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A series of 6-amidinobenzothiazoles, linked via phenoxymethylene or directly to the 1,2,3-triazole ring with a p -substituted phenyl or benzyl moiety, were synthesised and evaluated in vitro against four human tumour cell lines and the protozoan parasite Trypanosoma brucei . The influence of the type of amidino substituent and phenoxymethylene linker on antiproliferative and antitrypanosomal activities was observed, showing that the imidazoline moiety had a major impact on both activities. Benzothiazole imidazoline 14a , which was directly connected to N -1-phenyl-1,2,3-triazole, had the most potent growth-inhibitory effect (IC 50 = 0.25 µM) on colorectal adenocarcinoma (SW620), while benzothiazole imidazoline 11b , containing a phenoxymethylene linker, exhibited the best antitrypanosomal potency (IC 90 = 0.12 µM). DNA binding assays showed a non-covalent interaction of 6-amidinobenzothiazole ligands, indicating both minor groove binding and intercalation modes of DNA interaction. Our findings encourage further development of novel structurally related 6-amidino-2-arylbenzothiazoles to obtain more selective anticancer and anti-HAT agents.

The novel 1,2,3-triazolyl-appended N - and O -heterocycles containing amidine 4 - 11 and amidoxime 12 - 22 moiety were prepared and evaluated for their antiproliferative activities in vitro. Among the series of amidine-substituted heterocycles, aromatic diamidine 5 and coumarine amidine 11 had the most potent growth-inhibitory effect on cervical carcinoma (HeLa), hepatocellular carcinoma (HepG2) and colorectal adenocarcinoma (SW620), with IC 50 values in the nM range. Although compound 5 was toxic to non-tumor HFF cells, compound 11 showed certain selectivity. From the amidoxime series, quinoline amidoximes 18 and 20 showed antiproliferative effects on lung adenocarcinoma (A549), HeLa and SW620 cells emphasizing compound 20 that exhibited no cytostatic effect on normal HFF fibroblasts. Results of CD titrations and thermal melting experiments indicated that compounds 5 and 10 most likely bind inside the minor groove of AT-DNA and intercalate into AU-RNA. Compounds 6 , 9 and 11 bind to AT-DNA with mixed binding mode, most probably minor groove binding accompanied with aggregate binding along the DNA backbone.

Three novel 2-aminopyrazine Schiff bases derived from salicylaldehyde derivatives and their uranyl complexes were synthesized and characterized by elemental analysis, UV-vis, FTIR, molar conductance, and thermal gravimetric analysis (TGA). The proposed structures were optimized using density functional theory (DFT/B3LYP) and 6-311G ∗(d,p) basis sets. All uranyl complexes are soluble in DMSO and have low molar conductance, which indicates that all the complexes are nonelectrolytes. The DNA binding of those Schiff bases and their uranyl complexes was studied using UV-vis spectroscopy, and screening of their ability to bind to calf thymus DNA (CT-DNA) showed that the complexes interact with CT-DNA through an intercalation mode, for which the K b values ranged from 1 × 10 6 to 3.33 × 10 5 M -1 . The anticancer activities of the Schiff base ligands and their uranyl complexes against two ovarian (Ovcar-3) and melanoma cell lines (M14) were investigated, and the results indicated that uranyl complexes exhibit better results than the Schiff base ligands. Molecular docking identified the distance, energy account, type, and position of links contributing to the interactions between these complexes and two different cancer proteins (3W2S and 2OPZ).

Several complexes of general formula [Ru(halide)(η 6 -p-cymene)(α-diimine)] + , in the form of nitrate, triflate and hexafluorophosphate salts, including a newly synthesized iodide compound, were investigated as potential anticancer drugs and bactericides. NMR and UV-Vis studies evidenced remarkable stability of the complexes in water and cell culture medium. In general, the complexes displayed strong cytotoxicity against A2780 and A549 cancer cell lines with IC 50 values in the low micromolar range, and one complex (RUCYN) emerged as the most promising one, with a significant selectivity compared to the non-cancerous HEK293 cell line. A variable affinity of the complexes for BSA and DNA binding was ascertained by spectrophotometry/fluorimetry, circular dichroism, electrophoresis and viscometry. The performance of RUCYN appears associated to enhanced cell internalization, favored by two cyclohexyl substituents, rather than to specific interaction with the evaluated biomolecules. The chloride/iodide replacement, in one case, led to increased cellular uptake and cytotoxicity at the expense of selectivity, and tuned DNA binding towards intercalation. Complexes with iodide or a valproate bioactive fragment exhibited the best antimicrobial profiles., (Copyright © 2021 Elsevier B.V. All rights reserved.)

New analogs of the commercial asymmetric monomethine cyanine dyes thiazole orange (TO) and thiazole orange homodimer (TOTO) with hydroxypropyl functionality were synthesized and their properties in the presence of different nucleic acids were studied. The novel compounds showed strong, micromolar and submicromolar affinities to all examined DNA ds-polynucleotides and poly rA-poly rU. The compounds studied showed selectivity towards GC-DNA base pairs over AT-DNA, which included both binding affinity and a strong fluorescence response. CD titrations showed aggregation along the polynucleotide with well-defined supramolecular chirality. The single dipyridinium-bridged dimer showed intercalation at low dye-DNA/RNA ratios. All new cyanine dyes showed potent micromolar antiproliferative activity against cancer cell lines, making them promising theranostic agents.

We synthesized a series of novel 3-carboranyl-1,8-naphthalimide derivatives, mitonafide and pinafide analogs, using click chemistry, reductive amination and amidation reactions and investigated their in vitro effects on cytotoxicity, cell death, cell cycle, and the production of reactive oxygen species in a HepG2 cancer cell line. The analyses showed that modified naphthalic anhydrides and naphthalimides bearing ortho - or meta -carboranes exhibited diversified activity. Naphthalimides were more cytotoxic than naphthalic anhydrides, with the highest IC 50 value determined for compound 9 (3.10 µM). These compounds were capable of inducing cell cycle arrest at G0/G1 or G2M phase and promoting apoptosis, autophagy or ferroptosis. The most promising conjugate 35 caused strong apoptosis and induced ROS production, which was proven by the increased level of 2'-deoxy-8-oxoguanosine in DNA. The tested conjugates were found to be weak topoisomerase II inhibitors and classical DNA intercalators. Compounds 33 , 34 , and 36 fluorescently stained lysosomes in HepG2 cells. Additionally, we performed a similarity-based assessment of the property profile of the conjugates using the principal component analysis. The creation of an inhibitory profile and descriptor-based plane allowed forming a structure-activity landscape. Finally, a ligand-based comparative molecular field analysis was carried out to specify the (un)favorable structural modifications (pharmacophoric pattern) that are potentially important for the quantitative structure-activity relationship modeling of the carborane-naphthalimide conjugates.

