer gas. Prudent use of both of these standards can lead to improved measurement of accurate reduced mobility values.

"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.

"One Ring to Bind Them All"-Part II: Identification of Promising G-Quadruplex Ligands by Screening of Cyclophane-Type Macrocycles

A collection of 26 polyammonium cyclophane-type macrocycles with a large structural diversity has been screened for G-quadruplex recognition. A two-step selection procedure based on the FRET-melting assay was carried out enabling identification of macrocycles of high affinity (ΔT_1/2 up to 30°C) and high selectivity for the human telomeric G-quadruplex. The four selected hits possess sophisticated architectures, more particularly the presence of a pendant side-arm as well as the existence of a particular topological arrangement appear to be strong determinants of quadruplex binding. These compounds are thus likely to create multiple contacts with the target that may be at the origin of their high selectivity, thereby suggesting that this class of macrocycles offers unique advantages for targeting G-quadruplex-DNA.

G-quadruplex signaling probe for highly sensitive DNA detection

Ferrocene-conjugated oligonucleotides that can form intermolecular guanine (G)-quadruplexes are prepared and used as signaling probes for detecting target DNA, improving substantially assay characteristics (e.g. a considerably wider linear dynamic range and lower detection limit).

Evaluation of DNA/Ligand interactions by electrospray ionization mass spectrometry

Electrospray ionization mass spectrometry (ESI-MS) has enabled the detection and characterization of DNA/ligand complexes, including evaluation of both relative binding affinities and selectivities of DNA-interactive ligands. The noncovalent complexes that are transferred from the solution to the gas phase retain the signature of the native species, thus allowing the use of MS to screen DNA/ligand complexes, reveal the stoichiometries of the complexes, and provide insight into the nature of the interactions. Ligands that bind to DNA via metal-mediated modes and those that bind to unusual DNA structures, such as quadruplexes, are amenable to ESI. Chemical probe methods applied to DNA/ligand complexes with ESI-MS detection afford information about ligand-binding sites and conformational changes of DNA that occur upon ligand binding.

Frontiers of mass spectrometry in nucleic acids analysis

Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.

Colorimetric split G-quadruplex probes for nucleic acid sensing: improving reconstituted DNAzyme's catalytic efficiency via probe remodeling

Split G-rich DNA probes can assemble into active peroxidase-mimicking DNAzymes in the presence of bioanalytes such as DNA, thereby providing a simple and cheap means to detect analytes in biological samples. A comprehensive study designed to reveal the salient probe architectural features and reaction conditions that facilitate facile reconstitution into enzymatically proficient enzymes unveiled these important findings: (a) The loops that connect the G3-tracts in a G-quadruplex structure can be replaced with a stem-loop or loop-stem-loop motif without destabilizing the resulting quadruplex structure; endowing the split G-rich probes with regions of limited complementarity leads to more proficient reconstituted enzymes. (b) The addition of hemin to antiparallel G-quadruplex DNAzymes lead to a blue shift in the CD spectra of the G-quadruplex DNAzymes. (c) The architectures of the DNA motifs that lie adjacent to the G-quadruplex structure influence both the stability and the enzymatic proficiency of the reconstituted enzymes. (d) The nature of the monovalent cation that is present in excess is a key determinant of the turnover number of the G-quadruplex DNAzyme; decomposition of G-quadruplex DNAzymes is slower in buffers that contain ammonium ions than those that contain sodium or potassium ions. These findings are important for the design of bioassays that use peroxidase-mimicking G-quadruplexes as detection labels.

G-quadruplex aptamers with peroxidase-like DNAzyme functions: which is the best and how does it work?

Some G-quadruplex DNA aptamers have been found to strongly bind hemin to form DNAzymes with peroxidase-like activity. To help determine the most suitable DNAzymes and to understand how they work, five previously reported G-quadruplex aptamers were compared for their binding affinity and then the potential catalytic mechanism of their corresponding hemin-G-quadruplex DNAzymes was explored. Among these aptamers, a G-quadruplex named AGRO100 was shown to possess the highest hemin-binding affinity and the best DNAzyme function. This means that AGRO100 is the most ideal candidate for DNAzyme-based analysis. Furthermore, we found the peroxidase-like activity of DNAzyme to be primarily dependent on the concentration of H(2)O(2) and independent of that of the peroxidase substrate (that is, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)diammonium salt). Accordingly, a reaction mechanism for DNAzyme-catalyzed peroxidation is proposed. This study provides new insights into the G-quadruplex-based DNAzymes and will help us to further extend their applications in the analytical field.

Putative DNA G-quadruplex formation within the promoters of Plasmodium falciparum var genes

Background

Guanine-rich nucleic acid sequences are capable of folding into an intramolecular four-stranded structure called a G-quadruplex. When found in gene promoter regions, G-quadruplexes can downregulate gene expression, possibly by blocking the transcriptional machinery. Here we have used a genome-wide bioinformatic approach to identify Putative G-Quadruplex Sequences (PQS) in the Plasmodium falciparum genome, along with biophysical techniques to examine the physiological stability of P. falciparum PQS in vitro.

Results

We identified 63 PQS in the non-telomeric regions of the P. falciparum clone 3D7. Interestingly, 16 of these PQS occurred in the upstream region of a subset of the P. falciparum var genes (group B var genes). The var gene family encodes PfEMP1, the parasite's major variant antigen and adhesin expressed at the surface of infected erythrocytes, that plays a key role in malaria pathogenesis and immune evasion. The ability of the PQS found in the upstream regions of group B var genes (UpsB-Q) to form stable G-quadruplex structures in vitro was confirmed using ¹H NMR, circular dichroism, UV spectroscopy, and thermal denaturation experiments. Moreover, the synthetic compound BOQ1 that shows a higher affinity for DNA forming quadruplex rather than duplex structures was found to bind with high affinity to the UpsB-Q.

Conclusion

This is the first demonstration of non-telomeric PQS in the genome of P. falciparum that form stable G-quadruplexes under physiological conditions in vitro. These results allow the generation of a novel hypothesis that the G-quadruplex sequences in the upstream regions of var genes have the potential to play a role in the transcriptional control of this major virulence-associated multi-gene family.

A new method for the determination of the relative affinity of a ligand against various DNA sequences by electrospray ionization mass spectrometry. Application to a polyamide minor groove binder

A new method for the determination of the relative affinity of a ligand against various dsDNA sequences is presented by using electrospray ionization time-of-flight mass spectrometry (ESI-QTOF) mass spectrometry. The principle is described here through the complexation of double-stranded DNA by a polyamide ligand including twelve N-methylpyrrole rings. However this method could be applied to other ligands especially when dissociation constants (Kd) are in nanomolar range. This method does not require knowing the ligand concentration accurately. It allows determination of the relative affinity of a ligand against various dsDNA sequences for 1 : 1 complex stoichiometries in a quick manner without labeling.