The effect of manganese(II) on DNA structure: electronic and vibrational circular dichroism studies

Strain dependent UV degradation of Escherichia coli DNA monitored by Fourier transform infrared spectroscopy

In this work we present a method for detection of DNA isolated from nonpathogenic Escherichia coli strains, respectively. Untreated and UV irradiated bacterial DNAs were analyzed by FT-IR spectroscopy, to investigate their screening characteristic features and their structural radiotolerance at 253.7nm. FT-IR spectra, providing a high molecular structural information, have been analyzed in the wavenumber range 800-1800cm(-1). FT-IR signatures, spectroscopic band assignments and structural interpretations of these DNAs are reported. Also, UV damage at the DNA molecular level is of interest. Strain dependent UV degradation of DNA from E. coli has been observed. Particularly, alterations in nucleic acid bases, base pairing and base stacking have been found. Also changes in the DNA conformation and deoxyribose were detected. Based on this work, specific E. coli DNA-ligand interactions, drug development and vaccine design for a better understanding of the infection mechanism caused by an interference between pathogenic and nonpathogenic bacteria and for a better control of disease, respectively, might be further investigated using Fourier transform infrared spectroscopy. Besides, understanding the pathways for UV damaged DNA response, like nucleic acids repair mechanisms is appreciated.

Study on the interaction of homoisoflavonoids with RNA

Homoisoflavonoids (3-benzylidene-4-chromanones) are isomers of flavonoids and exhibit different biological activities because of hydroxyl groups attaching to different positions. This study is the first attempt to locate the binding sites of four synthetic homoisoflavonoids: (E)-3-(3,4-dihydroxybenzylidene)-7-methoxychroman-4-one (BMC), (E)-3-(3,4-dihydroxybenzylidene)-7-propoxychroman-4-one (BPC), (E)-3-(4-hydroxybenzylidene)-7-methoxychroman-4-one (HBMC) and (E) 3-(4-hydroxybenzylidene)-chroman-4-one (HBC) to RNA. The effect of the ligand complexation on RNA aggregation was investigated in aqueous solution at physiological conditions, using constant RNA concentration (6.25mM) and various ligand/polynucleotide (phosphate) ratios of 1/120, 1/80, 1/40, 1/20, 1/10 and 1/5. Fourier transform infrared (FTIR) and UV-Visible spectroscopic methods were used to determine the ligand binding modes, the binding constants, and the stability of ligand-RNA complexes in aqueous solution. Spectroscopic evidence showed external binding of homoisoflavonoids to RNA duplex with overall binding constants of KBMC-RNA = 1.06(± 0.09) × 10(4)M(-1), KBPC-RNA = 1.11(± 0.15) × 10(4)M (-1), KHBC-RNA = 3.82(± 0.09) × 10(3)M(-1) and KHBMC-RNA=5.82(± 0.04) × 10(3) M(-1). The affinity of homoisoflavonoid-RNA binding is in the order of BPC>BMC>HBMC>HBC. No biopolymer secondary structural changes were observed upon homoisoflavonoids interaction and RNA remains in the A-family structure in these complexes.

Fourier transform infrared spectroscopy of DNA from Borrelia burgdorferi sensu lato and Ixodes ricinus ticks

In this work we present a method for detection of motile and immotile Borrelia burgdorferi genomic DNA, in relation with infectious and noninfectious spirochetes. An FT-IR study of DNA isolated from B. burgdorferi sensu lato strains and from positive and negative Ixodes ricinus ticks, respectively, is reported. Motile bacterial cells from the species B. burgdorferi sensu stricto, Borrelia garinii and Borrelia afzelii were of interest. Also, FT-IR absorbance spectra of DNA from immotile spirochetes of B. burgdorferi sensu stricto, in the absence and presence of different antibiotics (doxycycline, erythromycin, gentamicin, penicillin V or phenoxymethylpenicillin, tetracycline, respectively) were investigated. FT-IR spectra, providing a high molecular structural information, have been analyzed in the wavenumber range 400-1800 cm(-1). FT-IR signatures, spectroscopic band assignments and structural interpretations of these DNAs are reported. Spectral differences between FT-IR absorbances of DNAs from motile bacterial cells and immotile spirochetes, respectively, have been found. Particularly, alterations of the sugar-phosphate B-form chain in the case of DNA from Borrelia immotile cells, as compared with DNA from B. burgdorferi sensu lato motile cells have been observed. Based on this work, specific B. burgdorferi sensu lato and I. ricinus DNA-ligand interactions, respectively, might be further investigated using Fourier transform infrared spectroscopy.