In view of their DNA intercalation activities as anticancer agents, novel twenty four [1,2,4]triazolo[4,3-a]quinoxaline derivatives have been designed, synthesized and evaluated against HepG2, HCT-116 and MCF-7 as DNA intercalators and Top II enzyme inhibitors. The data obtained from molecular modeling studies revealed that, our small aromatic molecules were concluded to act through two ways firstly, through non-covalent interaction with the directly bound proteins to DNA hence inhibit topoisomerase-II enzyme. The second is through non-covalently binding to double helical structures of DNA either by intercalating binder as in compounds 10 a and 11 d or by minor groove binding as in compounds 8 e and 8 c . Cytotoxic activity indicated that MCF-7 and HepG2 were the most sensitive cell lines to the influence of the new derivatives respectively. In particular, compounds 10 a , 11 d and 8 e were found to be the most potent derivatives overall the tested compounds against the three HepG2, HCT116 and MCF-7 cancer cell lines with IC 50 = (4.55 ± 0.3, 6.18 ± 0.8 and 3.93 ± 0.6 µM), (5.61 ± 0.5, 6.49 ± 0.5and 3.71 ± 0.3 µM) and (4.66 ± 0.3, 8.08 ± 0.8 and 5.11 ± 0.7 µM) respectively. The three derivatives exhibited higher activities than doxorubicin, (IC 50  = 7.94 ± 0.6, 8.07 ± 0.8 and 6.75 ± 0.4 µM respectively), against HepG2 and MCF-7 but 8 e exhibited nearly the same activity against HCT116 cancer cell lines respectively. The most active derivatives 8 a-e , 10 a , b , 11 b-e , 13 a and 14 b,c were evaluated for their DNA binding activities. The tested compounds displayed very good to moderate DNA-binding affinities. Compounds 10 a 11 d , 8 e , 8 c , 8 a and 8 b displayed the highest binding affinities. These compounds potently intercalate DNA at decreased IC 50 values of 25.27 ± 1.2, 27.47 ± 2.1, 27.54 ± 3.2, 27.78 ± 1.3, 29.15 ± 1.8 and 30.23 ± 3.7 µM respectively, which were less than that of doxorubicin (31.27 ± 1.8). Furthermore, the most active cytotoxic compounds 8 a , 8 b , 8 c , 8 e , 10 a and 11 d were selected to evaluate their inhibitory activities against Topo II enzyme. All the tested compounds could interfere with the Topo II activity. They exhibited very good inhibitory activities with IC 50 values ranging from 0.379 ± 0.07 to 0.813 ± 0.14 µM that were lower than that of doxorubicin (IC 50  = 0.94 ± 0.4 µM). For a great extent, the reported results were in agreement with that of in vitro cytotoxicity activity, DNA binding and molecular modeling studies., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Herein we report the design and synthesis of a new series of phthalazine derivatives as Topo II inhibitors and DNA intercalators. The synthesized compounds were in vitro evaluated for their cytotoxic activities against HepG-2, MCF-7 and HCT-116 cell lines. Additionally, Topo II inhibitory activity and DNA intercalating affinity were investigated for the most active compounds as a potential mechanism for the anticancer activity. Compounds 15h, 23c, 32a, 32b, and 33 exhibited the highest activities against Topo II with IC 50 ranging from 5.44 to 8.90 µM, while compounds 27 and 32a were found to be the most potent DNA binders at IC 50 values of 36.02 and 48.30 µM, respectively. Moreover, compound 32a induced apoptosis in HepG-2 cells and arrested the cell cycle at the G2/M phase. Besides, compound 32a showed Topo II poisoning effect at concentrations of 2.5 and 5 μM, and Topo II catalytic inhibitory effect at a concentration of10 μM. In addition, compound 32b showed in vivo a significant tumor growth inhibition effect. Furthermore, molecular docking studies were carried out against DNA-Topo II complex and DNA to investigate the binding patterns of the designed compounds., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2020 Elsevier Inc. All rights reserved.)

A new set of differently hydrated barium and strontium squarates, namely poly[[triaqua(μ-1,2-dioxocyclobut-3-ene-1,2-diolato)barium] monohydrate], {[Ba(C 4 O 4 )(H 2 O) 3 ]·H 2 O} n (1), poly[[diaqua(μ-1,2-dioxocyclobut-3-ene-1,2-diolato)strontium] monohydrate], {[Sr(C 4 O 4 )(H 2 O) 2 ]·H 2 O} n (2), and poly[[triaqua(μ-1,2-dioxocyclobut-3-ene-1,2-diolato)barium/strontium(0.85/0.15)] monohydrate], {[Ba 0.85 Sr 0.15 (C 4 O 4 )(H 2 O) 3 ]·H 2 O} n (3), is reported. The study of their crystal structures indicates that all the complexes crystallize in the triclinic space group P-1. Complexes 1 and 3 have a rare combination of squarate units coordinated through monodentate O atoms to two different metal atoms and through two bidentate O atoms to three different metal atoms. Furthermore, they have three coordinated water molecules to give a coordination number of nine. The squarate ligands in complex 2 exhibit two different coordination modes: (i) monodentate O atoms coordinated to four different Sr atoms and (ii) two monodentate O atoms coordinated to two different metal atoms with the other two O atoms bidentate to four different Sr atoms. All the compounds decompose to give the respective carbonates when heated to 800 °C, as evidenced by thermogravimetry/differential thermal analysis (TG-DTA), which are clusters of nanoparticles. Complexes 1 and 3 show additional endothermic peaks at 811 and 820 °C, respectively, indicating the phase transition of BaCO 3 from an orthorhombic (α-Pmcn) to a trigonal phase (β-R3m). All three complexes have significant DNA-binding constants, ranging from 2.45 × 10 4 to 9.41 × 10 4  M -1 against EB-CT (ethidium bromide-calf thymus) DNA and protein binding constants ranging from 1.1 × 10 5 to 8.6 × 10 5 with bovine serum albumin. The in vitro cytotoxicity of the complexes is indicated by the IC 50 values, which range from 128.8 to 261.3 µg ml -1 . Complex 3 shows better BSA binding, antioxidant activity against the DPPH radical and cytotoxicity than complexes 1 and 2.

