Molecular Anchoring of Duplex and Triplex DNA by Disubstituted Anthracene-9,10-diones: Calorimetric, UV Melting, and Competition Dialysis Studies

Role of Hoogsteen interaction in the stability of different phases of triplex DNA

A simple coarse-grained model of DNA which includes both Watson-Crick and Hoogsteen base pairing has been used to study the melting and unzipping of triplex DNA. Using Langevin dynamics simulations, we reproduce the qualitative features of one-step and two-step thermal melting of triplex as seen in experiments. The thermal melting phase diagram shows the existence of a stable interchain three-strand complex (bubble-bound state). Our studies based on the mechanical unzipping of a triplex revealed that it is mechanically more stable compared to an isolated duplex-DNA.

Modulation of DNA structure formation using small molecules

Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.

Thermodynamic signature of indoloquinolines interacting with G-quadruplexes: Impact of ligand side chain

Binding of indoloquinolines with different aliphatic side chains to a parallel G-quadruplex derived from the MYC promoter sequence was characterized by optical and calorimetric measurements. ITC experiments performed at different temperatures enabled the determination of molar heat capacity changes upon quadruplex binding and a partitioning of the total binding free enthalpy into contributing terms with hydrophobic effects being major driving forces for all derivatives. Whereas affinities increase for indoloquinolines equipped with a long and positively charged side arm, the highest contribution of specific intermolecular interactions anticipated to impart enhanced specificity is found for a ligand with an uncharged ether aliphatic tail. Obtained thermodynamic signatures may considerably aid in the rational selection of ligand side chains for G-quadruplex binders with enhanced affinity or selectivity.

Discovery of selective ligands for telomeric RNA G-quadruplexes (TERRA) through 19F-NMR based fragment screening

Telomeric repeat-containing RNA (TERRA) is a novel and very attractive antitumoral target. Here, we report the first successful application of (19)F-NMR fragment-based screening to identify chemically diverse compounds that bind to an RNA molecule such as TERRA. We have built a library of 355 fluorinated fragments, and checked their interaction with a long telomeric RNA as a target molecule. The screening resulted in the identification of 20 hits (hit rate of 5.6%). For a number of binders, their interaction with TERRA was confirmed by (19)F- and (1)H NMR as well as by CD melting experiments. We have also explored the selectivity of the ligands for RNA G-quadruplexes and found that some of the hits do not interact with other nucleic acids such as tRNA and duplex DNA and, most importantly, favor the propeller-like parallel conformation in telomeric DNA G-quadruplexes. This suggests a selective recognition of this particular quadruplex topology and that different ligands may recognize specific sites in propeller-like parallel G-quadruplexes. Such features make some of the resulting binders promising lead compounds for fragment based drug discovery.

Spectroscopic and calorimetric studies on the binding of an indoloquinoline drug to parallel and antiparallel DNA triplexes

11-Phenyl-substituted indoloquinolines have been found to exhibit significant antiproliferative potency in cancer cells but to show only moderate affinity toward genomic double-helical DNA. In this study, parallel as well as antiparallel triple-helical DNA targets are employed to evaluate the triplex binding of these ligands. UV melting experiments with parallel triplexes indicate considerable interactions with the drug and a strong preference for TAT-rich triplexes in line with an increasing number of potential intercalation sites of similar binding strength between two TAT base triads. Via substitution of a singly charged aminoethylamine side chain by a longer and doubly charged bis(aminopropyl)amine substituent at the ligand, binding affinities increase and also start to exhibit long-range effects as indicated by a strong correlation between the binding affinity and the overall length of the TAT tract within the triplex stem. Compared to parallel triplexes, an antiparallel triplex with a GT-containing third strand constitutes a preferred target for the indoloquinoline drug. On the basis of pH-dependent titration experiments and corroborated by a Job analysis of continuous variation, binding of the drug to the GT triplex not only is strongly enhanced when the solution pH is lowered from 7 to 5 but also reveals a pH-dependent stoichiometry upon formation of the complex. Calorimetric data demonstrate that stronger binding of a protonated drug at acidic pH is associated with a more exothermic binding process. However, at pH 7 and 5, binding is enthalpically driven with additional favorable entropic contributions.

