IR and Raman study on the interactions of the 5'-GMP and 5'-CMP phosphate groups with Mg(II), Ca(II), Sr(II), Ba(II), Cr(III), Co(II), Cu(II), Zn(II), Cd(II), Al(III) and Ga(III)

DNA-Assisted Creation of a Library of Ultrasmall Multimetal/Metal Oxide Nanoparticles Confined in Silica

Supported ultrasmall metal/metal oxide nanoparticles (UMNPs) with sizes in the range of 1-5 nm exhibit unique properties in sensing, catalysis, biomedicine, etc. However, the metal-support and metal-metal precursor interactions were not as well controlled to stabilize the metal nanoparticles on/in the supports. Herein, DNA is chosen as a template and a ligand for the silica-supported UMNPs, taking full use of its binding ability to metal ions via either electrostatic or coordination interactions. UMNPs thus are highly dispersed in silica via self-assembly of DNA and DNA-metal ion interactions with the assistance of a co-structural directing agent (CSDA). A large number of metal ions are easily retained in the mesostructured DNA-silica materials, and their growth is controlled by the channels after calcination. Based on this directing concept, a material library, consisting of 50 mono- and 54 bicomponent UMNPs confined within silica and with narrow size distribution, is created. Theoretical calculation proves the indispensability of DNA with combination of several organics in the synthesis of ultrasmall metal nanoparticles. The Pt-silica and Pt/Ni-silica chosen from the library exhibit good catalytic performance for toluene combustion. This generalizable and straightforward synthesis strategy is expected to widen the corresponding applications of supported UMNPs.

Stimuli-Responsive Nucleotide-Amino Acid Hybrid Supramolecular Hydrogels

The ability to assemble chemically different gelator molecules into complex supramolecular hydrogels provides excellent opportunities to construct functional soft materials. Herein, we demonstrate the formation of hybrid nucleotide–amino acid supramolecular hydrogels. These are generated by the silver ion (Ag⁺)-triggered formation of silver–guanosine monophosphate (GMP) dimers, which undergo self-assembly through non-covalent interactions to produce nanofilaments. This process results in a concomitant pH reduction due to the abstraction of a proton from the guanine residue, which triggers the in situ gelation of a pH-sensitive amino acid, N-fluorenylmethyloxycarbonyl tyrosine (FY), to form nucleotide–amino acid hybrid hydrogels. Alterations in the supramolecular structures due to changes in the assembly process are observed, with the molar ratio of Ag:GMP:FY affecting the assembly kinetics, and the resulting supramolecular organisation and mechanical properties of the hydrogels. Higher Ag:GMP stoichiometries result in almost instantaneous gelation with non-orthogonal assembly of the gelators, while at lower molar ratios, orthogonal assembly is observed. Significantly, by increasing the pH as an external stimulus, nanofilaments comprising FY can be selectively disassembled from the hybrid hydrogels. Our results demonstrate a simple approach for the construction of multicomponent stimuli-responsive supramolecular hydrogels with adaptable network and mechanical properties.

Environmentally benign pH-responsive cytidine-5′-monophosphate molecule-mediated akaganeite (5′-CMP-β-FeOOH) soft supramolecular hydrogels induced by the puckering of ribose sugar with efficient loading/release capabilities

A novel synthetic protocol for environmentally benign 5′-CMP-β-FeOOH soft hydrogels exhibiting a rapid pH-responsive reversible sol–gel transition, efficient adsorption and slow release capabilities is reported.

Spectroscopic Studies on Photoinduced Reactions of the Anticancer Prodrug, trans,trans,trans-[Pt(N3 )2 (OH)2 (py)2 ]

The photodecomposition mechanism of trans,trans,trans-[Pt(N3 )2 (OH)2 (py)2 ] (1, py=pyridine), an anticancer prodrug candidate, was probed using complementary Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR), transient electronic absorption, and UV/Vis spectroscopy. Data fitting using Principal Component Analysis (PCA) and Multi-Curve Resolution Alternating Least Squares, suggests the formation of a trans-[Pt(N3 )(py)2 (OH/H2 O)] intermediate and trans-[Pt(py)2 (OH/H2 O)2 ] as the final product upon 420 nm irradiation of 1 in water. Rapid disappearance of the hydroxido ligand stretching vibration upon irradiation is correlated with a -10 cm-1 shift to the antisymmetric azido vibration, suggesting a possible second intermediate. Experimental proof of subsequent dissociation of azido ligands from platinum is presented, in which at least one hydroxyl radical is formed in the reduction of PtIV to PtII . Additionally, the photoinduced reaction of 1 with the nucleotide 5'-guanosine monophosphate (5'-GMP) was comprehensively studied, and the identity of key photoproducts was assigned with the help of ATR-FTIR spectroscopy, mass spectrometry, and density functional theory calculations. The identification of marker bands for some of these photoproducts (e.g., trans-[Pt(N3 )(py)2 (5'-GMP)] and trans-[Pt(py)2 (5'-GMP)2 ]) will aid elucidation of the chemical and biological mechanism of anticancer action of 1. In general, these studies demonstrate the potential of vibrational spectroscopic techniques as promising tools for studying such metal complexes.