Synthesis, crystal structure and interaction of L-valine Schiff base divanadium(V) complex containing a V2O3 core with DNA and BSA

A divanadium(V) complex, [V2O3(o-van-val)2] (o-van-val=Schiff base derived from o-vanillin and L-valine), has been synthesized and structurally characterized. The crystal structure shows that both of the vanadium centers in the complex have a distorted octahedral coordination environment composed of tridentate Schiff base ligand. A V2O3 core in molecular structure adopts intermediate between cis and trans configuration with the O1V1⋯V1AO1A torsion angle 115.22 (28)° and the V1⋯V1A distance 3.455Å. The binding properties of the complex with calf thymus DNA (CT-DNA) have been investigated by UV-vis absorption, fluorescence, CD spectra and viscosity measurement. The results indicate that the complex binds to CT-DNA in non-classical intercalative mode. Meanwhile, the interaction of the complex with bovine serum albumin (BSA) has been studied by UV-vis absorption, fluorescence and CD spectra. Results indicated that the complex can markedly quench the intrinsic fluorescence of BSA via a static quenching process, and cause its conformational change. The calculated apparent binding constant Kb was 1.05×10(6)M(-1) and the binding site number n was 1.18.

DNA Interaction with Naturally Occurring Antioxidant Flavonoids Quercetin, Kaempferol, and Delphinidin

Flavonoids are strong antioxidants that prevent DNA damage. The anticancer and antiviral activities of these natural products are implicated in their mechanism of actions. However, there has been no information on the interactions of these antioxidants with individual DNA at molecular level. This study was designed to examine the interaction of quercetin (que), kaempferol (kae), and delphinidin (del) with calf-thymus DNA in aqueous solution at physiological conditions, using constant DNA concentration (6.5 mmol) and various drug/DNA(phosphate) ratios of 1/65 to 1. FTIR and UV-Visible difference spectroscopic methods are used to determine the drug binding sites, the binding constants and the effects of drug complexation on the stability and conformation of DNA duplex. Structural analysis showed quercetin, kaempferol, and delphinidin bind weakly to adenine, guanine (major groove), and thymine (minor groove) bases, as well as to the backbone phosphate group with overall binding constants K(que) = 7.25 x 10(4)M(-1), K(kae) = 3.60 x 10(4)M(-1), and K(del) = 1.66 x 10(4)M(-1). The stability of adduct formation is in the order of que>kae>del. Delphinidin with a positive charge induces more stabilizing effect on DNA duplex than quercetin and kaempferol. A partial B to A-DNA transition occurs at high drug concentrations.

New modulated design and synthesis of chiral CuII/SnIV bimetallic potential anticancer drug entity: in vitro DNA binding and pBR322 DNA cleavage activity

A new chiral ligand scaffold L derived from (R)-2-amino-2-phenyl ethanol and diethyl oxalate was isolated and thoroughly characterized by various spectroscopic methods. The ligand L was allowed to react with CuCl(2)·2H(2)O and NiCl(2)·6H(2)O to achieve monometallic complexes 1 and 2, respectively. Subsequently modulation of 1 and 2 was carried out in the presence of SnCl(4)·5H(2)O to obtain heterobimetallic potential drug candidates 3 and 4 possessing (Cu(II)/Sn(IV) and Ni(II)/Sn(IV)) metallic cores, respectively and characterized by elemental analysis and spectroscopic data including (1)H, (13)C and (119)Sn NMR in case of 3 and 4. In vitro DNA binding studies revealed that complex 3 avidly binds to DNA as quantified by K(b) and K(sv) values. Complex 3 exhibits a remarkable DNA cleavage activity (concentration dependent) with pBR322 DNA and the cleavage activity of 3 was significantly enhanced in the presence of activators and follows the order H(2)O(2)>Asc>MPA>GSH. Complex 3 cleave pBR322 DNA via hydrolytic pathway and accessible to major groove of DNA.

β-Cell subcellular localization of glucose-stimulated Mn uptake by X-ray fluorescence microscopy: implications for pancreatic MRI

Manganese (Mn) is a calcium (Ca) analog that has long been used as a magnetic resonance imaging (MRI) contrast agent for investigating cardiac tissue functionality, for brain mapping and for neuronal tract tracing studies. Recently, we have extended its use to investigate pancreatic β-cells and showed that, in the presence of MnCl(2), glucose-activated pancreatic islets yield significant signal enhancement in T(1)-weigheted MR images. In this study, we exploited for the first time the unique capabilities of X-ray fluorescence microscopy (XFM) to both visualize and quantify the metal in pancreatic β-cells at cellular and subcellular levels. MIN-6 insulinoma cells grown in standard tissue culture conditions had only a trace amount of Mn, 1.14 ± 0.03 × 10(-11)µg/µm(2), homogenously distributed across the cell. Exposure to 2 mM glucose and 50 µM MnCl(2) for 20 min resulted in nonglucose-dependent Mn uptake and the overall cell concentration increased to 8.99 ± 2.69 × 10(-11) µg/µm(2). When cells were activated by incubation in 16 mM glucose in the presence of 50 µM MnCl(2), a significant increase in cytoplasmic Mn was measured, reaching 2.57 ± 1.34 × 10(-10) µg/µm(2). A further rise in intracellular concentration was measured following KCl-induced depolarization, with concentrations totaling 1.25 ± 0.33 × 10(-9) and 4.02 ± 0.71 × 10(-10) µg/µm(2) in the cytoplasm and nuclei, respectively. In both activated conditions Mn was prevalent in the cytoplasm and localized primarily in a perinuclear region, possibly corresponding to the Golgi apparatus and involving the secretory pathway. These data are consistent with our previous MRI findings, confirming that Mn can be used as a functional imaging reporter of pancreatic β-cell activation and also provide a basis for understanding how subcellular localization of Mn will impact MRI contrast.

