Probing site specificity of DNA binding metallointercalators by NMR spectroscopy and molecular modeling

Exploring DNA-6MP interactions to develop a receptor with selective binding properties

This study focuses on identifying DNA sequences capable of selectively binding 6-mercaptopurine (6MP) or its analog, azathioprine (Aza), as a potential bioreceptor for biosensing methods. The approach used in the study is based on instrumental analysis methods such as UV-Vis spectroscopy, high performance liquid chromatography (HPLC), and nuclear magnetic resonance techniques to describe the interaction, its mode, and strength as well as selectivity of selected DNA sequences toward thiopurines. Thus, of the sequences tested, dsDNA GGCAGGACGGAG poses the ability to form complexes with 6MP, with an affinity constant of 2.52·103 M-1 as determined by DOSY NMR. Studies performed by HPLC technique confirmed the selectivity of the indicated strand toward selected interferents like natural metabolites and active pharmaceutical ingredients (API) used during azathioprine treatment. Further insights into the DNA-6MP interaction were provided by TOCSY and NOESY NMR experiments, highlighting the preference for guanine-rich sequences in binding, indicating a potential 6MP binding site in the dsDNA. The results also indicate the rapid conversion of azathioprine to 6-mercaptopurine upon contact with DNA, indirectly confirming the pro-drug nature of azathioprine. This research contributes to the development of DNA-based bioreceptors for selective determination of 6-mercaptopurine, with potential implications in personalized medicine and therapeutic drug monitoring.

Anti-cancer property and DNA binding interaction of first row transition metal complexes: A decade update

Metal ions carry out a wide variety of functions, including acid-base/redox catalysis, structural functions, signaling, and electron transport. Understanding the interactions of transition metal complexes with biomacromolecules is essential for biology, medicinal chemistry, and the production of synthetic metalloenzymes. After the coincidental discovery of cisplatin, importance of the metal complexes in biochemistry became a top priority for inquiry. In this review, a decade update on various synthetic strategies to first row transition metal complex and their interaction with DNA through non-covalent binding are explored. Moreover, this effort provides an excellent analysis on the efficacy of theoretical and practical approaches to the systematic generation of new non-platinum based metallodrugs for anti-cancer therapeutics.

A nanoscale electrochemical guanine DNA-biosensor based on a flower-like nanocomposite of Tb-doped ZnO for the sensitive determination of pemetrexed

Pemetrexed is an antineoplastic drug used in chemotherapeutic treatments, especially in malignant mesothelioma and non-small cell lung carcinoma, but can also cause a variety of complications, like stomach pain, nausea, burning, vomiting, numbness, and tingling, emphasizing the need for an approach to quantify the drug in biological matrices. Herein, a DNA-based biosensor was introduced for pemetrexed determination. A hydrothermal approach was used for synthesizing flower-like nanoparticles (NPs) of zinc oxide (ZnO) doped with Tb (FL-NP Tb3+/ZnO). Moreover, energy dispersive X-ray (EDX), field-emission scanning electron microscopy (FESEM), zeta potential, Brunauer-Emmett-Teller (BET), and X-ray diffraction (XRD) analyses were used for characterizing the as-prepared nanocomposite. According to the impedance analysis, FL-NP Tb3+/ZnO was accompanied by very good electrochemical functions for a simple transfer of electrons. In the case of the immobilization of double-stranded deoxyribonucleic acid (ds-DNA) on the FL-NP Tb3+/ZnO and polypyrrole (PP)-modified pencil graphite electrode (ds-DNA/PP/FL-NP Tb3+/ZnO/PGE), a considerable enhancement was found in the electrochemical oxidation of guanine in ds-DNA residue bases. Since there was an interaction between ds-DNA and pemetrexed, the voltammetric current of guanine over the ds-DNA/PP/FL-NP Tb3+/ZnO/PGE declined in the presence of pemetrexed in the electrolytic solution. Moreover, under optimum conditions (25 mg L-1 of ds-DNA and 10 min incubation time, in acetate buffer at 25 °C), a linear decrease in the guanine signal was observed on the ds-DNA/PP/FL-NP Tb3+/ZnO/PGE as the pemetrexed concentration increased in the range from 0.001 μM to 175.0 μM with a limit of detection of 0.17 nM. Finally, the new DNA-based biosensor was successfully used for determining pemetrexed in real samples, indicating its application potential.

Minimising sample volume and run times for circular dichroism spectroscopy

Circular dichroism (CD) spectroscopy is widely used to characterise chiral structures in solution, including to determine protein secondary structure content. However, protein CD experiments typically require 10-20 μg of protein. An additional challenge is that some proteins change their structure when their concentration is changed (they unfold or aggregate) so, particularly for protein biopharmaceuticals, it is attractive to have a range of different path lengths to hand. This paper reports the validation of demountable DMV Bio-cells of path lengths 0.5 mm, 0.2 mm and 0.125 mm, which have approximately 1 mm diameter windows, for CD spectroscopy. When complemented with a 10 cm focal length focusing lens positioned 9.5 cm in front of the sample, the signal : noise ratio of the final spectrum is equivalent to data collected on a standard cell wide enough to allow the full light beam to pass through. The DMV Bio-cells require 2-3% of the sample needed for a standard full-width cuvette and can be assembled without bubbles with the nominal path length. In addition, they are easy to clean and less likely to be chipped or broken than standard cuvettes which, together with the sample saved, compensates for their much higher price. For smaller path lengths the Jasco MSD-462 microsampling disk enabled fairly reproducible assembly at 4-7 μm depending on the sample viscosity and similarly high quality data.

