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G-quadruplex (G4) sequences, which can fold into higher-order G4 structures, are abundant in the human genome and are over-represented in the promoter regions of many genes involved in human cancer initiation, progression, and metastasis. They are plausible targets for G4-binding small molecules, which would, in the case of promoter G4s, result in the transcriptional downregulation of these genes. However, structural information is currently available on only a very small number of G4s and their ligand complexes. This limitation, coupled with the currently restricted information on the G4-containing genes involved in most complex human cancers, has led to the development of a phenotypic-led approach to G4 ligand drug discovery. This approach was illustrated by the discovery of several generations of tri- and tetra-substituted naphthalene diimide (ND) ligands that were found to show potent growth inhibition in pancreatic cancer cell lines and are active in in vivo models for this hard-to-treat disease. The cycles of discovery have culminated in a highly potent tetra-substituted ND derivative, QN-302, which is currently being evaluated in a Phase 1 clinical trial. The major genes whose expression has been down-regulated by QN-302 are presented here: all contain G4 propensity and have been found to be up-regulated in human pancreatic cancer. Some of these genes are also upregulated in other human cancers, supporting the hypothesis that QN-302 is a pan-G4 drug of potential utility beyond pancreatic cancer. [ABSTRACT FROM AUTHOR]

G-quadruplex (G4) sequences, which can fold into higher-order G4 structures, are abundant in the human genome and are over-represented in the promoter regions of many genes involved in human cancer initiation, progression, and metastasis. They are plausible targets for G4-binding small molecules, which would, in the case of promoter G4s, result in the transcriptional downregulation of these genes. However, structural information is currently available on only a very small number of G4s and their ligand complexes. This limitation, coupled with the currently restricted information on the G4-containing genes involved in most complex human cancers, has led to the development of a phenotypic-led approach to G4 ligand drug discovery. This approach was illustrated by the discovery of several generations of tri- and tetra-substituted naphthalene diimide (ND) ligands that were found to show potent growth inhibition in pancreatic cancer cell lines and are active in in vivo models for this hard-to-treat disease. The cycles of discovery have culminated in a highly potent tetra-substituted ND derivative, QN-302, which is currently being evaluated in a Phase 1 clinical trial. The major genes whose expression has been down-regulated by QN-302 are presented here: all contain G4 propensity and have been found to be up-regulated in human pancreatic cancer. Some of these genes are also upregulated in other human cancers, supporting the hypothesis that QN-302 is a pan-G4 drug of potential utility beyond pancreatic cancer.

G‐quadruplex DNA is a non‐canonical structure that forms in guanine‐rich regions of the genome. There is increasing evidence showing that G‐quadruplexes have important biological functions, and therefore molecular tools to visualise these structures are important. Herein we report on a series of new cyclometallated platinum(II) complexes which, upon binding to G‐quadruplex DNA, display an increase in their phosphorescence, acting as switch‐on probes. More importantly, upon binding to G‐quadruplexes they display a selective and distinct lengthening of their emission lifetime. We show that this effect can be used to selectively visualise these structures in cells using Phosphorescence Lifetime Imaging Microscopy (PLIM). [ABSTRACT FROM AUTHOR]

Three series of metal salophen complexes derived from Zn2+, Cu2+, Pt2+ and Ni2+ have been synthesized and their interaction with quadruplex DNA has been evaluated. The compounds differ on the number of ethyl piperidine substituents. They have been characterized by 1H NMR, IR and UV‐visible spectroscopies and by HR‐mass spectrometry. Their luminescent properties have been also evaluated and we can observe that, as expected, Zn2+ and Pt2+ complexes are those displaying more interesting luminescence with an emission band red‐shifted with respect to the corresponding uncoordinated ligand. DNA interactions with G4 and duplex DNA were evaluated by FRET melting assays (for the Zn2+, Cu2+ and Ni2+ complexes) and by emission titrations (for one Pt2+ complex) which indicated that the disubstituted compounds 2‐Ni and 2‐Pt are the only ones that display good affinity for G4 DNA structures. [ABSTRACT FROM AUTHOR]

G‐quadruplex (G4) is one of the non‐canonical nucleic acid structures that regulate multiple key biological processes. The formation of G4 hinders the progression of cancer. The molecular entities which can stabilize the G4 structure are very important to design anticancer therapeutics. Herein, it is described that a synthetic dendron‐like peptide, Cδ3‐(YYEE)‐E co‐assembles with G4 DNA in aqueous buffer containing Na+ ions. Various orthogonal biophysical studies have established the co‐assembly phenomenon. In silico, molecular docking studies also corroborate the results obtained from biophysical experiments. Importantly, the co‐assembly enhances the thermal stability of G4 DNA compared to free G4 DNA. The peptide inhibits the activity of telomerase enzyme which is found to be over‐expressed in most of the cancer cells and also down‐regulates the c‐Myc oncogenic expression. The peptide exhibits significant cytotoxic effect on cancer cells (HeLa and U2OS) compared to non‐cancer cells (HEK293) under similar experimental conditions. The study highlights the applicability of a synthetic bioactive peptide as a putative anticancer therapeutic. [ABSTRACT FROM AUTHOR]