The interaction of telomere DNA G-quadruplex with three bis-benzyltetrahydroisoquinoline alkaloids

Telomeres are important multifunctional nucleoprotein structures located at the ends of eukaryotic chromosomes. Telomerase regulates telomere elongation, and its activity is associated with tumorigenesis. Because the activity of telomerase can be inhibited by G-quadruplex (G4) formation (a four-stranded DNA with stacks of G-quartets formed by four guanines in a planar structure), the role of G4 in cancer therapy has attracted many research interests. We studied the effects of three natural alkaloids-tetrandrine, fangchinoline, and berbamine-on the stability and formation of telomere DNA G4 with circular dichroism melting spectroscopy (melting-CD), variable temperature ultraviolet (melting-UV), proton nuclear magnetic resonance spectroscopy ((1)H NMR), and molecular docking, and examined the relationships among the alkaloid structure and their activities. We further investigated their cytotoxicity with the 3-(4,5-dimethylthiazole-2-yl)-2,5-diphenyltetrazolium bromide assay (MTT) and flow cytometry (FCM). The results demonstrated that alkaloids increased G4 stability and induced its formation, which added structure diversity of G4-ligands. The results showed that -OH at R(1), -OCH(3) at R(2), and [Formula: see text] at R(3) had higher stability than other substituent groups for these alkaloids. We also found a transition of antiparallel to parallel G4 as the temperature increased. The result indicated the possible advantage of parallel G4 in adversity. In addition, the alkaloids demonstrated a moderate cytotoxicity and proved to be cell cycle blocker in the G(1) phase. These alkaloids have revealed promising potentials to be the agents for antitumor therapy.

Spectroscopic and calorimetric studies on the triplex formation with oligonucleotide-ligand conjugates

Several triplex-forming 9-mer oligonucleotide (TFO) conjugates with a methyl- or methoxy-substituted 5-phenyl-6H-indolo[3,2-b]quinoline (PIQ) attached at the 5'-terminus or 3'-terminus or at an internal C5 thymine position were synthesized and tested for their ability to form and stabilize a triple helix with a double-helical DNA target employing UV melting experiments, fluorescence titrations, and isothermal titration calorimetry (ITC). A considerable thermal stabilization by up to 14 degrees C at pH 6.0 was observed for the 5'- and 3'-conjugates with little influence on the type of substituent but also for a conjugate with the ligand tethered by a short linker to the interior of the 9-mer TFO. A detailed thermodynamic characterization of the unmodified TFO and its 5'-conjugate with a methyl-substituted ligand by ITC experiments yielded a DeltaDeltaG degrees of -1.8 kcal mol(-1) at pH 6.0 for the TFO-attached PIQ-triplex interaction and also revealed a favorable entropic contribution as the major determinant for the free energy of PIQ binding in the conjugate. The pH dependence of triplex thermal stability highlights the importance of ring protonation of the triplex-bound ligand for its effective interaction and triplex stabilization near physiological conditions.

New challenges for pharmaceutical formulations and drug delivery systems characterization using isothermal titration calorimetry

Long viewed as the 'method of choice' for characterizing thermodynamics and stoichiometry of molecular interactions, with high sensitivity, isothermal titration calorimetry (ITC) has been applied to many areas of pharmaceutical analysis. This review highlights ITC employment to measure binding thermodynamics and their use for pharmaceutical formulations and drug delivery system characterization particularly cyclodextrin-guest interactions, investigation of micellar-based systems, polyelectrolytes, nucleic acid interactions with multivalent cations and the optimization of DNA targeting and delivery. Furthermore, the potential of ITC for the characterization of different functionalities carried by nanoparticles as well as their interaction with living systems was outlined.

A competition dialysis assay for the study of structure-selective ligand binding to nucleic acids

Unique DNA structures represent potential targets for small molecules, and provide a promising new avenue for drug development. However, attempts to rationally design small molecules that bind selectively to a particular DNA structure have been hampered by the lack of a rapid and convenient assay for structural selectivity. Determination of structure-selective ligand binding using competition dialysis is described in this unit. The competition dialysis assay is simple, straightforward, and rapid once stock solutions of the nucleic acid structures of interest have been prepared as described.

Spectroscopic studies of DNA binding modes of cation-substituted anthrapyrazoles derived from emodin

The DNA binding properties of three cation-substituted anthrapyrazole derivatives of emodin with calf thymus DNA were characterized by spectroscopic methods and the specific binding modes were elucidated. At low drug and high DNA concentrations, compound 1 with a mono-cationic amino side chain exhibited an intercalative binding mode, 2 with a much longer and more flexible di-cationic side chain exhibited an external binding mode, and 3 with a rigid di-cationic side chain exhibited both intercalative and external binding modes. The DNA binding mode of compounds was altered after structural modification. The molecular structure-DNA binding relationships found from this study may be useful for the design of anthrapyrazole derivatives with desired binding characteristics.