Metal ion-promoted conformational changes of oligonucleotides

The review will discuss the influence of metal ions on conformational changes of oligonucleotides. First, a short definition of the torsion angles is given, followed by a concise yet critical overview of the commonly applied experimental techniques. Finally, the possible role of metals upon the following conformational changes of oligonucleotides is discussed: (i) the denaturation of double-strands, (ii) the transition from B- to A-DNA, (iii) the transition from right- to left-handed DNA and RNA, (iv) the condensation, (v) and other conformational changes. We conclude with a summary and outlook.

Study on the interaction of glycyrrhizin and glycyrrhetinic acid with RNA

Glycyrrhizin is a well known pharmacologically bioactive natural glycoside. Glycyrrhizin (GL) has been widely used as a therapeutic agent for chronic active liver diseases. Glycyrrhetinic acid is an aglycone and an active metabolite of glycyrrhizin. This study is the first attempt to locate the binding sites of glycyrrhizin and glycyrrhetinic acid to RNA. The effect of the ligand complexation on RNA aggregation was investigated in aqueous solution at physiological conditions, using constant RNA concentration (6.25 mM) and various ligand/polynucleotide (phosphate) ratios of 1/280, 1/240, 1/120, 1/80, 1/40, 1/20, 1/10, 1/5, 1/2 and 1/1. Fourier transform infrared (FTIR) and UV-Visible spectroscopic methods as well as molecular modeling were used to determine the ligand binding modes, the binding constants, and the stability of ligands-RNA complexes in aqueous solution. Spectroscopic evidence showed that glycyrrhizin and glycyrrhetinic acid bind RNA via G-C and A-U base pairs as well as the backbone phosphate group with overall binding constants of K(GL-RNA)=3.03×10(3)M(-1), K(GA-RNA)=2.71×10(3)M(-1). The affinity of ligands-RNA binding is in the order of glycyrrhizin>glycyrrhetinic acid. RNA remains in the A-family structure, while biopolymer aggregation occurred at high triterpenoid concentrations.

Design, synthesis, characterization and DNA-binding studies of a triphenyltin(IV) complex of N-glycoside (GATPT), a sugar based apoptosis inducer: in vitro and in vivo assessment of induction of apoptosis by GATPT

The novel organotin complex 1-{(2-hydroxyethyl)amino}-2-amino-1,2-dideoxy-D-glucose triphenyltin(iv) (GATPT) was synthesized by the reaction of N-glycoside ligand and triphenyltin(iv) chloride. GATPT was characterized by elemental analyses, polarimetry, IR, CD, UV and multinuclear ((1)H, (13)C, (119)Sn) 1D and 2D NMR. The interaction of GATPT with calf thymus DNA was studied by using viscometry, absorption, emission and circular dichoric spectral methods. The DNA binding results suggested the intercalative mode of binding for GATPT with DNA along with simultaneous electrostatic interaction between the Sn(iv) center and the phosphate backbone of the DNA helix. GATPT was tested for its cytotoxic properties against SY5Y, PC-12 and N2A neuronal tumor cell lines. GATPT induced significant apoptosis in the PC-12 cell line characterized by DNA fragmentation and chromosome condensation. Treatment of PC-12 cells with GATPT resulted in a dramatic up-regulation of Bax and Bak and down-regulation of the anti-apoptotic factor Bcl-2. Apoptotic induction by GATPT was shown to be mediated in a p53-dependent manner and loss of p53 impaired the release of cytochrome c from mitochondria to cytosol. Caspase-3 was found to be indispensable for the GATPT triggered apoptosis signaling pathway. Furthermore, in vivo studies using a nude mice model revealed that GATPT exhibits significant antiproliferative activity against tumor development with minimal cytotoxicity. These findings warrant further clinical investigations of GATPT as a therapeutic agent for cancer chemotherapy.

De novo design, synthesis and spectroscopic characterization of chiral benzimidazole-derived amino acid Zn(II) complexes: Development of tryptophan-derived specific hydrolytic DNA artificial nuclease agent

Novel ternary dizinc(II) complexes 1-3, derived from 1,2-bis(1H-benzimidazol-2-yl)ethane-1,2-diol and l-form of amino acids (viz., tryptophan, leucine and valine) were synthesized and characterized by spectroscopic (IR, (1)H NMR, UV-vis, ESI-MS) and other analytical methods. To evaluate the biological preference of chiral drugs for inherently chiral target DNA, interaction of 1-3 with calf thymus DNA in Tris-HCl buffer was studied by various biophysical techniques which reveal that all these complexes bind to CT DNA non-covalently via electrostatic interaction. The higher K(b) value of L-tryptophan complex 1 suggested greater DNA binding propensity. Further, to evaluate the mode of action at the molecular level, interaction studies of complexes 1 and 2 with nucleotides (5'-GMP and 5'-TMP) were carried out by UV-vis titrations, (1)H and (31)P NMR which implicates the preferential selectivity of these complexes to N3 of thymine rather than N7 of guanine. Furthermore, complex 1 exhibits efficient DNA cleavage with supercoiled pBR322. The complex 1 cleaves DNA efficiently involving hydrolytic cleavage pathway. Such chiral synthetic hydrolytic nucleases with asymmetric centers are gaining considerable attention owing to their importance in biotechnology and drug design, in particular to cleave DNA with sequence selectivity different from that of the natural enzymes.