The number of (TTAGGG)n repeats at the ends of chromosomes is highly variable between individual chromosomes, between different cells and between species. Progressive loss of telomere repeats limits the proliferation of pre-malignant human cells but also contributes to aging by inducing apoptosis and senescence in normal cells. Despite enormous progress in understanding distinct pathways that result in loss and gain of telomeric DNA in different cell types, many questions remain. Further studies are needed to delineate the role of damage to telomeric DNA, replication errors, chromatin structure, liquid-liquid phase transition, telomeric transcripts (TERRA) and secondary DNA structures such as guanine quadruplex structures, R-loops and T-loops in inducing gains and losses of telomere repeats in different cell types. Limitations of current telomere length measurements techniques and differences in telomere biology between species and different cell types complicate generalizations about the role of telomeres in aging and cancer. Here some of the factors regulating the telomere length in embryonic and adult cells in mammals are discussed from a mechanistic and evolutionary perspective. [ABSTRACT FROM AUTHOR]

Eleven novel 10-O-aryl-substituted berberrubine and berberine derivatives were synthesized by the Cu2+-catalyzed Chan–Evans–Lam coupling of berberrubine with arylboronic acids and subsequent 9-O-methylation. The reaction is likely introduced by the Cu2+-induced demethylation of berberrubine and subsequent arylation of the resulting 10-oxyanion functionality. Thus, this synthetic route represents the first successful Cu-mediated coupling reaction of berberine substrates. The DNA-binding properties of the 10-O-arylberberine derivatives with duplex and quadruplex DNA were studied by thermal DNA denaturation experiments, spectrometric titrations as well as CD and LD spectroscopy. Fluorimetric DNA melting analysis with different types of quadruplex DNA revealed a moderate stabilization of the telomeric quadruplex-forming oligonucleotide sequence G3(TTAG3)3. The derivatives showed a moderate affinity towards quadruplex DNA (Kb = 5–9 × 105 M−1) and ct DNA (Kb = 3–5 × 104 M−1) and exhibited a fluorescence light-up effect upon complexation to both DNA forms, with slightly higher intensity in the presence of the quadruplex DNA. Furthermore, the CD- and LD-spectroscopic studies revealed that the title compounds intercalate into ct DNA and bind to G4-DNA by terminal stacking.

Films of four different DNA quadruplex-forming (G4) sequences (c-KIT, c-MYC, HTelo, and BCL2) on gold surfaces were investigated by electrochemical impedance spectroscopy (EIS) to evaluate whether they evoke unique electrochemical responses that can be used for their identification. This could render EIS an alternative means for the determination of G4 sequences of unknown structure. Towards, this end, cation-dependent topology changes in the presence of either K+, K+ in combination with Li+, or Pb2+ in the presence of Li+ were first evaluated by circular dichroism (CD) spectroscopy, and electrochemical studies were performed subsequently. As a result, G4-sequence specific charge transfer resistance (RCT) patterns were in fact observed for each G4 sequence, allowing their discrimination by EIS. [ABSTRACT FROM AUTHOR]

Molybdenum carbonyl complexes with chalcone ligands incorporating pyridyl and anthryl units were synthesized via microwave activation. The incorporation of the chalcone moiety was found to improve the cytotoxicity and quadruplex DNA binding of these complexes. [Display omitted] • Molybdenum carbonyl complexes with chalcone ligands incorporating pyridyl and anthryl units were synthesized via microwave activation. • The structures of products with 2-pyridyl ligands were different from those with 3- or 4-pyridyl moieties. • The incorporation of the chalcone moiety was found to improve the cytotoxicity and quadruplex DNA binding of these complexes. Microwave irradiation of a mixture of Mo(CO) 6 and pyridinecarboxaldehyde (pyca), acetylpyridine (acpy) and pyridyl-anthryl chalcones with tetrahydrofuran solvent in a closed vessel afforded products in good yields without the need for an inert atmosphere. While the reaction with 3- and 4-pyridyl moieties gave the cis -disubstituted complexes Mo(CO) 4 (L) 2 , the reaction with 2-pyridyl entities yielded complexes with a range of structures such as Mo(CO) 2 (L) 2 , Mo(CO) 4 L and Mo 2 (CO) 6 (L) 2. All the novel complexes have been characterised by IR and 1H NMR spectroscopy as well as elemental analysis. In addition, the solid-state structure of one of the chalcone-ligated compounds has been determined by single-crystal X-ray diffraction. The chalcone-ligated complexes were found to be cytotoxic through the brine shrimp lethality assay, and were able to bind to quadruplex DNA. On the other hand, the pyca- and acpy-ligated compounds did not display any lethality and were unable to interact with DNA. The results indicate that the inclusion of a chalcone ligand plays an important role in improving the cytotoxicity and DNA binding capabilities of molybdenum carbonyl compounds. [ABSTRACT FROM AUTHOR]