This study describes a series of newly synthesized phosphine/diimine ruthenium complexes containing the lawsone as bioligand with enhanced cytotoxicity against different cancer cells, and apoptosis induction in prostatic cancer cells DU-145. The complexes [Ru(law)(N-N) 2 ]PF 6 where N-N is 2,2'-bipyridine (1) or 1,10-phenanthroline (2) and [Ru(law)(dppm)(N-N)]PF 6 , where dppm means bis(diphenylphosphino)methane, N-N is 2,2'-bipyridine (3) or 1,10-phenanthroline (4), and law is lawsone, were synthesized and fully characterized by elemental analysis, molar conductivity, NMR, UV-vis, IR spectroscopies and cyclic voltammetry. The interaction of the complexes (1-4) with DNA was evaluated by circular dichroism, gel electrophoresis, and fluorescence, and the complexes presented interactions by the minor grooves DNA. The phosphinic series of complexes exhibited a remarkably broad spectrum of anticancer activity with approximately 34-fold higher than cisplatin and 5-fold higher than doxorubicin, inhibiting the growth of 3D tumor spheroids and the ability to retain the colony survival of DU-145 cells. Also, the complex (4) inhibits DU-145 cell adhesion and migration potential indicating antimetastatic properties. The mechanism of its anticancer activity was found to be related to increased reactive oxygen species (ROS) generation, increased the BAX/BCL-2 ratio and subsequent apoptosis induction. Overall, these findings suggested that the complex (4) could be a promising candidate for further evaluation as a chemotherapeutic agent in the prostate cancer treatment., (Copyright © 2019 Elsevier Inc. All rights reserved.)

New dithiocarbamate chalcone-based derivatives were synthesized, their structures were elucidated using different spectroscopic techniques. They were subjected to antimicrobial screening against selected Gram negative bacteria focusing on microbial resistance. Bacterial resistance was targeted via phosphoethanolamine transferase enzyme. Most of the synthesized compounds showed equal or higher activity to colistin standard. Compound 24 proved to be the most active candidate with MIC of 8 µg/ml against both Ps12 and K4 and MBC of 32 µg/ml against Ps12 and 16 µg/ml against K4 Molecular docking study showed that 20, 22, 24 and 25 had good binding affinity with active site residues via Thr280. DNA macromolecule was further targeted. Compounds 28 and 34 were recorded to have better DNA binding than doxurubucin with IC 50 of 27.48 and 30.97 µg/ml respectively, suggesting that it could have a role in their higher antibacterial effect. Their docking into DNA has shown a clear intercalation matching with antibacterial data. Pharmacokinetics parameters of active compounds showed that they have better absorption through GIT., (Copyright © 2019. Published by Elsevier Inc.)

Nonsteroidal anti-inflammatory drugs (NSAIDs) are the most widely used drugs in the world but some NSAIDs such as diclofenac and tolfenamic acid display levels of cytotoxicity, an effect which has been attributed to the presence of diphenylamine contained in their structures. A novel series of diphenylamine derivatives were synthetised and evaluated for their cytotoxic activities and proliferation inhibition. The most active compounds in the cytotoxicity tests were derivative 6g with an IC 50 value of 2.5 ± 1.1 × 10 -6  M and derivative 6f with an IC 50 value of 6.0 ± 3.0 × 10 -6  M (L1210 cell line) after 48 h incubation. The results demonstrate that leukemic L1210 cells were much more sensitive to compounds 6f and 6g than the HEK293T cells (IC 50  = 35 × 10 -6  M for 6f and IC 50  > 50 × 10 -6  M for 6g) and NIH-3T3 (IC 50  > 50 × 10 -6  M for both derivatives). The IC 50 values show that these substances may selectively kill leukemic cells over non-cancer cells. Cell cycle analysis revealed that a primary trend of the diphenylamine derivatives was to arrest the cells in the G 1 -phase of the cell cycle within the first 24 h. UV-visible, fluorescence spectroscopy and circular dichroism were used in order to study the binding mode of the novel compounds with DNA. The binding constants determined by UV-visible spectroscopy were found to be in the range of 2.1-8.7 × 10 4  M -1 . We suggest that the observed trend for binding constant K is likely to be a result of different binding thermodynamics accompanying the formation of the complexes., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Guanine-rich nucleic acid sequences can fold into four-stranded G-quadruplex (G4) structures. Despite growing evidence for their biological significance, considerable work still needs to be done to detail their cellular occurrence and functions. Herein, we describe an optimized core-extended naphthalene diimide (cex-NDI) to be exploited as a G4 light-up sensor. The sensing mechanism relies on the shift of the aggregate-monomer equilibrium towards the bright monomeric state upon G4 binding. In contrast with the majority of other ligands, this novel cex-NDI is able to discriminate among G4s with different topologies, with a remarkable fluorescent response for the parallel ones. We investigate this sensing by means of biophysical methods, comparing the lead compound to a non-selective analogue. We demonstrate that mitigating the affinity of the binding core for G4s results in an increased selectivity and sensitivity of the fluorescent response. This is achieved by replacing positively charged substituents with diethylene glycol (DEG) side chains. Remarkably, the limit of detection values obtained for parallel G4s are more than one order of magnitude lower than those of the parallel-selective ligand N-methyl mesoporphyrin IX (NMM). Interestingly, the classical fluorescent intercalator displacement (FID) assay failed to reveal binding of cex-NDI to G4 because of the presence a ternary complex (G4-TO-cex-NDI) revealed by electrospray-MS. Our study thus provides a rational basis to design or modify existent scaffolds to redirect the binding preference of G4 ligands.

Fluorophore-linked, sequence-specific DNA binding reagents can visualize sequence information on a large DNA molecule. In this paper, we synthesized newly designed TAMRA-linked polypyrrole to visualize adenine and thymine base pairs. A fluorescent image of the stained DNA molecule generates an intensity profile based on A/T frequency, revealing a characteristic sequence composition pattern. Computer-aided comparison of this intensity pattern with the genome sequence allowed us to determine the DNA sequence on a visualized DNA molecule from possible intensity profile pattern candidates for a given genome. Moreover, TAMRA-polypyrrole offers robust advantages for single DNA molecule detection: no fluorophore-mediated photocleavage and no structural deformation, since it exhibits a sequence-specific pattern alone without the use of intercalating dyes such as YOYO-1. Accordingly, we were able to identify genomic DNA fragments from Escherichia coli cells by aligning them to the genomic A/T frequency map based on TAMRA-polypyrrole-generated intensity profiles. Furthermore, we showed band and interband patterns of polytene chromosomal DNA stained with TAMRA-polypyrrole because it prefers to bind AT base pairs.