A new bio-active asymmetric-Schiff base: synthesis and evaluation of calf thymus DNA interaction, topoisomerase IIα inhibition, in vitro antiproliferative activity, SEM analysis and molecular docking studies

In this paper, the asymmetric-Schiff base 2-(4-(2-hydroxybenzylideneamino)benzylideneamino)benzoic acid (SB-2) was newly synthesized and characterized by various spectroscopic methods. The interaction of SB-2 with calf thymus DNA was investigated by UV-vis, fluorescence spectroscopy and molecular docking methods. It was determined that SB-2 effectively binds to DNA via the intercalation mode. DNA electrophoretic mobility experiments displayed that topoisomerase IIα could not cleave pBR322 plasmid DNA in the presence of SB-2, confirming that the Schiff base acts as a topo II suppressor. In the molecular docking studies, SB-2 was found to show an affinity for both the DNA-topoisomerase IIα complex and the DNA. In vitro antiproliferative activity of SB-2 was screened against HT-29 (colorectal) and HeLa (cervical) human tumor cell lines by MTT assay. SB-2 diminished the cell viability in a concentration- and incubation time-dependent manner. The ability of SB-2 to measure DNA damage in tumor cells was evaluated with cytokinesis-block micronucleus assay after incubation 24 h and 48 h. Light and scanning electron microscopy experiments of tumor cells demonstrated an incubation time-dependent increase in the proportion of apoptotic cells (nuclear condensation and apoptotic bodies) suggesting that autophagy and apoptosis play a role in the death of cells. Based on the obtained results, it may be considered that SB-2 is a candidate for DNA-targeting antitumor drug.Communicated by Ramaswamy H. Sarma.

Design and synthesis of fatty acid derived 4-methoxybenzylamides as antimicrobial agents

A new series of fatty acid amides viz. N-(4-methoxybenzyl)undec-10-enamide (5), (9Z, 12R)-12-Hydroxy-N-(4-methoxybenzyl)octadec-9-enamide (6) and N-(4-methoxy benzyl)oleamide (7) were synthesized by using a suitable synthetic route involving DCC and DMAP as catalysts. The synthesized compounds were characterized through FTIR, NMR spectroscopy, and mass spectrometry. DNA binding studies through spectroscopy and molecular docking were performed to evaluate the binding mechanism of molecules (5-7) with (ctDNA). The inhibition zone with reference to standards, Minimum Inhibitory Concentration (MIC) and Minimum Killing Concentration (MKC) values were determined to study the in vitro antimicrobial activity for tested compounds. Among all the tested compounds, the compound 6 containing hydroxy group at the fatty acid chain showed most powerful antifungal as well as antibacterial activity.

Synthesis, characterization, DNA binding, topoisomerase inhibition, and apoptosis induction studies of a novel cobalt(III) complex with a thiosemicarbazone ligand

In this study, 9-anthraldehyde-N(4)-methylthiosemicarbazone (MeATSC) 1 and [Co(phen)2(O2CO)]Cl·6H2O 2 (where phen = 1,10-phenanthroline) were synthesized. [Co(phen)2(O2CO)]Cl·6H2O 2 was used to produce anhydrous [Co(phen)2(H2O)2](NO3)33. Subsequently, anhydrous [Co(phen)2(H2O)2](NO3)33 was reacted with MeATSC 1 to produce [Co(phen)2(MeATSC)](NO3)3·1.5H2O·C2H5OH 4. The ligand, MeATSC 1 and all complexes were characterized by elemental analysis, FT IR, UV-visible, and multinuclear NMR (1H, 13C, and 59Co) spectroscopy, along with HRMS, and conductivity measurements, where appropriate. Interactions of MeATSC 1 and complex 4 with calf thymus DNA (ctDNA) were investigated by carrying out UV-visible spectrophotometric studies. UV-visible spectrophotometric studies revealed weak interactions between ctDNA and the analytes, MeATSC 1 and complex 4 (Kb = 8.1 × 105 and 1.6 × 104 M-1, respectively). Topoisomerase inhibition assays and cleavage studies proved that complex 4 was an efficient catalytic inhibitor of human topoisomerases I and IIα. Based upon the results obtained from the 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay on 4T1-luc metastatic mammary breast cancer cells (IC50 = 34.4 ± 5.2 μM when compared to IC50 = 13.75 ± 1.08 μM for the control, cisplatin), further investigations into the molecular events initiated by exposure to complex 4 were investigated. Studies have shown that complex 4 activated both the apoptotic and autophagic signaling pathways in addition to causing dissipation of the mitochondrial membrane potential (ΔΨm). Furthermore, activation of cysteine-aspartic proteases3 (caspase 3) in a time- and concentration-dependent manner coupled with the ΔΨm, studies implicated the intrinsic apoptotic pathway as the major regulator of cell death mechanism.