• Eight diruthenium sawhorse and cationic complexes were synthesized and characterized. • Electrochemical studies were conducted on the complexes with ferrocenyl moieties. • The cationic complexes could dissolve in water and were able to bind to quadruplex DNA. A total of eight diruthenium sawhorse and cationic complexes incorporating carboxylated chalcones with phenyl or ferrocenyl units have been synthesized and characterized. The electrochemical behavior of the sawhorse and cationic complexes incorporating the ferrocenyl moiety have been studied by cyclic voltammetry. For the cationic complexes both the diruthenium core and the ferrocenyl unit undergo oxidation, in contrast only the ferrocenyl moieties for the sawhorse complexes were oxidized. The enhanced solubility of the cationic complexes over the neutral sawhorse compounds in aqueous medium enabled DNA binding studies to be undertaken for the former. All of the cationic complexes could bind to DNA, and displayed better selectivity for quadruplex over duplex DNA. These results indicate that diruthenium cationic complexes are able to bind to quadruplex DNA and have the potential to function as telomerase inhibitors. Diruthenium sawhorse and cationic complexes with carboxylated chalcone ligands incorporating phenyl and ferrocenyl units were synthesized and characterized. Electrochemical studies were conducted on the complexes with ferrocenyl moieties. The cationic complexes could dissolve in water and were able to bind to quadruplex DNA. [Display omitted] [ABSTRACT FROM AUTHOR]

Genes encoding 45S ribosomal RNA (rDNA) are known for their abundance within eukaryotic genomes and for their unstable copy numbers in response to changes in various genetic and epigenetic factors. Commonly, we understand as epigenetic factors (affecting gene expression without a change in DNA sequence), namely DNA methylation, histone posttranslational modifications, histone variants, RNA interference, nucleosome remodeling and assembly, and chromosome position effect. All these were actually shown to affect activity and stability of rDNA. Here, we focus on another phenomenon – the potential of DNA containing shortly spaced oligo-guanine tracts to form quadruplex structures (G4). Interestingly, sites with a high propensity to form G4 were described in yeast, animal, and plant rDNAs, in addition to G4 at telomeres, some gene promoters, and transposons, suggesting the evolutionary ancient origin of G4 as a regulatory module. Here, we present examples of rDNA promoter regions with extremely high potential to form G4 in two model plants, Arabidopsis thaliana and Physcomitrella patens. The high G4 potential is balanced by the activity of G4-resolving enzymes. The ability of rDNA to undergo these “structural gymnastics” thus represents another layer of the rich repertoire of epigenetic regulations, which is pronounced in rDNA due to its highly repetitive character.

Abstract Background Many studies have shown that guanine-rich DNA sequences form quadruplex structures (G4) in vitro but there is scarce evidence of guanine quadruplexes in vivo. The majority of potential quadruplex-forming sequences (PQS) are located in transposable elements (TEs), especially close to promoters within long terminal repeats of plant LTR retrotransposons. Results In order to test the potential effect of G4s on retrotransposon expression, we cloned the long terminal repeats of selected maize LTR retrotransposons upstream of the lacZ reporter gene and measured its transcription and translation in yeast. We found that G4s had an inhibitory effect on translation in vivo since “mutants” (where guanines were replaced by adenines in PQS) showed higher expression levels than wild-types. In parallel, we confirmed by circular dichroism measurements that the selected sequences can indeed adopt G4 conformation in vitro. Analysis of RNA-Seq of polyA RNA in maize seedlings grown in the presence of a G4-stabilizing ligand (NMM) showed both inhibitory as well as stimulatory effects on the transcription of LTR retrotransposons. Conclusions Our results demonstrate that quadruplex DNA located within long terminal repeats of LTR retrotransposons can be formed in vivo and that it plays a regulatory role in the LTR retrotransposon life-cycle, thus also affecting genome dynamics.

Genes encoding 45S ribosomal RNA (rDNA) are known for their abundance within eukaryotic genomes and for their unstable copy numbers in response to changes in various genetic and epigenetic factors. Commonly, we understand as epigenetic factors (affecting gene expression without a change in DNA sequence), namely DNA methylation, histone posttranslational modifications, histone variants, RNA interference, nucleosome remodeling and assembly, and chromosome position effect. All these were actually shown to affect activity and stability of rDNA. Here, we focus on another phenomenon – the potential of DNA containing shortly spaced oligo-guanine tracts to form quadruplex structures (G4). Interestingly, sites with a high propensity to form G4 were described in yeast, animal, and plant rDNAs, in addition to G4 at telomeres, some gene promoters, and transposons, suggesting the evolutionary ancient origin of G4 as a regulatory module. Here, we present examples of rDNA promoter regions with extremely high potential to form G4 in two model plants, Arabidopsis thaliana and Physcomitrella patens. The high G4 potential is balanced by the activity of G4-resolving enzymes. The ability of rDNA to undergo these "structural gymnastics" thus represents another layer of the rich repertoire of epigenetic regulations, which is pronounced in rDNA due to its highly repetitive character. [ABSTRACT FROM AUTHOR]