In this work, we report on the synthesis of two new mono-alkylated tetrandrine derivatives with acridine and anthracene units, MAcT and MAnT. The compounds were fully characterized by physicochemical techniques and single-crystal X-ray diffraction analysis. In addition, both derivatives were studied as nucleotide receptors and double-stranded DNA binders in aqueous phosphate buffer at pH = 7.2 using UV-vis and fluorescence spectroscopy. According to the molecular recognition studies, MAcT and MAnT exhibit high affinity (K ∼ 10 5  M -1 ) and selectivity for ds-DNA, presumably in an intercalation mode. Finally, the anti-proliferative effects of the tetrandrine derivatives on different cancer cell lines were explored, revealing promising activities. Particularly, the mono-anthracene tetrandrine derivative MAnT showed an IC 50 of 2.74 μg/mL on the HeLa cervical cancer cell line, representing a value 3.3 times smaller than that obtained for unsubstituted tetrandrine. Examination of the cytotoxic effects on the HeLa cell line by inverted microscopy suggests that the cell death mechanism consists basically in apoptosis. The molecular modelling of three ds-DNA-MAcT complexes, suggested that the macrocycles may use an intercalation binding mode towards DNA. MAcT is predicted to bind into the major groove of the ds-DNA providing non-covalent interactions such as electrostatic, van der Waals and hydrophobic interactions that lead to selectivity. Overall experimental data supports the mode of action of MAnT and MAcT as cytotoxic compounds against cancer cell lines via a DNA interaction mechanism., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Background: The pentacyclic lupane-type (6-6-6-6-5 type) triterpenoid, Betulinic acid (BA) is a potent inhibitor of topoisomerases and is of immense interest as anticancer drugs. However, the compound being highly lipophilic, has limited in vivo uptake capacity. BA derivatives with halogen substituent at C-2 have improved membrane permeability and cytotoxicity against cancer cells., Aim: The halogenated triterpenoid, 2α-bromo-dihydrobetulonic acid (B1) was synthesized from betulinic acid (BA) isolated from Bischofia javanica. Aim of the study was to determine whether B1 could act as a more efficient inhibitor of Topo IIα activity and HeLa cell proliferation, in comparison to BA., Result: B1 displayed efficient inhibition of DNA relaxation activity of topoisomerase IIα and the inhibitory effect was markedly improved upon pre-incubation of the compound with enzyme. Topoisomerase IIα inhibition by B1 was relieved in presence of increasing concentrations of DNA suggesting the compound as a reversible catalytic inhibitor. Subsequent UV and fluorescence spectroscopy studies indicated that B1 interacts and intercalates with DNA at concentrations signicantly greater than that required for topoisomerase IIα inhibition. The compound showed cytotoxic activity against HeLa cells with significantly lower IC 50 value (7.5 μM) as compared to that of BA (30 μM) and had very low damaging/cytotoxic effect on normal cells. Treatment of B1 impaired HeLa cell proliferation by inducing Go-G1 arrest through lowered expression of cyclin D1 and PCNA polypeptides, and enhanced expression of p21. B1 treatment also increased the accumulation of early and late apoptotic cells in a concentration dependent manner as indicated by annexin V-FITC/PI binding assay., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Pyrazolone based metal complexes have strong bio-activity but the anti-cancer mechanism of these derivatives is not fully understood. In recent years, Cu(II) complexes have attracted the interest of researchers increasingly because of their high antitumor activities that are usually related to DNA binding. The reaction of three different derivatives (I) PPMP [3-methyl-1-phenyl-4-propionyl-1H-pyrazol-5(4H)-one], (II) TMCPMP [1-(3-chlorophenyl)-3-methyl-4-(4-methylbenzoyl)-1H-pyrazol-5(4H)-one] and (III) PPTPMP [3-methyl-4-propionyl-1-p-tolyl-1H-pyrazol-5(4H)-one] of 3-methyl-1-phenyl-1H-pyrazol-5(4H)-one and 2.2' bipyridyl along with Cu(NO3)2·3H2O under methanolic condition allowed us to isolate and characterize a series of new mixed ligand complexes [Cu(TMCPMP) (Bipy)NCS] (1) [Cu(PPMP) (Bipy)NCS] (2) and [Cu(PPTPMP) (Bipy)NCS] (3). All complexes are well characterized by elemental analysis, metal estimation, molar conductivity, FT-IR and UV-Vis spectroscopy. The molecular geometry of these complexes has been determined by single crystal X-ray study. The single-crystal X-ray structures of complexes 1 and 2 exhibit square pyramidal geometry, while complex 3 revealed slightly distorted square-pyramidal geometry. The DNA binding of these compounds with Calf-Thymus DNA (CT-DNA) has been explored by emission titration methods, which revealed that 1-3 could interact with CT-DNA through intercalation mode. The complexes also exhibited a strong binding with Bovine Serum Albumin (BSA) over the ligands. Complexes were evaluated for their in vitro cytotoxic activities against lung cancer cell lines (A549) as well as noncancerous rat cardiomyocytes (H9C2) cell lines, which showed that all three complexes exhibited substantial cytotoxic activity with minimum effect on noncancerous cells. Complex 1 with more hydrophobic environment exhibited relatively high cytotoxic activity towards A549 cells. In summary, this new series of compounds belongs to a class of copper-pyrazolonate complexes that target many biochemical sites and with potential anti-cancer activity. All these results collectively suggested that complexes could serve as promising pharmacologically active substance against lung cancer., (Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.)

Two novel coordination compounds of half-sandwiched ruthenium(II) containing 2-(5-fluorouracil)-yl-N-(pyridyl)-acetamide were synthesized, and their intercalation binding modes with calf thymus DNA were revealed by hyperchromism of ultraviolet-visible spectroscopy; the binding constants were determined according to a Langmuir adsorption equation that was deduced on the base of careful cyclic voltammetry measurements. The two compounds exhibited DNA intercalation binding activities with the binding constants of 1.13×106 M-1 and 5.35 ×105 M-1, respectively.

Diverse actinomycetes produce a family of structurally and biosynthetically related non-ribosomal peptide compounds which belong to the chromodepsipeptide family. These compounds act as bisintercalators into the DNA helix. They give rise to antitumor, antiparasitic, antibacterial and antiviral bioactivities. These compounds show a high degree of conserved modularity (chromophores, number and type of amino acids). This modularity and their high sequence similarities at the genetic level imply a common biosynthetic origin for these pathways. Here, we describe insights about rules governing this modular biosynthesis, taking advantage of the fact that nowadays five of these gene clusters have been made public (thiocoraline, triostin, SW-163 and echinomycin/quinomycin). This modularity has potential application for designing and producing novel genetic engineered derivatives, as well as for developing new chemical synthesis strategies. These would facilitate their clinical development.