Interaction of glycyrrhizin and glycyrrhetinic acid with DNA

Glycyrrhizin (GL), a molecule of glycyrrhetinic acid (GA), is an aqueous extract from licorice root. These compounds are well known for their anti-inflammatory, hepatocarcinogenesis, antiviral, and interferon-inducing activities. This study is the first attempt to investigate the binding of GL and GA with DNA. The effect of ligand complexation on DNA aggregation and condensation was investigated in aqueous solution at physiological conditions, using constant DNA concentration (6.25 mM) and various ligands/polynucleotide (phosphate) ratios of 1/240, 1/120, 1/80, 1/40, 1/20, 1/10, 1/5, 1/2, and 1/1. Fourier transform infrared and ultraviolet (UV)-visible spectroscopic methods were used to determine the ligand binding modes, the binding constants, and the stability of ligand-DNA complexes in aqueous solution. Spectroscopic evidence showed that GL and GA bind DNA via major and minor grooves as well as the backbone phosphate group with overall binding constants of K(GL-DNA)=5.7×10(3) M(-1), K(GA-DNA)=5.1×10(3) M(-1). The affinity of ligand-DNA binding is in the order of GL>GA. DNA remained in the B-family structure, whereas biopolymer aggregation occurred at high triterpenoid concentrations.

Spectroscopic detection of DNA quadruplexes by vibrational circular dichroism

The four-stranded G-quadruplex motif is a conformation frequently adopted by guanine-rich nucleic acids that plays an important role in biology, medicine, and nanotechnology. Although vibrational spectroscopy has been widely used to investigate nucleic acid structure, association of particular spectral features with the quadruplex structure has to date been ambiguous. In this work, experimental IR absorption and vibrational circular dichroism (VCD) spectra of the model quadruplex systems d(G)(8) and deoxyguanosine-5'-monophosphate (5'-dGMP) were analyzed using molecular dynamics (MD) and quantum-chemical modeling. The experimental spectra were unambiguously assigned to the quadruplex DNA arrangement, and several IR and VCD bands related to this structural motif were determined. Involvement of MD in the modeling was essential for realistic simulation of the spectra. The VCD signal was found to be more sensitive to dynamical structural variations than the IR signal. The combination of the spectroscopic techniques with multiscale simulations provides extended information about nucleic acid conformations and their dynamics.

Synthesis and enantiopreferential DNA-binding profile of late 3d transition metal R- and S-enantiomeric complexes derived from N,N-bis-(1-benzyl-2-ethoxyethane): Validation of R-enantiomer of copper(II) complex as a human topoisomerase II inhibitor

To evaluate the biological preference of chiral drug candidates for molecular target DNA, new potential metal-based chemotherapeutic agents 1-3 (a and b) of late 3d transition metals Ni(II), Cu(II), and Zn(II), respectively, derived from (R)- and (S)-2-amino-2-phenylethanol with CH(2) CH(2)  linker were synthesized and thoroughly characterized. Interaction studies of 1-3 (a and b) with calf thymus DNA in Tris buffer were studied by electronic absorption titrations, luminescence titrations, cyclic voltammetry, and circular dichroism. The results reveal that the extent of DNA binding of R-enantiomer of copper 1a was highest in comparison to rest of the complexes via electrostatic interaction mode. The nuclease activity of 1(a and b) with supercoiled pBR322 DNA was further examined by gel electrophoresis, which reveals that complex 1a exhibits a remarkable DNA cleavage activity (concentration dependent) with pBR322DNA, and the cleavage activity of both enantiomers of complex 1 was significantly enhanced in the presence of activators. The activating efficiency follows the order Asc > H(2) O(2) > MPA for 1a, and reverse order was observed for 1b, because of the differences in enantioselectivity and conformation. Further, it was observed that cleavage reaction involves singlet oxygen species and superoxide radicals via oxidative cleavage mechanism. In addition, complex 1a exhibits significant inhibitory effects on the topoisomerase II (topo II) activity at a very low concentration ∼24 μM, which suggest that complex 1a is indeed catalytic inhibitor or (poison) of human topo II.

Applications of the Cartesian coordinate tensor transfer technique in the simulations of vibrational circular dichroism spectra of oligonucleotides

The application of the Cartesian coordinate tensor transfer (CCT) technique for simulations of the IR absorption and vibrational circular dichroism (VCD) spectra of relatively large nucleic acid fragments is demonstrated on several case studies. The approach is based on direct ab initio calculations of atomic tensors, determining molecular properties, for relatively small fragments, and subsequent transfer of these tensors to the larger systems in Cartesian coordinates. This procedure enables precise computations of vibrational spectra for large biomolecular systems, currently with up to several thousands of atoms. The versatile ability of the CCT methods is emphasized on the examples of VCD and IR absorption spectra calculations for B- and Z-forms of DNA, single-, double-, and triple-stranded RNA helices and DNA structures with different base content and sequences. The development and recent improvements of the methodology are followed, including utilization of the constrained normal mode optimization (NMO) strategy and combined quantum mechanics and molecular dynamics simulations. Advantages, drawbacks, and recommendations for future improvements of the CCT method as applied to nucleic acid spectra calculations are discussed.