Study of the Binding Interaction between Wortmannin and Calf Thymus DNA: Multispectroscopic and Molecular Docking Studies

INTRODUCTION

Wortmannin (WTN) is a steroid metabolite that inhibits phosphatidylinositol 3-kinase and other signaling pathways. Structurally, the WTN consists of a cyclopentanophenanthrene-like structure with several oxygen-rich moieties which have the potential to interact with deoxyribonucleic acid (DNA) molecules.

METHODS

We aim to evaluate the WTN and calf thymus DNA (ct-DNA) interaction with molecular docking using the AutoDock 4.2 software. UV and fluorescence spectroscopy and viscosity techniques were performed to confirm the in silico analysis.

RESULTS

Molecular docking showed that the WTN interacted with ct-DNA via hydrogen bonds at guanine-rich sequences. The number of hydrogen bonds between the WTN and DNA was 1-2 bonds (average 1.2) per WTN molecule. The in silico binding constant was 2 × 103 M-1. UV spectroscopy showed that the WTN induced a hyperchromic feature without wavelength shifting. The WTN and DNA interaction led to quenching of DNA-emitted fluorescence. The different concentrations of WTN had no effect on DNA viscosity. Taken together, our results demonstrated WTN interacts with DNA in the nonintercalating mode, which is considered as a new mechanism of action.

CONCLUSION

These results suggest that the WTN may exert its biological effects, at least in part, via interaction with DNA.

Synthesis of steroidal imidazolidinthiones as potential apoptotic agents: Investigation by theoretical and experimental studies

New steroidal imidazolidinthione derivatives (4-6) were synthesized from steroidal thiosemicarbazones and dichloroethane. The synthesized compounds were characterized using spectral data analysis. Theoretical DFT involving B3LYP/6-31G∗∗ level of theory was employed to gain insights into the molecular structure of the target compounds. MEPS and FMO analysis were carried out. HOMO-LUMO energy gap was determined which helped to evaluate various global descriptors like hardness, chemical potential, electronegativity, nucleophilicity and electrophilicity index, etc. The calculated properties established that the synthesized products are more or less similar in their reactivity behaviour. To explore their biological potential, interaction studies of compounds (4-6) with DNA were carried out using various biophysical techniques. The compounds bind DNA preferentially through electrostatic and hydrophobic interactions with K_b of 3.21 × 10³ M^-1, 2.79 × 10³ M^-1 and 2.26 × 10³ M^-1, respectively indicating the higher binding affinity of compound 4 towards DNA. Gel electrophoresis of compound 4 demonstrated strong interaction during the concentration dependent cleavage activity with pBR322 DNA. It was observed that these steroidal imidazolidinthiones are minor groove binders of DNA which was validated using molecular docking studies. An in vitro cytotoxicity screening using MTT assay revealed that the compounds (4-6) exhibit potential toxicity against different human cancer cells. Highest antiproliferative effect was observed on HeLa cells by compound 4. The results suggested that compounds 4-6 cause apoptotic cell death by cleaving apoptotic protein caspase-3 and suppress anti-apoptotic protein Bcl-2 in HeLa cancer cells.

Stepwise synthesis, characterization, DNA binding properties and cytotoxicity of diruthenium oligopyridine compounds conjugated with peptides

Although the interactions of oligopyridine ruthenium complexes with DNA have been widely studied, the biological activity of similar diruthenium oligopyridine complexes conjugated with peptides has not been investigated. Herein, we report the stepwise synthesis and characterization of diruthenium complexes with the general formula [(L^a)Ru(tppz)Ru(L^b)]ⁿ⁺ (tppz = 2,3,5,6-tetra(2-pyridyl)pyrazine, L^a = 2,2':6',2''-terpyridine or 4-phenyl-2,2':6',2''-terpyridine and L^b = 2,2':6',2''-terpyridine-4'-CO(Gly¹-Gly²-Gly³-LysCONH₂) (5), (6), n = 5; 2,2':6',2''-terpyridine-4'-CO(Gly¹-Gly²-Lys¹-Lys²CONH₂) (7), (8), n = 6; 2,2':6',2''-terpyridine-4'-CO(Ahx-Lys¹Lys²CONH₂) (9), (10), n = 5, Ahx = 6-aminohexanoic acid). The compounds [(trpy)Ru(tppz)Ru(trpy-CO₂H)](PF₆)₄, (2)(PF₆)₄, [(ptrpy)Ru(tppz)Ru(trpy-CO₂H)](PF₆)₄, (3)(PF₆)₄ and [(ptrpy)Ru(tppz)Ru(trpy)](PF₆)₄, (4)(PF₆)₄ were also characterized by single crystal X-ray methods. Moreover, the interactions of the chloride salts (5), (6) and (4) with the self-complementary dodecanucleotide duplex d(5'-CGCGAATTCGCG-3')₂ were studied by NMR spectroscopic techniques. The results show that complex (4) binds in the central part of the oligonucleotide, from the minor groove through the ligand ptrpy, while the ligand trpy, which was located on the other side of the diruthenium core, does not contribute to the binding. Complex (5) binds similarly, through the ligand ptrpy. However, the induced upfield shifts of the ptrpy proton signals are significantly lower than the corresponding ones in the case of (4), indicating much lower binding affinity. This is clear evidence that the tethered peptide Gly¹-Gly²-Gly³-Lys¹CONH₂ hinders the complex binding, even though it contains groups that are able to assist it (e.g., the positively charged amino group of lysine, the peptidic backbone, the terminal amide). Complex (6) shows a non-specific binding, interacting through electrostatic forces. The chloride salts of (4), (5) and (6) had insignificant effects on the cell cycle distribution and marginal cytotoxicity (IC₅₀ > 750 μM) against human lung cancer cell lines H1299 and H1437, indicating that their binding to the oligonucleotide is not a sufficient condition for their cytotoxicity.