Myotonic dystrophy type 2 (DM2) is an incurable neuromuscular disease caused by expanded CCUG repeats that may exhibit toxicity by sequestering the splicing regulator MBNL1. A series of triaminotriazine- and triaminopyrimidine-based small molecules (ligands 1-3) were designed, synthesized and tested as inhibitors of the MBNL1-CCUG interaction. Despite the structural similarities of the triaminotriazine and triaminopyrimidine units, the triaminopyrimidine-based ligands bind with low micromolar affinity to CCUG repeats (K(d) ∼ 0.1-3.6 µM) whereas the triaminotriazine ligands do not bind CCUG repeats. Importantly, these simple and small triaminopyrimidine ligands exhibit both strong inhibition (K(i) ∼ 2 µM) of the MBNL1-CCUG interaction and high selectivity for CCUG repeats over other RNA targets. These experiments suggest these compounds are potential lead agents for the treatment of DM2.

Four complexes [Pd(L)(bipy)Cl].4H(2)O (1), [Pd(L)(phen)Cl].4H(2)O (2), [Pt(L)(bipy)Cl].4H(2)O (3), and [Pt(L)(phen)Cl].4H(2)O (4), where L = quinolinic acid, bipy = 2,2'-bipyridyl, and phen = 1,10-phenanthroline, have been synthesized and characterized using IR, (1)H NMR, elemental analysis, and single-crystal X-ray diffractometry. The binding of the complexes to FS-DNA was investigated by electronic absorption titration and fluorescence spectroscopy. The results indicate that the complexes bind to FS-DNA in an intercalative mode and the intrinsic binding constants K of the title complexes with FS-DNA are about 3.5 x 10(4) M(-1), 3.9 x 10(4) M(-1), 6.1 x 10(4) M(-1), and 1.4 x 10(5) M(-1), respectively. Also, the four complexes bind to DNA with different binding affinities, in descending order: complex 4, complex 3, complex 2, complex 1. Gel electrophoresis assay demonstrated the ability of the Pt(II) complexes to cleave pBR322 plasmid DNA.

A series of novel water-soluble beta-carbolines bearing a flexible amino side chain was designed, synthesized and evaluated as potent cytotoxic and DNA intercatalating agents. The N(9)-arylated alkyl substituted beta-carbolines represented the most interesting cytotoxic activities. The results suggested that (1) the N(9)-arylated alkyl substituents of beta-carboline nucleus played a very important role in the modulation of the cytotoxic potencies; (2) the length of the alkylamino side chain significantly affected their cytotoxic potency, and N,N-dimethylaminopropylamino substituent were more favorable. In addition, these compounds were found to exhibit significant DNA intercalating potencies.

In the pathway of anticancer drug development, we designed and synthesized some 6H-indolo[2,3-b]quinoxaline derivatives (which act as DNA intercalators) by structural modification. The structure of the 6H-indolo[2,3-b]quinoxaline derivatives was confirmed by IR, NMR, Mass and elemental analysis. The compounds (IDQ-5, IDQ-10, IDQ-11, IDQ-13, and IDQ-14) exhibited significant in vitro activity against a human leukemia (HL-60) cell line. The QSAR derived for modeling the cytotoxic activity of 6H-indolo[2,3-b]quinoxaline derivatives suggests that candidate structures for increased cytotoxic potency should incorporate cyclic substituents or substituents with primary carbon atoms.

A new ruthenium(II) complex grafted with beta-d-allopyranoside, Ru(bpy)(2)(Happip)(ClO(4))(2) (where bpy = 2,2'-bipyridine; Happip = 2-(4-(beta-d-allopyranoside)phenyl)imidazo[4,5-f][1,10]phenanthroline), has been synthesized and characterized by elemental analysis, (1)H NMR spectroscopy, and mass spectrometry. The acid-base properties of the complex have been studied by UV-visible and luminescence spectrophotometric pH titrations, and ground- and excited-state ionization constants have been derived. The Ru(II) complex functions as a DNA intercalator as revealed by UV-visible and emission titrations, salt effects, steady-state emission quenching by [Fe(CN)(6)](4-), DNA competitive binding with ethidium bromide, DNA melting experiment, and viscosity measurements.

In the present overview, we describe the bases of intercalation of small molecules (cationic and polar neutral compounds) in DNA. We briefly describe the importance of DNA structure and principles of intercalation. Selected syntheses, possibilities and applications are shown to exemplify the importance, drawbacks and challenges in this pertinent, new, and exciting research area. Additionally, some clinical applications (molecular processes, cancer therapy and others) and trends are described.

Chemically modified oligonucleotides are increasingly applied in nucleic acid based therapeutics and diagnostics. LNA (locked nucleic acid) and its diastereomer alpha-L-LNA are two promising examples thereof that exhibit increased thermal and enzymatic stability. Herein, the synthesis, biophysical characterization, and molecular modeling of N2'-functionalized 2'-amino-alpha-L-LNA is described. Chemoselective N2'-functionalization of protected amino alcohol 1 followed by phosphitylation afforded a structurally varied set of target phosphoramidites, which were incorporated into oligodeoxyribonucleotides. Incorporation of pyrene-functionalized building blocks such as 2'-N-(pyren-1-yl)carbonyl-2'-amino-alpha-L-LNA (monomer X) led to extraordinary increases in thermal affinity of up to +19.5 degrees C per modification against DNA targets in particular. In contrast, incorporation of building blocks with small nonaromatic N2'-functionalities such as 2'-N-acetyl-2'-amino-alpha-L-LNA (monomer V) had detrimental effects on thermal affinity toward DNA/RNA complements with decreases of as much as -16.5 degrees C per modification. Extensive thermal DNA selectivity, favorable entropic contributions upon duplex formation, hybridization-induced bathochromic shifts of pyrene absorption maxima and increases in circular dichroism signal intensity, and molecular modeling studies suggest that pyrene-functionalized 2'-amino-alpha-L-LNA monomers W-Y having short linkers between the bicyclic skeleton and the pyrene moiety allow high-affinity hybridization with DNA complements and precise positioning of intercalators in nucleic acid duplexes. This rigorous positional control has been utilized for the development of probes for emerging therapeutic and diagnostic applications focusing on DNA targeting.