Extended ethidium bromide analogue as a triple helix intercalator: synthesis, photophysical properties and nucleic acids binding

Ethidium bromide has been extended by fusing an additional aromatic ring resulting in a larger intercalator with increased affinity for poly r(A) x r(U), poly d(A) x d(T) and triple helices when compared to the parent heterocycle.

Conformational transitions and aggregation in poly(dA)-poly(dT) system induced by Na+ and Mg2+ ions

Effects of Mg(2+) ions on thermally induced conformational transitions in the synthetic poly(dA).poly(dT) and poly(dA).2poly(dT) were studied in the buffered solutions (pH 6.9), containing 0.1 or 1M NaCl at polynucleotide concentration of 0.1-0.3mM (in nucleic bases). The experiments consist of measurements of the UV absorption and intensity of conventional visible static light scattering. The diagram of conformational transitions in the poly(dA)-poly(dT)-Mg(2+) system was constructed on a basis of experimental data obtained. Anomalously strong light scattering, like critical opalescence, has been revealed at 0.1M NaCl and [Mg(2+)]>/=20mM in the melting range of both polynucleotides, which eventually disappeared after the completion of polymer strands separation. The effect presumably is caused by a fluctuation process of polymer strands complexing which arises at a certain concentration of Mg(2+) ions.

Perylene diimide G-quadruplex DNA binding selectivity is mediated by ligand aggregation

Two N,N'-disubstituted perylene diimide G-quadruplex DNA ligands, PIPER [N,N'-bis-(2-(1-piperidino)ethyl)-3,4,9,10-perylene tetracarboxylic acid diimide] and Tel01 [N,N'-bis-(3-(4-morpholino)-propyl)-3,4,9,10-perylene tetracarboxylic acid diimide] were studied. Visible absorbance, resonance light scattering, and fluorescence spectroscopy were used to characterize the pH-dependent aggregation of these ligands. The G-quadruplex DNA binding selectivity of these ligands as monitored by absorption spectroscopy is also pH-dependent. The ligands bind to both duplex and G-quadruplex DNA under low pH conditions, where the ligands are not aggregated. At higher pH, where the ligands are extensively aggregated, the apparent G-quadruplex DNA binding selectivity is high.

Drug-DNA recognition: energetics and implications for design

In this article we review thermodynamic studies designed to examine the interaction of low molecular weight ligands or drugs with DNA. Over the past 10 years there has been an increase in the number of rigorous biophysical studies of DNA-drug interactions and considerable insight has been gained into the energetics of these binding reactions. The advent of high-sensitivity calorimetric techniques has meant that the energetics of DNA-drug association reactions can be probed directly and enthalpic and entropic contributions to the binding free energy established. There are two principal consequences arising from this type of work, firstly three-dimensional structures of DNA-drug complexes from X-ray and NMR studies can be put into a thermodynamic context and the energetics responsible for stabilizing the observed structures can be more fully understood. Secondly, any rational approach to structure-based drug design requires a fundamental base of knowledge where structural detail and thermodynamic data on complex formation are intimately linked. Therefore these types of studies allow a set of general guidelines to be established, which can then be used to develop drug design algorithms. In this review we describe recent breakthroughs in duplex DNA-directed drug design and also discuss how similar principles are now being used to target higher-order DNA molecules, for example, triplex (three-stranded) and tetraplex (four-stranded) structures.

G-quadruplex DNA: a potential target for anti-cancer drug design

In addition to the familiar duplex DNA, certain DNA sequences can fold into secondary structures that are four-stranded; because they are made up of guanine (G) bases, such structures are called G-quadruplexes. Considerable circumstantial evidence suggests that these structures can exist in vivo in specific regions of the genome including the telomeric ends of chromosomes and oncogene regulatory regions. Recent studies have demonstrated that small molecules can facilitate the formation of, and stabilize, G-quadruplexes. The possible role of G-quadruplex-interactive compounds as pharmacologically important molecules is explored in this article.

NB-506, an indolocarbazole topoisomerase I inhibitor, binds preferentially to triplex DNA

A novel competition dialysis method was used to study the structural selectivity of the nucleic acid binding of NB-506, a promising indolocarbazole anticancer agent. A pronounced preference for NB-506 binding to the DNA triplex poly [dA]:(poly[dT])(2) was observed among potential binding to 12 different nucleic acid structures and sequences. Structures included in the assay ranged from single-stranded DNA, through a variety of right-handed DNA duplexes, to multistranded triplex and tetraplex forms. RNA and left-handed Z DNA were also included in the assay. The preferential binding to triplex was confirmed by UV melting experiments. The novel and unexpected structural selectivity shown by NB-506 may arise from a complementary shape between its extended aromatic ring system and the planar triplex stack.