DNA binding, artificial nuclease activity and cytotoxic studies of newly synthesized steroidal pyrimidines

The new steroidal pyrimidine derivatives (4-6) were synthesized by the reaction of steroidal thiosemicarbazones with (2-methyl) diethyl malonate in absolute ethanol. After characterization by spectral and analytical data, the DNA interaction studies of compounds (4-6) were carried out by UV-vis, fluorescence spectroscopy, hydrodynamic measurements, molecular docking and gel electrophoresis. The compounds bind to DNA preferentially through electrostatic and hydrophobic interactions with K_b; 2.31×10³M^-1, 1.93×10³M^-1 and 2.05×10³M^-1, respectively indicating the higher binding affinity of compound 4 towards DNA. Gel electrophoresis demonstrated that compound 4 showed a strong interaction during the concentration dependent cleavage activity with pBR322 DNA. The molecular docking study suggested the intercalation of steroidal pyrimidine moiety in the minor groove of DNA. During in vitro cytotoxicity, compounds (4-6) revealed potential toxicity against the different human cancer cells (MTT assay). During DAPI staining, the nuclear fragmentations on cells occurred after treatment with compounds 4 and 5. Western blotting analysis clearly indicates that compound 4 causes apoptosis in MCF-7 cancer cells. The results revealed that compound 4 has better prospectus to act as a cancer chemotherapeutic candidate, which warrants further in vivo anticancer investigations.

Correlation Between Molecular Modelling and Spectroscopic Techniques in Investigation With DNA Binding Interaction of Ruthenium(II) Complexes

The DNA binding studies of rutheniumu(II) polypyridyl complexes {[Ru(phen)₂Mipc]²⁺, [Ru(bpy)₂Mipc]²⁺, [Ru(dmb)₂Mipc]²⁺, [Ru(phen)₂BrIPC]²⁺, [Ru(bpy)₂BrIPC]²⁺, [Ru(dmb)₂BrIPC]²⁺, [Ru(phen)₂PIP-Cl]²⁺, [Ru(bpy)₂PIP-Cl]²⁺, [Ru(dmb)₂PIP-Cl]²⁺, [Ru(phen)₂IPPBA]²⁺, [Ru(bpy)₂IPPBA]²⁺, [Ru(dmb)₂IPPBA]²⁺} with DNA investigated by electronic absorption titration, emission and molecular modelling studies to identify the binding interactions. All these complexes are showing good binding constant values ~10⁴ to 10⁵. The intercalative ligands makes the binding of the ruthenium(II) complex with DNA as intercalation mode. The ancillary ligands 1,10-phenanthroline (phen), 4,4'-Dimethyl-2,2'-dipyridyl (dmb) and 2,2'-dipyridine (bpy) having been discovered found to be involved in bond formation with the phosphate backbone of nucleotide base pairs in ruthenium(II) complex-DNA docked complex. The molecular docking results are good agreement with experimental results. The molecular modelling technic should help to extend knowledge about the nature (or) mode of binding of these ruthenium(II) complexes with (calf thymus) CT-DNA.

DNA-binding study of anticancer drug cytarabine by spectroscopic and molecular docking techniques

The interaction of anticancer drug cytarabine with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multispectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove-binding mode, while the binding constant of UV-vis and the number of binding sites were 4.0 ± 0.2 × 10⁴ L mol^-1 and 1.39, respectively. The fluorimetric studies showed that the reaction between the drugs with CT-DNA is exothermic. Circular dichroism spectroscopy was employed to measure the conformational change of DNA in the presence of cytarabine. Furthermore, the drug induces detectable changes in its viscosity for DNA interaction. The molecular modeling results illustrated that cytarabine strongly binds to groove of DNA by relative binding energy of docked structure -20.61 KJ mol^-1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the interaction of small molecular pollutants and drugs with biomacromolecules for clarifying the molecular mechanism of toxicity or side effect in vivo.

Theoretical studies on binding modes of copper-based nucleases with DNA

In the present work, molecular simulations were performed for the purpose of predicting the binding modes of four types of copper nucleases (a total 33 compounds) with DNA. Our docking results accurately predicted the groove binding and electrostatic interaction for some copper nucleases with B-DNA. The intercalation modes were also reproduced by "gap DNA". The obtained results demonstrated that the ligand size, length, functional groups and chelate ring size bound to the copper center could influence the binding affinities of copper nucleases. The binding affinities obtained from the docking calculations herein also replicated results found using MM-PBSA approach. The predicted DNA binding modes of copper nucleases with DNA will ultimately help us to better understand the interaction of copper compounds with DNA.