A new coumarin derivative (8-methylcoumaro-4a,10a-pyrone-3-carbaldehyde benzoyl hydrazone) ligand and its novel Cu(II) complex have been synthesized and characterized on the basis of elemental analyses, molar conductivities, (1)H-NMR, IR spectra, UV-visible spectroscopy and thermal analyses. In addition, the interactions of the Cu(II) complex and the ligand with calf-thymus DNA were investigated by spectrometric titrations, ethidium bromide displacement experiments and viscosity measurements. It was found that both the two compounds, specially the Cu(II) complex, strongly bind with calf-thymus DNA, presumably via an intercalation mechanism.

Bulge insertions of conjugated intercalators into the DNA triplex structure are found to give a dramatic contribution to the triplex stability. On the other hand insertions of conjugated intercalators are found to diminish quadruplex structures and in this way breaking down the self association of G-rich oligonucleotides under physiologically potassium ion conditions. A large number of intercalators are described here and they all result in dramatic increases of thermal stability of the corresponding triplexes. Another interesting aspect of conjugated intercalators is their use for assembling alternate strand triplexes. Targeting of neighbouring purine sequences on each their strand in the duplex DNA is a challenge for the 5'- 5' connectivity of the TFOs because of a large distance between the 5'-ends. The intercalator approach offers a linkage with the proper combination of flexibility and rigidity to produce alternate strand triplexes with higher stability than a similar wild type triplex of the same total length.

Naphthalenediimide (1) carrying two beta-cyclodextrins (beta CDs) was successfully synthesized by click chemistry between pentynylnaphthalenediimide and azido beta CD. Absorption spectra of 1 showed hypochromic and red shifts upon addition of sonicated calf thymus DNA as a double stranded DNA. Kinetic studies showed its slow association with and dissociation from calf thymus DNA. These results suggested that 1 can bind to double stranded DNA by the threading mode, where one of the beta CD is required to go through adjacent base pairs of double stranded DNA. If this is proven, beta CD is one of the largest groups ever reported which can go through a DNA duplex for threading.

The interaction of the linear dibenzo[b,g]quinolizinium (5a) and the angular dibenzo[a,f]quinolizinium (6) with DNA was studied in detail in order to evaluate the influence of the shape of polycyclic quinolizinium ions on their DNA-binding properties. First, the synthesis and the thermally induced dimerization of 5a were reinvestigated because the preparation and isolation of the bromide salt of 5a according to literature procedures turned out to be problematic. The dibenzo[b,g]quinolizinium bromide [5a(Br)] tends to dimerize in solution with a highly selective and unprecedented formation of the corresponding anti-head-to-head dimer. Nevertheless, it was observed that careful exclusion of bromide ions from the reaction mixture suppresses the formation of the dimer. Moreover, the dimer may be transformed to the monomer by a remarkably rapid photoinduced electron-transfer reaction with 1-methoxynaphthalene. The association of 5a and 6 with nucleic acids was investigated by spectrophotometric and spectrofluorimetric DNA titrations, CD and LD spectroscopy, DNA thermal denaturation studies, and competition-dialysis techniques. Both dibenzoquinolizinium ions 5a and 6 exhibit an intercalative mode of binding to double-stranded DNA with moderate binding constants (K = 1-7 x 10(5) M(-1)) and a slight preference for association with GC-rich DNA regions. The structures of the intercalation complexes were calculated by molecular modeling methods. Competition-dialysis studies reveal that the isomers 5a and 6 bind selectively to triple-helical DNA (poly[dA]-poly[dT]2) as compared to selected synthetic and native double-stranded nucleic acids. Notably, the selectivity of the linear dibenzo[b,g]quinolizinium 5a toward triplex DNA is higher than the one of the angular derivative 6. In contrast, the DNA thermal denaturation studies reveal a higher stabilization of triple-helical DNA in the presence of 6 (DeltaTm3-->2 = 28 degrees C at r = 0.5) as compared to the stabilization by 5a (DeltaTm3-->2 = 14 degrees C at r = 0.5). This comparison emphasizes the importance of the extended pi system for the interaction of annelated quinolizinium ions with DNA. Moreover, the comparison between 5a and 6 demonstrates the significant influence of the shape of the pi system on the duplex- and triplex-stabilizing properties of the dibenzoquinolizinium ions.

Peptide bioconjugates combine the molecular recognition features of the polypeptide from a DNA-binding protein and the DNA-sensitive fluorescence of an intercalating dye. Here, DNA template-directed assembly of two bioconjugate probes was examined by steady-state fluorescence resonance energy transfer and time-resolved single photon counting. The Förster critical distance was determined to be approximately 26 A for the oxazole yellow and thiazole orange donor-acceptor pair. The efficiency of energy transfer for two bioconjugates was a function of the number of intervening base pairs between two DNA cognate sites. These probes were sufficiently sensitive to detect sequence dependent curvature and polypeptide induced bending of the DNA. Molecular probes capable of examining spatial aspects of protein complexes at promoter sites could yield important information about the early events in transcription initiation.

A series of symmetrical 1,5-diamidoanthraquinone derivatives with potentially bioreducible groups has been synthesized and their cytostatic activity against the panel of various cancer cell lines in vitro has been studied. Preliminary structure-activity relationships were established. The results indicated that compounds 5 and 18 exhibited significant potent cytotoxicity at 1.24-1.75 microM for Hepa G2 cell line; compounds 5, 16, and 18 exhibited cytotoxicity at 0.14-1.82 microM for 2.2.15 cell line as determined by XTT colorimetric assay. Two structurally related compounds, mitoxantrone and adriamycin, were tested in parallel as positive controls. In addition, it was found that compounds 5 and 18 were a more potent and specific human hepatoma cell line than mitoxantrone and showed comparable activity to adriamycin. Among them, compound 18 was the most potent for 2.2.15 cells. We have demonstrated that the anthraquinone moiety is essential for activity and that less sterically hindered substituents contribute to enhanced in vitro efficacy. Implications for amidoanthraquinone cytotoxicity as potential anticancer agents are discussed. We further delineate the nature of the pharmacophore for this class of compounds, which provides a rational basis for the structure-activity relationships.

A novel ruthenium(II) complex of [Ru(bpy)2(Hbopip)](ClO4)2 (in which bpy=2,2'-bipyridine, Hbopip=2-(4-benzoxazolyl)phenylimidazo[4,5-f][1,10]phenanthroline) was synthesized and characterized. The spectrophotometric pH titrations of the complex showed that it acted as a pH-induced luminescence "off-on-off" switch: a luminescence off-on switch with a luminescence enhancement factor of IpH=3.0/IpH=1.0=20 occurring over a narrow pH range of 1.00-3.00 plus a luminescence on-off switch with a luminescence enhancement factor of 3 over a pH range of 3.20-9.40. The excited-state ionization constant of the complex derived, pKa1*=3.06, is 1.36 pKa units greater than the ground-state pKa1=1.70, and pKa2*=5.01 and pKa3*=8.22 are comparable to the ground-state pKa2=5.23 and pKa3=8.22, respectively. The complex avidly bound to calf thymus DNA with a large binding constant of (1.2+/-0.3)x10(7) M-1 in buffered 50 mM NaCl, as evidenced by UV-vis and luminescence titrations, steady-state emission quenching by [Fe(CN)6]4-, DNA competitive binding with ethidium bromide, viscosity measurements, and DNA melting experiments.