Herein, we described the synthesis of two l-phenylalanines α-derivatized with a terminal alkyne moiety whose structures differed by phenyl ring halogen substitution (two o-Cl in 1 vs. one p-Br in 2) and investigated their effect on biological macromolecules and living cells. We explored their interaction with quadruplex DNA (G4 DNA), using tel26 and c-myc as models, and bovine serum albumin (BSA). By CD spectroscopy, we found that 1 caused minor tel26 secondary structure changes, leading also to a slight thermal stabilization of this hybrid antiparallel/parallel G4 structure, while the c-myc parallel topology remained essentially unchanged upon 1 binding. Other CD evidences showed the ability of 1 to bind BSA, while molecular docking studies suggested that the same molecule could be housed into the hydrophobic cavity between sub-domains IIA, IIB, and IIIA of the protein. Furthermore, preliminary aggregation studies, based on concentration-dependent spectroscopic experiments, suggested the ability of 1 to aggregate forming noncovalent polymeric systems in aqueous solution. Differently from 1, the bromine-modified compound was able to bind Cu(II) ion, likely with the formation of a CuL2 complex, as found by UV spectroscopy. Finally, cell tests excluded any cytotoxic effect of both compounds toward normal cells, but showed slight antiproliferative effects of 2 on PC3 cancerous cells at 24 h, and of 1 on both T98G and MDA-MB-231 cancer cells at 48 h. [ABSTRACT FROM AUTHOR]

Genomic DNA exhibits an innate ability to manifest diverse sequence-dependent secondary structures, serving crucial functions in gene regulation and cellular equilibrium. While extensive research has confirmed the formation of G-quadruplex structures by guanine-rich sequences in vitro and in cells, recent investigations have turned the quadruplex community's attention to the cytosine (C)-rich complementary strands that can adopt unique tetra-stranded conformation, termed as intercalated motif or i-motif. I-motifs are stabilized by hemi-protonated C:CH + base pairs under acidic conditions. Initially, the in vivo occurrence of i-motifs was underestimated because their formation is favored at non-physiological pH. However, groundbreaking research utilizing the structure-specific iMab antibody and high-throughput sequencing have recently detected their conserved dispersion throughout the genome, challenging previous assumptions. Given the evolving nature of this research field, it becomes imperative to conduct independent in vitro experiments aimed at identifying potential i-motif formation in C-rich sequences and consolidating the findings to address the properties of i-motifs. This chapter serves as an introductory guide for the swift identification of novel i-motifs, where we present an experimental framework for investigating and characterizing i-motif sequences in vitro. In this chapter, we selected a synthetic oligonucleotide (C 7 T 3 ) sequence and outlined appropriate methodologies for annealing the i-motif structure into suitable buffers. Then, we validated its formation by CD (Circular Dichroism) and NMR (Nuclear Magnetic Resonance) spectroscopy. Finally, we provided a thorough account of the step-by-step procedures to investigate the effect of i-motif formation on the stalling or retardation of DNA replication using high resolution primer extension assays., (Copyright © 2024. Published by Elsevier Inc.)

A phosphate-substituted, zwitterionic berberine derivative was synthesized and its binding properties with duplex DNA and G4-DNA were studied using photometric, fluorimetric and polarimetric titrations and thermal DNA denaturation experiments. The ligand binds with high affinity toward both DNA forms (Kb = 2–7 × 105 M−1) and induces a slight stabilization of G4-DNA toward thermally induced unfolding, mostly pronounced for the telomeric quadruplex 22AG. The ligand likely binds by aggregation and intercalation with ct DNA and by terminal stacking with G4-DNA. Thus, this compound represents one of the rare examples of phosphate-substituted DNA binders. In an aqueous solution, the title compound has a very weak fluorescence intensity (Φfl < 0.01) that increases significantly upon binding to G4-DNA (Φfl = 0.01). In contrast, the association with duplex DNA was not accompanied by such a strong fluorescence light-up effect (Φfl < 0.01). These different fluorimetric responses upon binding to particular DNA forms are proposed to be caused by the different binding modes and may be used for the selective fluorimetric detection of G4-DNA.

Ruthenium arene complexes containing mono-carbonyl analogues of curcumin (MAC) functioning as pendant or bridging ligands displayed anti-proliferative activity on MOLT-4 cells. The complex incorporating the bridging MAC ligand bound to human telomeric DNA more tightly than the complex with the pendant MAC ligand. Four ruthenium(II) arene complexes containing mono-carbonyl analogues of curcumin (MAC) functioning as pendant or bridging ligands as well as chlorido ancillary ligands have been synthesized and structurally characterized by IR and 1H NMR spectroscopies, ESI mass spectrometry and elemental analysis. Anti-proliferative activity of the complexes determined on MOLT-4 human leukemia cells revealed good to moderate activity. Two of the compounds, 3b and 4b , both of which incorporated cyclohexanone as part of the MAC structural motif, displayed potency comparable to cisplatin. In intercalative binding studies, while the organic MACs did not display any interaction with quadruplex DNA, the ruthenium complexes were found to be able to stabilize quadruplex DNA, with 3b and 4b displaying the greatest selectivity for HTelo over c-myc. Compound 4b , in which the MAC ligand is bridged by two organoruthenium centres, bound to HTelo more tightly than 3b , in which the MAC functions as a pendant ligand towards a single ruthenium arene core. These results suggest that minor changes to the structural motif of the MAC ligand, as well as the presence of the ruthenium arene moiety play an important role in achieving selective quadruplex DNA stabilization. [ABSTRACT FROM AUTHOR]