Anomalous behavior of pentacoordinate copper complexes of dimethylphenanthroline and derivatives of terpyridine ligands: Studies on DNA binding, cleavage and apoptotic activity

Copper(II) complexes with substituted terpyridine ligands, namely [Cu(itpy)(dmp)](NO3)2 (1) and [Cu(ptpy)(dmp)](NO3)2 (2) have been synthesized and characterized. The interaction of the complexes with CT-DNA has been explored using spectroscopic techniques and viscosity. Complexes 1 and 2 bind in the grooves of DNA, interestingly 1 in the minor and 2 in the major groove. Both the complexes have been found to promote DNA cleavage; complex 1 through hydrolytic and 2 oxidative. Complexes 1 and 2 have been found to be cytotoxic and bring about apoptosis of human lung cancer cell line A549.

Cytogenetic evaluation and DNA interaction studies of the food colorants amaranth, erythrosine and tartrazine

Food coloring agents, amaranth, erythrosine and tartrazine have been tested at 0.02-8mM in human peripheral blood cells in vitro, in order to investigate their genotoxic, cytotoxic and cytostatic potential. Amaranth at the highest concentration (8mM) demonstrates high genotoxicity, cytostaticity and cytotoxicity. The frequency of SCEs/cell was increased 1.7 times over the control level. Additionally, erythrosine at 8, 4 and 2mM shows a high cytotoxicity and cytostaticity. Finally, tartrazine seems to be toxic at 8 and 4mM. No signs of genotoxicity were observed. Reversely, tartrazine showed cytotoxicity at 1 and 2mM. Furthermore, spectroscopic titration studies for the interaction of these food additives with DNA showed that these dyes bind to calf thymus DNA and distinct isosbestic points are observed clearly suggesting binding of the dyes to DNA. Additionally DNA electrophoretic mobility experiments showed that these colorants are obviously capable for strong binding to linear dsDNA causing its degradation. PCR amplification of all DNA fragments (which previously were pre-treated with three different concentrations of the colorants, extracted from agarose gel after separation and then purified), seems to be attenuated with a manner dye concentration-dependent reflecting in a delayed electrophoretic mobility due to the possible binding of some molecules of the dyes. Evaluation of the data and curves were obtained after quantitative and qualitative analysis of the lanes of the gel by an analyzer computer program. Our results indicate that these food colorants had a toxic potential to human lymphocytes in vitro and it seems that they bind directly to DNA.

Bioinspired interactions studied by vibrational circular dichroism

Vibrational circular dichroism (VCD) spectra are reliable indicators of the spatial structure of chiral molecules. The specific and characteristic feature of vibrational spectroscopy, and therefore also of VCD, where the energy of some vibrational modes is predominantly focused to a specific part of the molecule, enables monitoring both the structure of the molecule dissolved in different solvents and under different physicochemical conditions and molecular interactions. This minireview deals with recent contributions covering structural information on the bioinspired interactions obtained by means of VCD, especially in the following areas: interaction of DNA with biomolecules and biogenic metals, guanine tetramers and quadruplexes, biointeractions of bile pigments, and polypeptide and protein interactions with other biomolecules.

A comparative study on the interaction of cis- and trans-platin with DNA and RNA

Cis-diamminedichloroplatinum(II) is a frequently used and very effective chemotherapeutic drug for treatment of various malignancies; however, the trans isomer is clinically ineffective. Cis-platin exerts its antitumor activity by binding to DNA via intrastrand cross-links to d(GpG) (dG = deoxyguanosine) and to d(ApG) (dA = deoxyadenosine), interfering with DNA replication and transcription and causing cell death. The trans-diamminedichloroplatinum(II) isomer also binds DNA, but is clinically ineffective. This study was designed to examine the interactions of cis- and trans-platin with calf thymus DNA and yeast RNA in aqueous solution at physiological conditions, using a constant DNA and RNA concentration (6.25 mM) and various platin salts/polynucleotide (phosphate) ratios of 1/100, 1/50, 1/25, and 1/12.5. Fourier transform infrared, ultraviolet-visible spectroscopic methods were used to determine the drug binding modes, the binding constants, and the stability of cis- and trans-platin-DNA and -RNA complexes in aqueous solution. Spectroscopic evidence showed that cis- and trans-platin bind to the major and minor grooves of DNA (via G, A, T, and C bases), while RNA binding is through G, U, A, and C bases with some degree of the pt-phosphate (PO(2)) interaction for both isomers and overall binding constants of K((cis-platin-DNA)) = 5.51 x 10(4) M(-1), K((trans-platin-DNA)) = 2.26 x 10(4) M(-1), K((cis-platin-RNA)) = 1.9 x 10(4) M(-1), and K((trans-platin-RNA)) = 1.75 x 10(4) M(-1). DNA and RNA aggregations occurred at high platin concentrations. No biopolymer conformational changes were observed upon cis- and trans-platin interactions, while DNA remains in the B-family, and RNA retains its A-family structure. The order of platin compound-polymer stability was cis-platin-DNA > trans-platin-DNA > cis-platin-RNA > trans-platin-RNA.