Pyrimido[5,4-c]cinnoline and pyrimido[5,4-c]quinoline derivatives have been tested as potential intercalators. All of them embody stuctural properties alike to afford intercalating activity. Their cytotoxicity was determined on the two human leukemia cell lines, the promyelocytic HL-60 and the lymphoblastic NALM-6. The viability of cells exposed continuously to tested compounds was estimated by the trypan-blue exclusion assay. IC50 data for the NALM-6 cell line are lower than for the HL-60 cell line, what suggested that the HL-60 leukemia cells are more resistant to toxic action of tested compounds. All compounds exerted moderate cytotoxic activity. The compounds were analyzed with the HyperChem/ChemPlus software trying to find basic structure-activity relationships.

Several dioxocyclams containing quinoxaline moieties, as well as their nickel(II) complexes were synthesized and studied for their ability to bind and oxidatively cleave DNA. Although no evidence for binding by intercalation was found, the ability of the Ni(II) complexes to cleave DNA in the presence of Oxone was strongly dependent on both the nature and the spatial orientation of the quinoxaline moieties, suggesting at least transient association of these complexes with DNA.

The synthesis and electron paramagnetic resonance (EPR) spectroscopic properties of three novel aromatic nitroxides and potential DNA intercalators, the carbazole-based 3,6-dimethylcarbazole-9-oxyl, as well as the acridane-based 9-acridanylidenemalonitrile-10-oxyl and 9-ethylacridanylidenecyanoacetate-10-oxyl, are described. The two acridane-based nitroxides can be isolated and are stable in solution as well as in the solid state for several days. Continuous wave X-band EPR measurements and density functional theory (DFT) calculations demonstrated that the spin density is delocalized over the whole molecule in all three cases. Furthermore, the DFT calculations provided insight into the molecular and electronic structures of these nitroxides and yielded hyperfine coupling constants which are in very good agreement with the experimental data allowing therefore an unambiguous assignment of the hyperfine couplings.

The tandem amine-exchange/heterocyclization of enaminoketones is successfully applied to the regioselective preparation of a series of new 4,5-diarylpyrazoles by reaction of phenylhydrazine and several 3-N,N-(dimethylamino)-1,2-diarylpropenones. The comparison of a vast array of biaryl coupling procedures provides general, complementary approaches to new phenanthro[9,10-d]pyrazoles. The most efficient procedures for this final step in the construction of the tetracyclic system are based on a Stille-type tandem stannylation-biaryl coupling of o,o'-dihalogenated diarylpyrazoles and an hypervalent iodine-mediated nonphenolic oxidative coupling of nonhalogenated precursors.

The development of a solution phase synthesis of azatriostin A (2) suitable for the preparation of combinatorial libraries enlisting only liquid-liquid acid/base extractions for the isolation and purification of all intermediates and the final product is disclosed.

The synthesis and triplex stabilizing properties of oligodeoxyribonucleotides functionalized at the 5'- and/or 3'-termini with a naphthalene diimide-based (NDI) intercalator is described. The NDI intercalator was prepared in a single step from the corresponding dianhydride and was attached to the 5'-terminus of an oligodeoxyribonucleotide following a reverse coupling procedure. The DMT protecting group was removed and the sequence phosphitylated to generate the phosphoramidite derivative on the 5'-terminus of the support-bound oligodeoxyribonucleotide. The NDI intercalator with a free hydroxyl was then added in the presence of tetrazole. Attachment of the NDI to the 3'-terminus relied upon a tethered amino group that could be functionalized first with the naphthalene dianhydride, which was subsequently converted to the diimide. Using both procedures, an oligonucleo-tide conjugate was prepared having the NDI intercalator at both the 5'- and 3'-termini. Thermal denaturation studies were used to determine the remarkable gain in stability for triplexes formed when the NDI-conjugated oligonucleotide was present as the third strand in the complex.

Tetra-acridinyl peptide 2 was synthesized from Fmoc-Lys(Boc)-OH and Fmoc-Lys(Acr)-OH (1) with the peptide synthesizer. The CD measurement suggested that 2 forms a special organized structure by itself in buffered solution. Peptide 2 binds to double stranded DNA with a very large affinity constant, which is 10(3)-times larger than that of quinacrine. Spectrophotometric and hydrodynamic studies suggested that all of the acridinyl parts of 2 contribute to the intercalating interaction for the DNA binding. Our finding in this experiment demonstrates that polyintercalators such as 2 can be assembled quickly by the automated synthesizer.

DAPI analogs containing an imidazoline ring or a tetrahydropyrimidine ring have been synthesized to study DNA binding properties. Spectroscopic (absorption, CD, flow dichroism and fluorescence) and viscosity measurements indicate that DAPI analogs interact with DNA both by intercalation and by groove binding. The solution structures of complexes between DAPI analog and DNA oligomers have been characterized by proton NMR spectroscopy.

On the basis of theoretical computations, we have recently synthesised [Perrée-Fauvet, M. and Gresh, N., Tetrahedron Lett., 36 (1995) 4227] a bisarginyl conjugate of a tricationic porphyrin (BAP), designed to target, in the major groove of DNA, the d(GGC GCC)2 sequence which is part of the primary binding site of the HIV-1 retrovirus site [Wain-Hobson, S. et al., Cell, 40 (1985) 9]. In the theoretical model, the chromophore intercalates at the central d(CpG)2 step and each of the arginyl arms targets O6/N7 belonging to guanine bases flanking the intercalation site. Recent IR and UV-visible spectroscopic studies have confirmed the essential features of these theoretical predictions [Mohammadi, S. et al., Biochemistry, 37 (1998) 6165]. In the present study, we compare the energies of competing intercalation modes of BAP to several double-stranded oligonucleotides, according to whether one, two or three N-methylpyridinium rings project into the major groove. Correspondingly, three minor groove binding modes were considered, the arginyl arms now targeting N3, O2 sites belonging to the purine or pyrimidine bases flanking the intercalation site. This investigation has shown that: (i) in both the major and minor grooves, the best-bound complexes have the three N-methylpyridinium rings in the groove opposite to that of the phenyl group bearing the arginyl arms; (ii) major groove binding is preferred over minor groove binding by a significant energy (29 kcal/mol); and (iii) the best-bound sequence in the major groove is d(GGC GCC)2 with two successive guanines upstream from the intercalation. On the other hand, due to the flexibility of the arginyl arms, other GC-rich sequences have close binding energies, two of them being less stable than it by less than 8 kcal/mol. These results serve as the basis for the design of derivatives of BAP with enhanced sequence selectivities in the major groove.