A series of mono imine (C=N) group that contained Wittig-based Schiff-Base ligands was optimized using the DFT-based computational method and Gaussian 09 program package. These optimized molecules were docked with Quadruplex DNA (PDB ID: 1KF1) and duplex DNA (PDB ID: 1BNA) using AutoDock Vina program along with the reference molecules. Schiff-Base ligands derived from fused aromatic rings contained amines and precursor aldehyde (PA-5 both Z and E isomers) showed lower binding energy for G-quadruplex DNA among all and N-5 category both Z and E isomer Schiff-Base ligands have shown high selectivity for G-quadruplex DNA over duplex DNA which is a very important phenomenon to develop the G-quadruplex DNA stabilizers. For a few Schiff-Base molecules like Ligand-6 (1-{[2-Hydroxy-5-(2-pyren-1-yl-vinyl)-benzylidene]-amino}-naphthalen-2-ol) of N-5 category both Z and E isomers with groove binding and end stacking modes, molecular dynamic calculations were carried out. The study revealed that Ligand-6 of N-5 category E isomer with groove binding mode has higher stabilizing effect on G-quadruplex DNA in spite of having the higher binding energy value. Among Schiff-Base copper(II) complexes, Complex-3 (E-(1-{[2-Hydroxy-5-(2-pyren-1-yl-vinyl)-benzylidene]-amino}-naphthalen-2-ol)Cu) is having high binding affinity for G-quadruplex DNA as compared to others. [ABSTRACT FROM AUTHOR]

Plant flavonols are the best known class of naturally occurring organic molecules exhibiting ultrafast excited state intramolecular proton transfer (ESIPT) leading to ‘two color’ fluorescence emissions, which are exquisitely sensitive to the environment. On a different scenario, flavonols and related polyphenolic compounds of the flavonoid group, have attracted enormous attention as novel prophylactic and therapeutic drugs for free radical mediated and other human diseases. Their high potency and low cyto-toxicity make them viable alternatives to conventional therapeutics. In this context, identification of their physiological target molecules, mode of interactions with such targets, structure-affinity relationships and related aspects, have been key areas of investigations. This article presents perspectives, illustrating the potential usefulness of bioactive plant flavonols as their own fluorescence ‘reporters’ for exploring their interactions with duplex and quadruplex DNA molecules of potential interest as therapeutic targets. Representative and recent findings from our laboratory, and other relevant studies, exemplifying novel uses of flavonols as multiparametric fluorescence probes, are appropriately highlighted. [ABSTRACT FROM AUTHOR]

Ruthenium arene complexes with chalcone ligands incorporating pyridyl and anthryl units were synthesized and studied for their interaction with DNA. The binding strength of these complexes with human telomeric DNA was influenced by the ancillary chloro or oxalato ligands, the structure of the chalcone ligand as well as the charge of the complex. [Display omitted] • Twelve ruthenium arene complexes were synthesized and studied for their interaction with DNA. • The binding strength with HTelo DNA was influenced by the nature of the ligands and the charge of the complex. Twelve ruthenium(II) arene complexes incorporating chalcone ligands with pyridyl and anthryl units, as well as chlorido or oxalato ancillary ligands, have been synthesized and structurally characterized by 1H NMR spectroscopy, ESI mass spectrometry and elemental analysis. Compared to the oxalato compounds, the chlorido complexes were less stable and more susceptible to aquation in solution; the dissociation was suppressed in the presence of chloride ions. All six of the chlorido complexes and three of the oxalato complexes were able to bind to quadruplex DNA, exhibiting greater selectivity for HTelo over c-myc. The cationic species 3f , in which the chalcone chelates to the metal center, was found to bind to HTelo most strongly. These results indicate that the ancillary ligand, the location of the N -donor atom in the pyridyl ring, the position of the α,β-unsaturated ketone relative to the pyridyl and anthryl entities in the chalcone moiety, as well as the presence of the metal center all play significant roles in improving the binding of such complexes to quadruplex DNA. [ABSTRACT FROM AUTHOR]

G-quadruplex DNA is a non-canonical structure that forms in guanine-rich regions of the genome. There is increasing evidence showing that G-quadruplexes have important biological functions, and therefore molecular tools to visualise these structures are important. Herein we report on a series of new cyclometallated platinum(II) complexes which, upon binding to G-quadruplex DNA, display an increase in their phosphorescence, acting as switch-on probes. More importantly, upon binding to G-quadruplexes they display a selective and distinct lengthening of their emission lifetime. We show that this effect can be used to selectively visualise these structures in cells using Phosphorescence Lifetime Imaging Microscopy (PLIM)., Competing Interests: The authors declare no conflict of interest., (© 2023 The Authors. Angewandte Chemie published by Wiley-VCH GmbH.)