Effects of Mn2+ on oligonucleotide-gold nanoparticle hybrids for colorimetric sensing of Hg2+: improving colorimetric sensitivity and accelerating color change

In this paper, we present a simple and rapid colorimetric assay--using the polythymine oligonucleotide T(33), citrate-capped gold nanoparticles (AuNPs), and phosphate-buffer saline (PBS) in the presence of Mn(2+)--for the highly selective and sensitive detection of Hg(2+) in an aqueous solution. Citrate-capped AuNPs adsorbed on randomly coiled T(33) were dispersed well in PBS because of strong electrostatic repulsion between DNA molecules. In the presence of Hg(2+), the formation of Hg(2+)-T(33) complexes enabled the removal of T(33) molecules from the NP surface, resulting in salt-induced NP aggregation. However, the T(33)-capped AuNPs (T(33)-AuNPs) were dispersed in PBS solution after the addition of 1.0 microM Hg(2+), indicating that T(33)-AuNPs had poor colorimetric sensitivity toward Hg(2+). We uncovered that the addition of Mn(2+) to a solution containing 0.75 nM T(33)-AuNPs and 0.2x PBS resulted in an acceleration of the analysis time (within 5 min) and a 100-fold sensitivity improvement for the detection of Hg(2+). As a result, the present approach enables the analysis of Hg(2+) with a minimum detectable concentration that corresponds to 10 nM. This is probably attributed to that Mn(2+) binds strongly to the phosphate backbone of DNA, thereby accelerating Hg(2+)-induced aggregation of the T(33)-AuNPs. Because Mn(2+) can stabilize the folded structure of the Hg(2+)-T(33) complex, Hg(2+) facilitates the removal of T(33) from the NP surface in the presence of Mn(2+). This probe was successfully applied to the determination of Hg(2+) in pond water.

RNA binding to antioxidant flavonoids

Flavonoids are an interesting group of natural polyphenolic compounds that exhibit extensive bioactivities such as scavenging free radical, antitumor and antiproliferative effects. The anticancer and antiviral effects of these natural products are attributed to their potential biomedical applications. While flavonoids complexation with DNA is known, their bindings to RNA are not fully investigated. This study was designed to examine the interactions of three flavonoids; morin (Mor), apigenin (Api) and naringin (Nar) with yeast RNA in aqueous solution at physiological conditions, using constant RNA concentration (6.25 mM) and various pigment/RNA (phosphate) ratios of 1/120 to 1/1. FTIR, UV-visible spectroscopic methods were used to determine the ligand binding modes, the binding constant and the stability of RNA in flavonoid-RNA complexes in aqueous solution. Spectroscopic evidence showed major binding of flavonoids to RNA with overall binding constants of K(morin) = 9.150 x 10(3) M(-1), K(apigenin)=4.967 x 10(4) M(-1), and K(naringin)=1.144 x 10(4) M(-1). The affinity of flavonoid-RNA binding is in the order of apigenin>naringin>morin. No biopolymer secondary structural changes were observed upon flavonoid interaction and RNA remains in the A-family structure in these pigment complexes.

Fourier transform infrared microspectroscopy identifies symmetric PO(2)(-) modifications as a marker of the putative stem cell region of human intestinal crypts

Complex biomolecules absorb in the mid-infrared (lambda = 2-20 microm), giving vibrational spectra associated with structure and function. We used Fourier transform infrared (FTIR) microspectroscopy to "fingerprint" locations along the length of human small and large intestinal crypts. Paraffin-embedded slices of normal human gut were sectioned (10 microm thick) and mounted to facilitate infrared (IR) spectral analyses. IR spectra were collected using globar (15 microm x 15 microm aperture) FTIR microspectroscopy in reflection mode, synchrotron ( Collapse

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MESH Headings

• Biomarkers/analysis
• Humans
• Immunohistochemistry
• Intestinal Mucosa/cytology
• Principal Component Analysis
• Spectroscopy, Fourier Transform Infrared
• Stem Cells/cytology

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Grants

• BB/D010055/1 Biotechnology and Biological Sciences Research Council

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Affiliation(s)

Michael J Walsh Biomedical Sciences Unit, Department of Biological Sciences, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
Tariq G Fellous
Azzedine Hammiche
Wey-Ran Lin
Nigel J Fullwood
Olaug Grude
Fariba Bahrami
James M Nicholson
Marine Cotte
Jean Susini
Hubert M Pollock
Mairi Brittan
Pierre L Martin-Hirsch
Malcolm R Alison
Francis L Martin

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Collaborators Collapse

Degradation of DNA into 5'-monodeoxyribonucleotides in the presence of Mn(2+) ions