To elucidate the kinetics of DNA strand breaks caused by low-energy Auger electron emitters in proximity to DNA molecules, we synthesized (125)I-labeled 2-iodoacridine (2-(125)IA), which intercalates with DNA, and 4-iodoacridine (4-(125)IA), which does not. Supercoiled DNA from pBR322 plasmid, labeled with 3H, was purified and incubated with 2-(125)IA or 4-(125)IA in aqueous solution. Reaction mixtures were stored at 4 degrees C to accumulate radiation dose from the decay of (125)I, and DNA was resolved by gel electrophoresis into supercoiled (DNA-I), nicked-circular (DNA-II) and linear (DNA-III) forms, representing undamaged DNA, single-strand breaks (SSBs) and double-strand breaks (DSBs), respectively. Gamma irradiation from an external (137)Cs source led to an exponential decrease in DNA-I with a D0 value of 10.8 +/- 0.3 Gy. Under identical conditions, the D0 values for 2-(125)IA and 4-(125)IA were 22.4 +/- 0.6 x 10(11) disintegrations and 4.7 +/- 0.4 x 10(11) disintegrations, respectively. External gamma irradiation and 4-(125)IA produced SSB/DSB ratios of 26.5 +/- 2.1 and 15.9 +/- 2, respectively, while that for 2-(125)IA was 0.6. The average number of DSBs from each decay of (125)I was 0.67 for 2-(125)IA and 0.27 for 4-(125)IA. The results indicate that the decay of (125)I bound to a DNA-intercalating compound produces DSBs 2.5-fold more efficiently than (125)I bound to a nonintercalating compound and support the theoretical expectations that predict a DSB yield that is highly dependent on the proximity of the Auger electron emitter to DNA.

4-Picoloine-2,2':6',2"-terpyridine-platinum(II) is shown in a ligation assay to unwind and so intercalate into DNA. Circular dichroism is used to determine an equilibrium binding constant of approximately 2 x 10(7) M(-1) for the most stable binding mode of 4-picoline-2,2':6',2"-terpyridine-platinum(II) to poly[d(A-T)2] with a site size of about 4 base pairs, and about 1 x 10(6) M(-1) for a second binding mode with a site size of about 2 base pairs. Fluorescence spectroscopy provides further evidence for the strong equilibrium binding constant of 4-picoline-2,2':6',2"-terpyridine-platinum(II) in that it displaces ethidium bromide bound to DNA. The double positive charge on 4-picoline-2,2':6',2"-terpyridine-platinum(II), together with the intercalative binding mode is probably responsible for the large binding constant.

The synthesis of three new monopyrazole analogues of the antiviral compound distamycin A is reported. Suitably protected 4-amino-1-methylpyrrole-2-carboxylic acid and 3-amino-1-methylpyrazole-5-carboxylic acid derivatives were chosen as starting materials. The construction of the trimeric polyamide framework was accomplished by assembly of the monomeric precursors under condensing conditions by analogy with our previous methodology, although with significant improvements in some pivotal steps. After chromatographic purification and spectroscopic characterisation, the analogues were assayed for antiviral activity. Compounds 7a-c inhibited vaccinia virus at a concentration similar to or lower than distamycin A and the related antibiotic netropsin. Analogues 7b and 7c exhibited an antiviral effect comparable to those of distamycin A and netropsin against HSV-1 and HSV-2, whereas their antiviral activity against several other viruses including HIV-1 and HIV-2 was somewhat lower. The cellular toxicity of 7a-c toward different host cell types proved to be of similar magnitude or lower than those of distamycin A and netropsin.

The electrophoretic movement and Brownian motion of T4DNA, lambda DNA and their complexes with polyacrylamide (PAAm) via intercalative unit from 5-[(4-acryloylamino)phenyl]-3-amino-7-(dimethylamino)-2-methylp henazinium chloride were observed using fluorescence microscopy. It was found that T4DNA/PAAm complex migrates slower than T4DNA alone in gel electrophoresis, although they exhibit similar conformational change during the migration. Quantitative analyses of the translational diffusion of the lambda DNA and its complex in solution demonstrate that the DNA molecules extend due to intercalative binding of PAAm, suggesting the pseudo-grafting structure of the complex.

The rigidity of the linking chain of bifunctional intercalators in the ditercalinium series was shown to be critical for antitumor activity. In order to study the influence of the rigidity of the linking chain on the DNA-binding properties of DNA bifunctional intercalators, fluorescent 9-aminoacridine and 2-methoxy-6-chloro-9-aminoacridine analogues with chains of variable rigidity were synthesized. 1H-NMR studies show that the conformation of 9-aminoacridine dimers is almost independent of the nature of the linking chain. A strong self-stacking of the aromatic rings of the 2-methoxy-6-chloro-9-aminoacridine is observed for dimers with flexible chains but not for those with rigid chains. All the dimers having a linking chain long enough to bisintercalate in DNA according to the excluded site model are indeed bisintercalators. The kinetic association constant of all monomers and dimers for poly[d(A-T)].poly[d(A-T)] are in the same range (2-4 x 10(7) M-1 s-1). The large increase of DNA binding affinity observed for the dimers is always associated with the expected decrease of the dissociation rate constant. The effect of chain rigidity and pH on the calf thymus DNA binding of 9-aminoacridine and 2-methoxy-6-chloro-9-aminoacridine dimers is quite different. In the series of 9-aminoacridine the pKa of the dimers remains high and therefore no difference of DNA-binding affinity is observed between pH 5 and 7.4. The rigidity of the linking chain does not significantly alter the DNA-binding affinity. In the 2-methoxy-6-chloro-9-aminoacridine series, the pKa of all dimers became smaller than the physiological pH and a dramatic decrease of DNA-binding affinity is observed when the pH is increased from pH 5 to 7.4. This decrease appears significantly smaller for dimers with rigid chains. A similar dramatic decrease of binding affinity at pH 7.4 is not observed for poly[d(A-T)].poly[d(A-T)]. This factor makes these dimers strongly specific for the alternating polymer at pH 7.4.