The present study reports the synthesis and evaluation of nonlinear optical property and G-Quadruplex DNA Stabilization of five novel copper(II) mixed ligand complexes. They were synthesized from copper(II) salt, 2,5- and 2,3- pyridinedicarboxylic acid, diethylenetriamine and amide based ligand (AL). The crystal structure of these complexes were determined through X-ray diffraction and supported by ESI-MAS, NMR, UV–Vis and FT-IR spectroscopic methods. Their nonlinear optical property was studied using Gaussian09 computer program. For structural optimization and nonlinear optical property, density functional theory (DFT) based B3LYP method was used with LANL2DZ basis set for metal ion and 6-31G ∗ for C,H,N,O and Cl atoms. The present work reveals that pre-polarized Complex-2 showed higher β value (29.59 × 10 −30 e.s.u) as compared to that of neutral complex-1 (β = 0.276 × 10 −30 e.s.u.) which may be due to greater advantage of polarizability. Complex-2 is expected to be a potential material for optoelectronic and photonic technologies. Docking studies using AutodockVina revealed that complex-2 has higher binding energy for both G-Quadruplex DNA (−8.7 kcal/mol) and duplex DNA (−10.1 kcal/mol). It was also observed that structure plays an important role in binding efficiency. [ABSTRACT FROM AUTHOR]

The interactions of the ILPR sequence (ILPR = "insulin-linked polymorphic region") a2 [d(ACAG4TGTG4ACAG4TGTG4)] with [2.2.2]heptamethinecyanine derivatives 1a–e and with the already established quadruplex ligands coralyne (2), 3,3′-[2,6-pyridinediylbis(carbonylimino)]bis[1-methylquinolinium] (3), 4,4′,4′′,4′′′-(21H,23H-porphine-5,10,15,20-tetrayl)tetrakis[1-methylpyridinium] (4), naphtho[2,1-b:3,4-b′:6,5-b′′:7,8-b′′′]tetraquinolizinium (5) and thiazole orange (6) were studied. It is demonstrated with absorption, fluorescence and CD spectroscopy that all investigated ligands bind with relatively high affinity to the ILPR-quadruplex DNA a2 (0.2–5.5 × 106 M−1) and that in most cases the binding parameters of ligand-ILPR complexes are different from the ones observed with other native quadruplex-forming DNA sequences.

Several tridentate hydrazone-based ligands, synthesized by a condensation reaction of either 2-(1-methylhydrazinyl)pyridine or 2-(1-methylhydrazinyl)quinoline with an aldehyde (picolinaldehyde, 1 H -pyrrole-2-carbaldehyde, 2-mercaptobenzaldehyde, 2-aminobenzaldehyde) have been reacted with palladium(II) and platinum(II) salts and precursor complexes to yield nine new metal complexes. These planar complexes were investigated with respect to their capability to interact with guanine quadruplex DNA. Two sequences (H-telo, derived from the human telomeric sequence, and c-myc , representing an excerpt of the promoter region of the c-Myc oncogene) were investigated. Circular dichroism (CD) spectroscopy, temperature-dependent CD spectroscopy, UV–Vis spectroscopy and a fluorescent intercalator displacement (FID) assay were applied in this respect. The spectroscopic data show that the complexes indeed interact with guanine quadruplex DNA. According to the FID assay, some of the complexes belong to the highest-affinity metal-containing quadruplex binders reported so far. Their affinity towards quadruplex DNA is up to 80-fold higher than to a reference double helix. These findings make the metal complexes good candidates as anticancer drugs, as guanine quadruplexes have been proposed as potential targets in anticancer drug design. [ABSTRACT FROM AUTHOR]

Study on anticancer agents that act via stabilization of telomeric G-quadruplex DNA has emerged as novel and exciting field for anticancer drug discovery. The interaction of carbohydrate containing anticancer alkaloid aristololactam-β-D-glucoside (ADG) with human telomeric G-quadruplex DNA sequence was characterized by different biophysical techniques. The binding parameters were compared with daunomycin (DAN), a well-known chemotherapeutic drug. The Scatchard binding isotherms revealed noncooperative binding for both with the binding affinity values of (1.01 ± 0.05) × 106 and (1.78 ± 0.18) × 106 M−1 for ADG and DAN, respectively. Circular dichroism, ferrocyanide quenching study, anisotropy study, thiazole orange displacement, optical melting, differential scanning calorimetry study, and molecular docking study suggest significant stacking and stabilizing efficiency of ADG with comparison to DAN. The energetics of the interaction for ADG and DAN revealed that both reactions were predominantly entropy driven. Negative heat capacity values were obtained from the temperature dependence of the enthalpy change. The standard molar Gibbs energy change exhibited only marginal alterations with temperature suggesting the occurrence of enthalpy-entropy compensation. These findings indicate that ADG can act as a stabilizer of telomeric G-quadruplex DNA and thereby can be considered as a potential telomerase inhibitor. [ABSTRACT FROM AUTHOR]

Guanine is the most readily oxidized of the four DNA bases, and guanine oxidation products cause G:C-T:A and G:C-C:G transversions through DNA replication. 8-Oxo-7,8-dihydroguanine (8-oxoG) causes G:C-T:A transversions but not G:C-C:G transversions, and is more readily oxidized than guanine. This review covers four major findings. (i) 2,2,4-Triamino-5(2H)-oxazolone (Oz) is produced from guanine and 8-oxoG under various oxidative conditions. Guanine is incorporated opposite Oz by DNA polymerases, except REV1. (ii) Several enzymes exhibit incision activity towards Oz. (iii) Since the redox potential of GG is lower than that of G, contiguous GG sequences are more readily oxidized by a one-electron oxidant than a single guanine, and OzOz is produced from GG in double-stranded DNA. Unlike most DNA polymerases, DNA polymerase ζ efficiently extends the primer up to full-length across OzOz. (iv) In quadruplex DNA, 3'-guanine is mainly damaged by one-electron oxidation in quadruplex DNA, and this damage depends on the highest occupied molecular orbital (HOMO). The oxidation products in quadruplex DNA are different from those in single-stranded or double-stranded DNA. [ABSTRACT FROM AUTHOR]