DNA is known to be aggregated by metal ions including Mn(2+) ions, but analysis of the aggregation process from a chemical viewpoint, which means identification of the product yielded during the process, has not been performed yet. On examination of the kinds of degraded materials that were in the supernatant obtained on centrifugation of a DNA mixture aggregated under conditions of 10 mM Mn(2+) ions ([Mn]/[P] = 46.3) at 70 degrees C for 1 h, the degradation products were found to be dAMP, dCMP, dGMP, and TMP. These dNMPs were purified by HPLC on TSKgel ODS-80Ts and identified by LC-TOF/MS. The degradation activity was lost on pretreatment of the DNA with a phenol-chloroform mixture, and the activity was recovered by pretreatment with a mixture of DMSO and a buffer containing surfactants. Mn(2+), Co(2+), Ni(2+), Cu(2+), Zn(2+), and Cd(2+), as transition element metal ions, were effective as to the degradation into dNMP. Mg(2+), Ca(2+), Sr(2+), and Ba(2+), as alkali earth element metal ions, were not effective as to the degradation. Monovalent anions such as Cl(-), CH(3)OO(-), and NO(3)(-) were found to increase the degradation rate. Sixty mug of the 120 mug of the starting DNA in 450 mul was degraded into dNMP on reaction for 1 h in the presence of 100 mM NaCl and 10 mM Mn(2+) ions. In this process, aggregation did not occur, and thus was not considered to be necessary for degradation. The degradation was found not to occur at pH 7.0, and to be very sensitive to pH. The OH(-) ion should have a critical role in cleavage of the phosphodiester linkages in this case. The dNMP obtained in the degradation process was found to be only 5'-NMP, based on the H(1)NMR spectra. This prosess should prove to be a new process for the production of 5'-dNMP in addtion to the exonuclease.

Interaction of tRNA with Safranal, Crocetin, and Dimethylcrocetin

Saffron is the red dried stigmas of Crocus sativus L. flowers and used both as a spice and as a drug in traditional therapeutic. The biological activity of saffron in modern medicine is in development. Its numerous applications as an anti-oxidant and anti-cancer agent are due to its secondary metabolites and their derivatives (safranal, crocins, crocetin, dimethylcrocetin). The aim of this study was to examine the interaction of transfer RNA with safranal, crocetin, and dimethylcrocetin in aqueous solution at physiological conditions. Constant tRNA concentration (6.25 mM) and various drug/tRNA (phosphate) molar ratios of 1/48 to 1/8 were used. FT-IR and UV-Visible difference spectroscopic methods have been applied to determine the drug binding mode, the binding constants and the effects of drug complexation on the stability and conformation of tRNA duplex. External binding mode was observed for safranal crocetin and dimethylcrocetin, with overall binding constants K(safranal) = 6.8 (+/- 0.34) x 10(3) M(-1), K(CRT) = 1.4 (+/- 0.31) x 10(4) M(-1), and K(DMCRT) = 3.4 (+/- 0.30) x 10(4) M(-1). Transfer RNA remains in the A-family structure, upon safranal, crocetin and dimethylcrocetin complexation.

Ca, Cd, Zn, and Their Ions Interacting with Cytosine: A Theoretical Study

Metal atoms play a major role in the chemical behavior of biological systems. In this work, known issues of the metal-base interactions, such as the stabilization of different tautomers of cytosine that could be incompatible with the DNA double helix, are researched using DFT methods. Ca-, Zn-, and Cd-cytosine in neutral and ionic forms were studied at the B3LYP/LANL2DZ level. Several neutral and ionic isomers were found within an interval of 10 kcal/mol of relative stability, with the most stable isomer in each group being a compound derived from the canonical isomer of cytosine, except for the dications where two iso-energetic isomers were found. Interatomic lengths from each metal atom to the nearest atoms in cytosine's ring were larger than 2 A, discouraging the possibility of a covalent interaction, as supported by additional evidence from molecular orbitals. The interaction between metal and cytosine, electrostatic in nature, is reinforced with the increase of the metal's nuclear charge. Additionally, the ionization energies of the metal-cytosine compounds exhibit a significant reduction (below 6 eV) compared with that of plain cytosine (8.7 eV), posing an interesting possibility with respect to the experimental determination of the photoelectron spectra of these compounds. Analyses of the energetics of the global reactions to form cationic species show that metal cations bind more strongly to neutral cytosine than to neutral metals. Metal dications form the most stable compounds with neutral cytosine, and the stabilities of these systems decrease as (Zn-cyt)2+ > (Cd-cyt)2+ > (Ca-cyt)2+. Aromaticities computed via the HOMA indexes also support the observation regarding the greater affinity of cytosine for metal cations.