Synthesis of new steroidal imidazo [1,2-a] pyridines: DNA binding studies, cleavage activity and in vitro cytotoxicity

A one-pot strategy for the catalytic synthesis of series of new 5α-cholestan-6-spiro-5'-phenylamino-2H-imidazo [1',2'-a] pyridines (4-14) has been investigated. The synthesized products were obtained in good yields (85-90%) and the protocol uses Multi-component Reaction (MCR) involving steroidal ketones, 2-aminopyridines, isocyanides and propylphosphonic anhydride (®T3P) as a catalyst. After characterization by spectral and analytical data, the interaction studies of compounds (4-6) with DNA were studied by UV-vis, fluorescence spectroscopy, gel electrophoresis and molecular docking. The compounds bind to DNA preferentially through electrostatic and hydrophobic interactions with Kb; 2.35×10(4), 3.71×10(4) and 3.24×10(4) M(-1), respectively, indicating the higher binding affinity of compound 5 towards DNA. Gel electrophoresis showed the concentration dependent cleavage activity of compounds 4-6 with DNA. Molecular docking studies suggested that compounds bind through minor groove to DNA. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay depicted promising anti-proliferative activity of compound 4-9 against different given cancer cells. In Western blotting, the expressions of relevant apoptotic markers depicted an apoptosis by steroidal imidazopyridines in A549 cells. Annexin V-FITC/PI staining data indicated that compounds could effectively induce apoptosis in A549 cells in a dose-dependent manner. FACS analysis shows that the compound 6 bring about cell cycle arrest at 2.62 μM concentration.

Spectroscopic and molecular docking studies on the interaction of the drug olanzapine with calf thymus DNA

The present study investigated the binding interaction between olanzapine and calf thymus DNA (ct-DNA) using emission, absorption, circular dichroism, viscosity measurements and molecular modeling. Thermodynamic parameters (ΔH<0 and ΔS<0) indicated that hydrogen bond and van der Waals play main roles in the binding of the drug to ct-DNA. Spectrophotometric studies of the interaction of olanzapine with DNA have shown that it could bind to ct-DNA (Kb=2×10(3)M(-1)). The binding constant is comparable to standard groove binding drugs. Competitive fluorimetric studies with Hoechst 33258 have shown that olanzapine exhibits the ability to displace the DNA-bound Hoechst 33258 indicating that binds strongly in minor groove of DNA helix. Furthermore, the drug induces detectable changes in the CD spectrum of ct-DNA as well as changes in its viscosity. All of the experimental results prove that the groove binding must be predominant. The results obtained from experimental data were in good agreement with molecular modeling studies.

Reactivity of hexanuclear ruthenium metallaprisms towards nucleotides and a DNA decamer

The reactivity of three hexacationic arene ruthenium metallaprisms towards isolated nucleotides and a short DNA strand was investigated using NMR spectroscopy, ESI mass spectrometry, UV/Vis and circular dichroism spectroscopy. The metallaprism built from oxalato-bridging ligands reacts rapidly in the presence of deoxyguanosine monophosphate (dGMP) and deoxyadenosine monophosphate, while the benzoquinonato derivative only reacts with dGMP. On the other hand, the larger metallaprism incorporating naphtoquinonato bridges remains stable in the presence of nucleotides. The reactivity of the three hexacationic metallaprisms with the decameric oligonucleotide d(CGCGATCGCG)2 was also investigated. Analysis of the NMR, MS, UV/Vis and CD data suggests that no adducts are formed between the oligonucleotide and the metallaprisms, but electrostatic interactions, leading to partial unwinding of the double-stranded oligonucleotide, were evidenced.

Single and double chain surfactant–cobalt(iii) complexes: the impact of hydrophobicity on the interaction with calf thymus DNA, and their biological activities

Single chain surfactant–cobalt(iii) complexes interact with minor grooves of CT-DNA, whereas double chin surfactant–cobalt(iii) complexes bind with CT-DNA through partial intercalation.

Experimental and molecular docking studies on DNA binding interaction of adefovir dipivoxil: advances toward treatment of hepatitis B virus infections

The toxic interaction of adefovir dipivoxil with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove binding mode. The binding constant of UV-visible and the number of binding sites were 3.33±0.2×10(4) L mol(-1)and 0.99, respectively. The fluorimetric studies showed that the reaction between the drug and CT-DNA is exothermic (ΔH=34.4 kJ mol(-1); ΔS=184.32 J mol(-1) K(-1)). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of CT-DNA in the presence of adefovir dipivoxil, which verified the groove binding mode. Furthermore, the drug induces detectable changes in its viscosity. The molecular modeling results illustrated that adefovir strongly binds to groove of DNA by relative binding energy of docked structure -16.83 kJ mol(-1). This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the toxic interaction of small molecular pollutants and drugs with bio macromolecules, which contributes to clarify the molecular mechanism of toxicity or side effect in vivo.