To study a series of new acridine derivatives containing two basic fragments able to bind to quadruplex DNA at C-4 and C-9 positions as potential telomerase inhibitors. Methods. TRAP assay was used to determine the activity of compounds in vitro. Results. A number of acridines inhibiting the enzyme at micromolar concentrations were found, with IC50 = 2.6 μM for the most active compound. Conclusions. The introduction of a highly basic N,N-dimethylaminoalkyl group at the C-9 position of the acridine core results in a strong increase of biological activity of compounds, and a 5-methyl substituent further enhances it. [ABSTRACT FROM AUTHOR]

ABSTRACT Regulatory regions in the genome can act through a variety of mechanisms that range from the occurrence of histone modifications to the presence of protein-binding loci for self-annealing sequences. The final result is often the induction of a conformational change of the DNA double helix, which alters the accessibility of a region to transcription factors and consequently gene expression. A ∼300 kb regulatory region on chromosome 14 at the 3' end (3'RR) of immunoglobulin (Ig) heavy-chain genes shows very peculiar features, conserved in mammals, including enhancers and transcription factor binding sites. In primates, the 3'RR is present in two copies, both having a central enhancer named hs1.2. We previously demonstrated the association between different hs1.2 alleles and Ig plasma levels in immunopathology. Here, we present the analysis of a putative G-quadruplex structure (tetraplex) consensus site embedded in a variable number tandem repeat (one to four copies) of hs1.2 that is a distinctive element among the enhancer alleles, and an investigation of its three-dimensional structure using bioinformatics and spectroscopic approaches. We suggest that both the role of the enhancer and the alternative effect of the hs1.2 alleles may be achieved through their peculiar three-dimensional-conformational rearrangement. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 768-778, 2016. [ABSTRACT FROM AUTHOR]

There is an escalating interest of using double stranded DNA molecules as a chiral scaffold to construct metal-biomacromolecule hybrid catalysts for asymmetric synthesis. Several recent studies also evaluated the use of G-quadruplex DNA-based catalysts for asymmetric Diels-Alder and Friedel-Crafts reactions. However, there is still a lack of understanding of how different oligonucleotides, salts (such as NaCl and KCl), metal ligands and co-solvents affect the catalytic performance of quadruplex DNA-based hybrid catalysts. In this study, we aim to systematically evaluate these key factors in asymmetric Michael addition reactions, and to examine the conformational and molecular changes of DNA by circular dichroism (CD) spectroscopy and gel electrophoresis. We achieved up to 95% yield and 50% enantiomeric excess (ee) when the reaction of 2-acylimidazole 1a and dimethylmalonate was catalyzed by 5′-G3(TTAG3)3−3′ (G4DNA1) in 20 mM MOPS (pH 6.5) containing 50 mM KCl and 40 µM [Cu(dmbipy)(NO3)2], and G4DNA1 was pre-sonicated in ice bath for 10 min prior to the reaction. G-quadruplex-based hybrid catalysts provide a new tool for asymmetric catalysis, but future mechanistic studies should be sought to further improve the catalytic efficiency. The current work presents a systematic study of asymmetric Michael addition catalyzed by G-quadruplex catalysts constructed via non-covalent complexing, and an intriguing finding of the effect of pre-sonication on catalytic efficiency. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:891-898, 2016 [ABSTRACT FROM AUTHOR]

Metalloporphyrins are efficient biomimetic models of heme enzymes such as cytochrome P450 and peroxidases. They are also endowed with high affinity for double-stranded and G-quadruplex DNA. The different DNA specific binding modes of porphyrins will be reviewed. After a summary of current knowledge on the mechanism of action of heme enzymes and their models some examples of the oxidation reactions carried out by porphyrins tightly bound to DNA are presented. The oxidation mediated by the porphyrin model may be directed toward DNA and the porphyrin/DNA complex leads to DNA damage (artificial nuclease) or may be directed toward small substrates present in the bulk (DNAzyme). The chosen examples of porphyrins interacting with either double-stranded DNA or G-quadruplex DNA hosts highlight how DNA participates in the reaction or contributes to a better understanding of the chemistry of porphyrin models. [ABSTRACT FROM AUTHOR]

The dicationic styrylimidazo[1,2-a]pyridinium dyes were synthesized and characterized using 1 H NMR, 13 C NMR, mass spectral techniques and elemental analysis. In addition, their photophysical and DNA-binding properties were investigated. The dyes absorb in the UV region with maxima at 342–358 nm, and the emission spectra of these derivatives show a maximum at 409–475 nm with moderate Stokes shift. It was shown with spectrophotometric, spectrofluorimetric and viscometric titrations as well as with Circular dichroism spectroscopic analysis that the dicationic styrylimidazo[1,2-a]pyridinium dyes associate as groove binders with double-stranded DNA with binding constants in the range of 10 5 –10 6 M −1 . Preliminary experiments revealed that these ligands also bind with reasonable affinity to telomeric quadruplex DNA. [ABSTRACT FROM AUTHOR]