DNA binding studies of novel Copper(II) complexes containing L-tryptophan as chiral auxiliary: in vitro antitumor activity of Cu-Sn2 complex in human neuroblastoma cells

Novel trinuclear complexes C23H31N6O6CuSn2Cl5 [1], C23H31N6O6CuZr2Cl5 [2], C23H31N6O6ZnSn2Cl5 [3], and C23H31N6O6ZnZr2Cl5 [4] were synthesized and characterized by spectroscopic (IR, 1H, 13C, 2D COSY, and 119Sn NMR, EPR, UV-vis, ESI-MS) and analytical methods. In complexes 1-4, the geometry of copper and zinc metal ions were described as square-based pyramidal with l-tryptophan coordinated to copper/zinc via carboxylate group while Sn/Zr was present in the hexacoordinate environment. The interaction of 1 and 2 with calf thymus DNA in Tris buffer was studied by electronic absorption titration, luminescence titration, cyclic voltammetry, circular dichroism, and viscometric measurements. The emission quenching of these complexes by [Fe(CN)6]4- depressed greatly when bound to DNA. Observed changes in the circular dichoric spectra of DNA in presence of 1 and 2 support the strong binding of complexes with DNA. The relative specific viscosity of DNA bound to 1 and 2 decreased, indicating that the complexes bind to DNA via covalent binding. The results reveal that the extent of DNA binding of 1 was greater than that of 2. To evaluate the mechanistic pathway of DNA inhibition, counting experiments and MTT assay were employed to assess the induction of apoptosis by 1. Western blot analysis of whole cell lysates and mitochondrial fractions with Bcl-2 and p-53 family proteins and caspase-3 colorimetry assay were also carried out on a human neuroblastoma cell line SY5Y.

Binding of oxovanadium ions to the major and minor grooves of DNA duplex: stability and structural models

Vanadate induces DNA strand breaks in cultured human fibroblasts at doses that are relative to the occupational exposure. Oxovanadium compounds also exert preventive effects against chemical carcinogenesis in animals and form complexes with DNA in vivo. This study was designed to examine the interaction of calf-thymus DNA with VO2+and VO3¯ions in aqueous solution at physiological pH, with a constant DNA concentration of 12.5 mmol/L and vanadium–DNA (phosphate) molar ratios (r) of 1:160 to 1:2. Capillary electrophoresis and Fourier transform infrared difference spectroscopy were used to determine the cation binding site, the binding constant, the helix stability, and DNA conformation in the oxovanadium–DNA complexes. Structural analysis showed that VO2+binds DNA through guanine and adenine N-7 atoms and the backbone PO2group with apparent binding constants of KG= 8.8 × 105(mol/L)–1and KA= 3.4 × 105(mol/L)–1. The VO3¯shows weaker binding through thymine, adenine, and guanine bases, with K = 1.9 × 104(mol/L)–1and no interaction with the backbone phosphate group. A partial B-to-A DNA transition occurred upon VO–DNA complexation, while DNA remains in the B-family structure in the VO3¯complexes.

Transfer RNA Binding to Human Serum Albumin: A Model for Protein–RNA Interaction

Protein-RNA complexation is essential in cell biological functions. Transfer RNAs are bound to aminoacyl-tRNA synthetases for the translation of the genetic code during protein synthesis, while ribonucleoproteins bind RNA in posttranscriptional regulation of gene expression. A recent report showed the interacton of human serum albumin (HSA) with DNA duplex, in which two binding sites with strong and weak association constants were detected. We now examine the interaction of tRNA with human serum albumin (HSA) in aqueous solution at physiological conditions, using a constant RNA concentration of 12.5 mM (phosphate) and various HSA contents of 0.04 to 0.6 mM. Affinity capillary electrophoresis and FTIR spectroscopic methods were used to determine the protein binding mode, the association constant, sequence preference, and the biopolymer secondary structural changes in the HSA-RNA complexes. Spectroscopic evidence showed two types of HSA-RNA complexes with an overall binding constant of K = 1.45 x 10(4) M(-1). The major binding sites were located on the G-C bases and the backbone PO2 group. The protein-RNA interaction stabilizes the HSA secondary structure, and no major alterations of A-RNA structure or protein conformation occurred.

Vibrational circular dichroism of matrix-assisted amino acid films in the mid-infrared region

Vibrational circular dichroism (VCD) spectra in the mid-infrared region of amino acid films are reported here for the first time. Amino acid films are formed from aqueous solutions with alpha-cyclodextrin (CD) serving as the matrix to facilitate the film formation. This film method eliminates the strong interfering water absorption seen in the solution study and makes it easier to measure the VCD in the 1800-1200 cm-1 region. VCD spectra for films of six amino acids, L-alanine, L-proline, L-methionine, Lhistidine, L-phenylalanine, and L-tryptophan, are obtained. For amino acids with low solubility (L-phenylalanine and L-tryptophan), VCD could not be measured in solution, so the film method is the only means of obtaining the VCD spectra for such amino acids. For amino acids with moderate solubility (L-alanine, L-proline, L-methionine, and L-histidine), VCD spectra are also obtained in the solution state and compared with their corresponding spectra in the film state. A good correlation is found between the film and solution spectra for both absorption and VCD. The VCD spectra of L-methionine, L-histidine, L-phenylalanine, and Ltryptophan are reported here in the mid-infrared region for the first time. The present study broadens the application range of the VCD technique and enhances its role in the detection and analysis of biologically important compounds.