Synthesis and characterization of ruthenium(II)-oligopyridine-peptide conjugates. Interactions of the diasteromeres Δ- and Λ-[Ru(bpy)2(4-COY-4'-Mebpy)]Cl2 (Y=Gly-Lys(1)-Lys(2)CONH2, Lys(1)-Gly-Lys(2)CONH2, Lys(1)-Lys(2)-GlyCONH2) with the oligonucleotide d(5'-CGCGAATTCGCG-3')2

Diastereomeric complexes of the general formulae Λ- and Δ-[Ru(bpy)2(4-COY-4'-Mebpy)]Cl2 where bpy=2,2'-bipyridine and Y=Gly-Lys(1)-Lys(2)CONH2, Lys(1)-Gly-Lys(2)CONH2, Lys(1)-Lys(2)-GlyCONH2, were synthesized and characterized. The ability of these compounds to bind to the oligonucleotide duplex d(5'-CGCGAATTCGCG-3') was studied with NMR techniques. Complex Λ-2, Λ-[Ru(bpy)2(4-COLys(1)-Gly-Lys(2)CONH2),4'-Mebpy)]Cl2 (Mebpy=methyl-2,2'-bipyridine), interacts non-specifically causing changes for both complex and oligonucleotide (1)H NMR signals. Both Λ-1, Λ-[Ru(bpy)2(4-COGly-Lys(1)-Lys(2)CONH2),4'-Mebpy)]Cl2 and Λ-3, Λ-[Ru(bpy)2(4-COLys(1)-Lys(2)-GlyCONH2),4'-Mebpy)]Cl2, were bound to the oligonucleotide through both lysine aliphatic chains, indicating that the side chains of the sequential lysines create a kind of "clamp" to connect the complex with the oligonucleotide. Complex Δ-1, Δ-[Ru(bpy)2(4-COGly-Lys(1)-Lys(2)CONH2),4'-Mebpy)]Cl2, interacts with the oligonucleotide duplex with both lysine side chains in a manner similar to Λ-1. Δ-2, Δ-[Ru(bpy)2(4-COLys(1)-Gly-Lys(2)CONH2),4'-Mebpy)]Cl2, interacts with the oligonucleotide with the bipyridine ligands. In addition, the formation of a hydrogen bond between the Gly-NH and the carbonyl groups of the oligonucleotide bases was detected. A completely different binding mode was observed for Δ-3 Δ-[Ru(bpy)2(4-COLys(1)-Lys(2)-GlyCONH2),4'-Mebpy)]Cl2, which at a ratio of 1:1 ([Ru]/[nucleotide]) opens the oligonucleotide strands. In addition, participation of all three peptidic NH of Δ-3 in hydrogen bonds was observed.

Synthesis of new heterometallic macromolecules: their DNA binding, cleavage activity and in vitro model electrochemotherapy study

The homodinuclear C(16)H(30)N(8)O(5)Sn(2)Cl(4) (1), heterotetranuclear C(16)H(38)N(8)O(9)Sn(2)Cu(2)Cl(8) (2) and C(16)H(38)N(8)O(9)Sn(2)Mn(2)Cl(8) (3) macrocyclic complexes were synthesized and characterized by elemental analysis, spectroscopic techniques and molar conductance measurements. The interaction studies of 1-3 with calf thymus DNA (CT-DNA) were carried out by UV-vis titration, fluorescence, cyclic voltammetry and viscosity measurements. These results were further authenticated by carrying out interaction studies of 1-3 with plasmid pBR322 DNA employing gel electrophoresis. To overcome the dose resistance, auto toxicity of the drugs, a model study based on electrochemotherapy (ECT) was carried out and the results were compared in the presence and in the absence of the applied electrical potential.

DNA binding and cytotoxicity of ruthenium(II) and rhenium(I) complexes of 2-amino-4-phenylamino-6-(2-pyridyl)-1,3,5-triazine

[Ru(tBu2bpy)2(2-appt)](PF6)2 [1.(PF6)2, tBu2bpy = 4,4'-di-tert-butyl-2,2'-bipyridine, 2-appt = 2-amino-4-phenylamino-6-(2-pyridyl)-1,3,5-triazine] and [Re(CO)3(2-appt)Cl] (2) were prepared and characterized by X-ray crystal analysis. The binding of 1.(PF6)2 and 2 to calf thymus DNA (ct DNA) led to increases in the DNA melting temperature (Delta Tm = +12 degrees C), modest hypochromism (29% and 5% of the absorption bands at lambda max = 450 and 376 nm, respectively), and insignificant shifts in the absorption maxima. The binding constants of 1.(PF6)2 and 2 with ct DNA, as determined by absorption titration, are (8.9 +/- 0.5) x 104 and (3.6 +/- 0.1) x 104 dm3 mol-1, respectively. UV-vis absorption titration, DNA melting studies, and competition dialysis using synthetic oligonucleotides [poly(dA-dT)2 and poly(dG-dC)2] revealed that 1.(PF6)2 and 2 exhibit a binding preference for AT sequences. A modeling study on the interaction between 1 or 2 and B-DNA revealed that the minor groove is the most favored binding site and an extensive hydrogen-bonding network is formed. As determined by MTT assays, 1.(PF6)2 and 2 exhibited moderate cytotoxicities toward several human cancer cell lines (KB-3-1, HepG2, and HeLa), as well as a multi-drug-resistant cancer cell line (KB-V-1). According to confocal microscopic and flow cytometric studies, 1.(PF6)2 and 2 induced apoptosis (50-60%) in cancer cells with <5% necrosis detected.