c-MYC DNA is an attractive target for drug design, especially for cancer chemotherapy. Around 90% of c-MYC transcription is controlled by NHE III1, whose 27-nt purine-rich strand has the ability to form G-quadruplex structure. In this investigation, interaction of ActD with 27-nt G-rich strand (G/c-MYC) and its equimolar mixture with the complementary sequence, (GC/c-MYC) as well as related C-rich oligonucleotide (C/c-MYC) was evaluated. Molecular dynamic simulations showed that phenoxazine and lactone rings of ActD come close to the outer G-tetrad nucleotides indicating that ActD binds through end-stacking to the quadruplex DNA. RMSD and RMSF revealed that fluctuation of the quadruplex DNA increases upon interaction with the drug. The results of spectrophotometry and spectrofluorometry indicated that ActD most probably binds to the c-MYC quadruplex and duplex DNA via end-stacking and intercalation, respectively and polarity of ActD environment decreases due to the interaction. It was also found that binding of ActD to the GC-rich DNA is stronger than the two other forms of DNA. Circular dichroism results showed that the type of the three forms of DNA structures doesn't change, but their compactness alters due to their interaction with ActD. Finally, it can be concluded that ActD binds differently to double stranded DNA, quadruplex DNA and i-motif. [ABSTRACT FROM AUTHOR]

Electrospray ionization mass spectrometry (ESI-MS) conditions were optimized for simultaneous observation of a bimolecular qDNA and a Watson-Crick base-paired duplex DNA/RNA hybrid. The DNA sequence used was telomeric DNA, and the RNA contained the template for telomerase-mediated telomeric DNA synthesis. Addition of RNA to the quadruplex DNA (qDNA) resulted in formation of the duplex DNA/RNA hybrid. Melting profiles obtained using circular dichroism spectroscopy confirmed that the DNA/RNA hybrid exhibited greater thermal stability than the bimolecular qDNA in solution. Binding of a 13-substituted berberine ( 1) derivative to the bimolecular qDNA stabilized its structure as evidenced by an increase in its stability in the mass spectrometer, and an increase in its circular dichroism (CD) melting temperature of 10°C. The DNA/RNA hybrid did not bind the ligand extensively and its thermal stability was unchanged in the presence of ( 1). The qDNA-ligand complex resisted unfolding in the presence of excess RNA, limiting the formation of the DNA/RNA hybrid. Previously, it has been proposed that DNA secondary structures, such as qDNA, may be involved in the telomerase mechanism. DNA/RNA hybrid structures occur at the active site of telomerase. The results presented in the current work show that if telomeric DNA was folded into a qDNA structure, it is possible for a DNA/RNA hybrid to form as is required during template alignment. The discrimination of ligand ( 1) for binding to the bimolecular qDNA over the DNA/RNA hybrid positions it as a useful compound for probing the role(s), if any, of antiparallel qDNA in the telomerase mechanism. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

[Display omitted] A series of 10-alkoxy-Anthryl-isoxazole-pyrrole-doubletails (RO-AIMs) were synthesized using a crown ether assisted nucleophilic aromatic substitution followed by a modified Schotten-Baumann reaction. The novel RO-AIMs described here exhibit robust growth inhibition for the human SNB19 CNS glioblastoma cell line, and biphenyl analog 8c had activity in the nanomolar regime, which represents the most efficacious compound in the AIM series to date. Computational modeling for RO-AIMs binding in a ternary complex with c- myc quadruplex DNA and its helicase DHX36 is presented which represents our current working hypothesis. [ABSTRACT FROM AUTHOR]

Highlights: [•] Selective NMR experiments give information on spermine structure and mobility. [•] Negative spermine NOEs observed on association with NHE quadruplexes. [•] TOCSY peak intensities support a quadruplex-induced spermine conformation change. [•] Parallel chain-reversal G-quadruplexes attenuate spermine mobility. [•] Five G-tracts within the NHE generate the most efficient spermine immobilisation. [ABSTRACT FROM AUTHOR]

Abstract: G-quadruplex DNA presents a potential target for the design and development of novel anticancer drugs. The porphyrin TMPyP4 was early reported to be a suitable motif for G-quadruplex DNA interaction. We inserted various metal ions such as Zn(II), Cu(II), Co(III) in the center of the aromatic core of tricationic TMPyP4-like porphyrin and examined their interactions with an antiparallel G-quadruplex DNA by a combination of spectroscopy and Job plot methods. Porphyrin metallation allowed the conclusion that the presence of one axial ligand perpendicular to the aromatic plane did not hamper π–π stacking interactions between quadruplex and the aromatic parts of porphyrin on the other face while porphyrin with two axial ligands was unable to undergo such interaction due to geometrical factors. Free base porphyrin and porphyrin without axial ligands are able to stabilize the quadruplex structure to a greater extent than the other metal complexes and thus may be potential anti-cancer drugs. [Copyright &y& Elsevier]

Triplex with a twist: Through metadynamics calculations, the thrombin binding aptamer (TBA) has been shown to adopt a stable G‐triplex structural motif, in addition to the usual G‐quadruplex (see scheme). An 11‐mer oligonucleotide was also shown to form a stable G‐triplex, whose structural and thermodynamic properties have been characterized. [ABSTRACT FROM AUTHOR]