Triple helix formation and the antigene strategy for sequence-specific control of gene expression

Specific gene expression involves the binding of natural ligands to the DNA base pairs. Among the compounds rationally designed for artificial regulation of gene expression, oligonucleotides can bind with a high specificity of recognition to the major groove of double helical DNA by forming Hoogsteen type bonds with purine bases of the Watson-Crick base pairs, resulting in triple helix formation. Although the potential target sequences were originally restricted to polypurine-polypyrimidine sequences, considerable efforts were devoted to the extension of the repertoire by rational conception of appropriate derivatives. Efficient tools based on triple helices were developed for various biochemical applications such as the development of highly specific artificial nucleases. The antigene strategy remains one of the most fascinating fields of triplex application to selectively control gene expression. Targeting of genomic sequences is now proved to be a valuable concept on a still limited number of studies; local mutagenesis is in this respect an interesting application of triplex-forming oligonucleotides on cell cultures. Oligonucleotide penetration and compartmentalization in cells, stability to intracellular nucleases, accessibility of the target sequences in the chromatin context, the residence time on the specific target are all limiting steps that require further optimization. The existence and the role of three-stranded DNA in vivo, its interaction with intracellular proteins is worth investigating, especially relative to the regulation of gene transcription, recombination and repair processes.

Recent advances in the development of telomerase inhibitors for the treatment of cancer

Telomerase is an holoenzyme responsible for the maintenance of telomeres, the protein-nucleic acid structures which exist at the ends of eukaryotic chromosomes that serve to protect chromosomal stability and integrity. Telomerase activity is essential for the sustained proliferation of most immortal cells, including cancer cells. Since the discovery that telomerase activity is expressed in 85 - 90% of all human tumours and tumour-derived cell lines but not in most normal somatic cells, telomerase has become the focus of much attention as a novel and potentially highly-specific target for the development of new anticancer chemotherapeutics. Herein we review recent advances in the development of telomerase inhibitors for the treatment of cancer. To date, these have included antisense strategies, reverse transcriptase inhibitors and compounds capable of interacting with high-order telomeric DNA tetraplex ('G-quadruplex') structures to prevent enzyme access to the necessary linear telomere substrate. In addition, a number of telomerase-inhibitory therapies have been shown to synergistically enhance the effects of clinically-established anticancer drugs. Critical appraisal of each individual approach is provided, together with highlighted areas of likely future development. We also review recent developments in telomere and telomerase biology, of which a more detailed understanding would be essential in order to further develop the present classes of telomerase inhibitors into viable, clinically applicable therapies.

Stabilization of DNA triple helices by a series of mono- and disubstituted amidoanthraquinones

We have used quantitative DNase I footprinting to measure the relative affinities of four disubstituted and two monosubstituted amidoanthraquinone compounds for intermolecular DNA triplexes, and have examined how the position of the attached base-functionalized substituents affects their ability to stabilize DNA triplexes. All four isomeric disubstituted derivatives examined stabilize DNA triplexes at micromolar or lower concentrations. Of the compounds studied the 2,7-disubstituted amidoanthraquinone displayed the greatest triplex affinity. The order of triplex affinity for the other disubstituted ligands decreases in the order 2,7 > 1,8 = 1,5 > 2,6, with the equivalent monosubstituted compounds being at least an order of magnitude less efficient. The 1,5-disubstituted derivative also shows some interaction with duplex DNA. These results have been confirmed by molecular modelling studies, which provide a rational basis for the structure-activity relationships. These suggest that, although all of the compounds bind through an intercalative mode, the 2,6, 2,7 and 1,5 disubstituted isomers bind with their two side groups occupying adjacent triplex grooves, in contrast with the 1,8 isomer which is positioned with both side groups in the same triplex groove.

Progress in developments of triplex-based strategies

Recognition of B-DNA by oligonucleotides that form triple helices is a unique method to specifically recognize sequences of double-stranded DNA. Recently, some significant limitations of the triple-based applications have been overcome. Stable intermolecular triplexes can be formed under physiologic conditions. Binding affinities of modified oligonucleotides to their target sequence due to Hoogsteen or reverse Hoogsteen hydrogen bonding interactions are now in the range of those obtained for duplex formation via Watson-Crick hydrogen bonding interactions even if the kinetics may be quite different. Progress has been made toward developing general procedures to determine the molecular mechanisms of action of triplex-forming oligonucleotides (TFO) administered to cultured cells to provide a rational proof-of-concept for antigene strategies. The antigene strategy has reached a point where TFOs can be used to interfere with several biologic progresses (replication, transcription, recombination, repair) in relevant systems both in vitro and ex vivo.