NMR analysis of duplex d(CGCGATCGCG)2 modified by Λ- and Δ-[Ru(bpy)2(m-GHK)]Cl2 and DNA photocleavage study

The interaction of the diastereomeric complexes Lambda-[Ru(bpy)2(m-GHK)]Cl2 and Delta-[Ru(bpy)2(m-GHK)]Cl2 (bpy is 2,2'-bipyridine, GHK is glycine-L-histidine-L-lysine) with the deoxynucleotide duplex d(5'-CGCGATCGCG)2 was studied by means of 1H NMR spectroscopy. At a Delta-isomer to DNA ratio of 1:1, significant shifts for the metal complex are observed, whereas there is negligible effect on the oligonucleotide protons and only one intermolecular nuclear Overhauser effect (NOE) is present at the 2D nuclear Overhauser enhancement spectroscopy spectrum. The 1Eta NMR spectrum at ratio 2:1 is characterized by a slight shift for the Delta-isomer's bpy aromatic protons as well as significant shifts for the decanucleotide G4 H1' and Eta2'', A5 H2, G10 H1', T6 NH and G2 NH protons. Furthermore, at ratio 2:1, 11 intermolecular NOEs are observed. The majority of the NOEs involve the sugar Eta2' and Eta2'' protons sited in the major groove of the decanucleotide. Increasing the Delta-isomer to d(CGCGATCGCG)2 ratio to 5:1 results in noteworthy spectral changes. The Delta-isomer's proton shifts are reduced, whereas significant shifts are observed for the decanucleotide protons, especially the sugar protons, as well as for the exchangeable protons. Interaction is characterized by the presence of only one intermolecular NOE. Furthermore, there is significant broadening of the imino proton signals as the ratio of the Delta-isomer to DNuAlpha increases, which is attributed to the opening of the two strands of the duplex. The Lambda-isomer, on the other hand, approaches the minor groove of the oligonucleotide and interacts only weakly, possibly by electrostatic interactions. Photocleavage studies were also conducted with the plasmid pUC19 and a 158-bp restriction fragment, showing that both diastereomers cleave DNA with similar efficiency, attacking mainly the guanines of the sequence probably by generating active oxygen species.

DNA-binding by functionalized gold nanoparticles: mechanism and structural requirements

A family of nanoparticles featuring surfaces of varying hydrophobicity was synthesized. The efficiency of DNA-binding was determined, demonstrating in a fivefold modulation in binding a 37-mer DNA strand. Nanoparticle-binding causes a reversible conformational change in the DNA structure, as demonstrated by circular dichroism and fluorescence experiments. Furthermore, the affinity of the nanoparticle for the DNA can be regulated by external agents, though stability of the complex is observed at relatively high ionic strengths.

Racemic D,L-[Co(phen)2dpq](3+)-DNA interactions: investigation into the basis for minor-groove binding and recognition

A study on the minor-groove recognition of B-DNA d(GTCGAC)2 by racemic D,L-[Co(phen)2dpq](3+), where phen and dpq stand for 1,10-phenanthroline and dipyrido [3,2-d:2,3-f]quinoxaline, respectively, was carried out with a one-, two-dimensional (1D, 2D) nuclear magnetic resonance (NMR) methodologies and molecular simulations. NMR investigations revealed that the metal complex intercalates into the DNA base stack from minor groove orientation with dpq as intercalator and dpq ligand participated in the nucleobase stack. Molecular docking simulations of these systems were consistent with the experimental results and revealed that the recognition shows obvious enantioselectivity: the L-isomer is favored at the pyrimidine-purine/purine-pyrimidine region, especially CG/GC sequence, while the D-isomer is favored at the pyrimidine-pyrimidine/purine-purine region, especially TC/AG sequence. Surprisingly, we found that the L-isomer would be enriched when racemic complex was employed. So contrary to general viewpoint, the L-isomer of complex recognized this right hand double helical DNA preferentially. Detailed analysis suggests that it is the electrostatic interactions that determine the steric interactions and then determine the whole recognition event.

A spectroscopic investigation of the self-association and DNA binding properties of a series of ternary ruthenium(II) complexes

Six ruthenium(II) complexes of the general form cis-alpha-[Ru(N4-tetradentate)(N2-bidentate)]Cl2 have been synthesized from the two related tetradentate ligands 1,6-di(2'-pyridyl)-2,5-dimethyl-2,5-diazahexane (picenMe2) and 1,6-di(2'-pyridyl)-2,5-dibenzyl-2,5-diazahexane (picenBz2) and the bidentate ligands 2,2'-bipyridine (bipy), 1,10-phenanthroline (phen) and dipyrido[3,2-f:2'3'-h]quinoxaline (dpq). Synthetic intermediate species of the general form cis-alpha-[Ru(II)(N4-tetradentate)(DMSO)Cl][PF6] were isolated. The N4-tetradentate ligand picenMe2 formed only the cis-alpha stereoisomer, while picenBz2 formed both the cis-alpha and cis-beta stereoisomers. These latter stereoisomers were resolved by fractional crystallisation. Dimer self-association constants, K(D), were estimated from the concentration dependence of the 1H NMR shifts for some of these complexes in aqueous solutions at 25 degrees C. The values of K(D) ranged from 0.6 to 7.9 M(-1) and a relationship was observed between the aromatic surface area of the bidentate component and the degree to which self-association occurred, whereby a greater level of self-association correlates with a larger surface area for the bidentate ligand. Some of these complexes demonstrate an ability to bind to DNA that is consistent with intercalation of the bidentate molecular component between the base pairs of the DNA molecule. Using calf-thymus DNA, the equilibrium binding constants, K(B), were determined for some of the complexes using intrinsic methods and these ranged from 3.32 to 5.11 M(-1), the intercalating abilities of the different bidentate ligands being in the order dp q > phen > bipy. This relationship between aromatic surface area of the bidentate ligand and the degree of DNA binding activity is the same as that observed in the self-association study.

Efficient DNA Binding by Optically Pure Ruthenium Tris(bipyridyl) Complexes Incorporating Carboxylic Functionalities. Solution and Structural Analysis

Herein, we report on the binding of optically pure ruthenium complexes Delta- or Lambda-[Ru(bpy)(2)(L-L)][PF(6)](2) [L-L = Hcmbpy = 4-carboxy-4'-methyl-2,2'-bipyridine (1), L-L = H(2)dcbpy = 4,4'-dicarboxy-2,2'-bipyridine (2)] to DNA. The binding constants of the two enantiomeric Delta-1 and Lambda-1 complexes to DNA were estimated from titration monitored by (1)H NMR spectroscopy. 2D transferred NOESY (TRNOESY) experiments support the conclusion that Delta-1 and Lambda-1 bind to DNA and that an intermediate-to-fast exchange occurs between bound and free Ru(II) complex. Further, evidence for enantioselective DNA cleavage by Delta-2 is provided by means of gel electrophoresis performed in the presence and in the absence of light; in contrast, the Lambda-2 enantiomer does not. The IR spectrum of enantiomer Delta-2 (or Lambda-2) compared to that of the racemate (rac-2) gives evidence that, in the latter form, the enantiomers are strongly associated. Moreover the X-ray structure of rac-2 was also determined and exhibits as an outstanding feature the formation of a one-dimensional supramolecular species in which the cohesion of the system is maintained by strong hydrogen bonding between carboxylic acid groups of enantiomers Delta-2 and Lambda-2 (cationic parts) with d(O...O) = 2.6 A in agreement with the infrared results. The conclusion that can be drawn from IR and X-ray spectroscopies together is that the self-association in rac-2 is strong.

Effect of a conjugated acridine moiety on the binding and reactivity of Cu(II)[9-acridinylmethyl-1,4,7-triazacyclononane] with DNA

The DNA binding orientation and dynamic behavior of Cu(II) complexes of 1,4,7-triazacyclononane ([9]aneN(3)), 1, and an acridine conjugate, 2, were investigated by DNA fiber EPR (EPR=electron paramagnetic resonance) spectroscopy. Crystal and molecular structure of 2 were determined by X-ray diffraction. It has been shown that 1 binds to DNA in two different modes at room temperature; one species is rapidly rotating and the other is immobilized randomly on the DNA. The introduction of acridine to [9]aneN(3) fixed the [Cu([9]aneN(3))](2+) moiety of 2 in two different environments on the DNA: the g(mid R:mid R:) axis of one species (g( parallel)=2.26) is aligned perpendicularly to the DNA fiber axis whereas that of the other (g( parallel)=2.24) aligns<90 degrees with the DNA fiber axis. The different DNA binding structures of 1 and 2 are reflected also in their different efficiencies of DNA cleavage; 2 was found to be more effective both in oxidative and hydrolytic cleavage reactions.

The DNA and RNA specificity of eilatin Ru(II) complexes as compared to eilatin and ethidium bromide

Eilatin-containing ruthenium complexes bind to a broad range of different nucleic acids including: calf thymus (CT) DNA, tRNA(Phe), polymeric RNAs and DNAs, and viral RNAs including the HIV-1 RRE and TAR. The nucleic acid specificity of Lambda- and Delta-[Ru(bpy)2eilatin]2+ have been compared to that of the 'free' eilatin ligand, and to the classic intercalating agent ethidium bromide. Interestingly, all four compounds appear to bind to nucleic acids by intercalation, but the trends in nucleic acid binding specificity are highly diverse. Unlike ethidium bromide, both eilatin and the eilatin-containing coordination complexes bind to certain single-stranded RNAs with high affinity (K(d) < or = 1 microM). Eilatin itself is selective for electron-poor polymeric purines, while the eilatin-coordination complexes exhibit preference for the polypyrimidine r(U). These results show how the binding specificity of an intercalating ligand can change upon its incorporation into an octahedral metal complex.

Secondary metabolites from Basotho medicinal plants. I. Bulbine narcissifolia

The medicinal plant Bulbine narcissifolia is used by the Basotho, Griqua, and whites of southern Africa for wound healing and as a mild purgative. Extraction of the powdered root has yielded acetosyringone, chrysophanol, knipholone, isoknipholone, 10,7'-bichrysophanol, and chrysalodin in addition to two new anthraquinone glycosides, knipholone-8-O-beta-D-gentiobioside (1) and chrysalodin-10-beta-D-gentiobioside (2). NMR spectroscopy was used to elucidate the structures of 1 and 2 and to show that 1 binds weakly to DNA.