Investigation of the roles of trace elements during hepatitis C virus infection using protein-protein interactions and a shortest path algorithm

BACKGROUND

Hepatitis is a type of infectious disease that induces inflammation of the liver without pinpointing a particular pathogen or pathogenesis. Type C hepatitis, as a type of hepatitis, has been reported to induce cirrhosis and hepatocellular carcinoma within a very short amount of time. It is a great threat to human health. Some studies have revealed that trace elements are associated with infection with and immune rejection against hepatitis C virus (HCV). However, the mechanism underlying this phenomenon is still unclear.

METHODS

In this study, we aimed to expand our knowledge of this phenomenon by designing a computational method to identify genes that may be related to both HCV and trace element metabolic processes. The searching procedure included three stages. First, a shortest path algorithm was applied to a large network, constructed by protein-protein interactions, to identify potential genes of interest. Second, a permutation test was executed to exclude false discoveries. Finally, some rules based on the betweenness and associations between candidate genes and HCV and trace elements were built to select core genes among the remaining genes.

RESULTS

12 lists of genes, corresponding to 12 types of trace elements, were obtained. These genes are deemed to be associated with HCV infection and trace elements metabolism.

CONCLUSIONS

The analyses indicate that some genes may be related to both HCV and trace element metabolic processes, further confirming the associations between HCV and trace elements. The method was further tested on another set of HCV genes, the results indicate that this method is quite robustness.

GENERAL SIGNIFICANCE

The newly found genes may partially reveal unknown mechanisms between HCV infection and trace element metabolism. This article is part of a Special Issue entitled "System Genetics" Guest Editor: Dr. Yudong Cai and Dr. Tao Huang.

Fourier Transform Infrared spectroscopy discloses different types of cell death in flow cytometrically sorted cells

Fourier Transform Infrared (FTIR) spectroscopy is a label free methodology showing promise in characterizing different types of cell death. Cervical adenocarcinoma (HeLa) and African monkey kidney (Vero) cells were treated with a necrosis inducer (methanol), novel apoptotic inducers (diphenylphosphino gold (I) complexes) and positive control, auranofin. Following treatment, cells stained with annexin-V and propidium iodide were sorted using a Fluorescence Activated Cell Sorter (FACS Aria) to obtain populations consisting of either viable, necrotic or apoptotic cells. Transmission Electron Microscopy confirmed successful sorting of all three populations. Four bands were identified which could discriminate between viable and necrotic cells namely 989 cm(-1), 2852 cm(-1), 2875 cm(-1) and 2923 cm(-1). In HeLa cells viable and induced apoptosis could be distinguished by 1294 cm(-1), while four bands were different in Vero cells namely; 1626 cm(-1), 1741 cm(-1), 2852 cm(-1) 2923 cm(-1). Principal Component Analysis showed separation between the different types of cell death and the loadings plots indicated an increase in an additional band at 1623 cm(-1) in dead cells. FTIR spectroscopy can be developed into an invaluable tool for the assessment of specific types of chemically induced cell death with notably different molecular signatures depending on whether the cells are cancerous and mechanism of cell death.

Cellular injury evidenced by impedance technology and infrared microspectroscopy

Fourier Transform Infrared (FTIR) spectroscopy is finding increasing biological application, for example in the analysis of diseased tissues and cells, cell cycle studies and investigating the mechanisms of action of anticancer drugs. Cancer treatment studies routinely define the types of cell-drug responses as either total cell destruction by the drug (all cells die), moderate damage (cell deterioration where some cells survive) or reversible cell cycle arrest (cytostasis). In this study the loss of viability and related chemical stress experienced by cells treated with the medicinal plant, Plectranthus ciliatus, was investigated using real time cell electronic sensing (RT-CES) technology and FTIR microspectroscopy. The use of plants as medicines is well established and ethnobotany has proven that crude extracts can serve as treatments against various ailments. The aim of this study was to determine whether FTIR microspectroscopy would successfully distinguish between different types of cellular injury induced by a potentially anticancerous plant extract. Cervical adenocarcinoma (HeLa) cells were treated with a crude extract of Pciliatus and cells monitored using RT-CES to characterize the type of cellular responses induced. Cell populations were then investigated using FTIR microspectroscopy and statistically analysed using One-way Analysis of Variance (ANOVA) and Principal Component Analysis (PCA). The plant extract and a cancer drug control (actinomycin D) induced concentration dependent cellular responses ranging from nontoxic, cytostatic or cytotoxic. Thirteen spectral peaks (915cm(-)(1), 933cm(-)(1), 989cm(-)(1), 1192cm(-)(1), 1369cm(-)(1), 1437cm(-)(1), 1450cm(-)(1), 1546cm(-)(1), 1634cm(-)(1), 1679cm(-)(1) 1772cm(-)(1), 2874cm(-)(1) and 2962cm(-)(1)) associated with cytotoxicity were significantly (p value<0.05, one way ANOVA, Tukey test, Bonferroni) altered, while two of the bands were also indicative of early stress related responses. In PCA, poor separation between nontoxic and cytostatic responses was evident while clear separation was linked to cytotoxicity. RT-CES detected morphological changes as indicators of cell injury and could distinguish between viable, cytostatic and cytotoxic responses. FTIR microspectroscopy confirmed that cytostatic cells were viable and could still recover while also describing early cellular stress related responses on a molecular level.

DNA damage induced by carbon ions (C³⁺) beam accessed by independent component analysis of infrared spectra

PURPOSE

To understand the degradation processes and role of secondary species on deoxyribonucleic acid (DNA)-damaged fragments as a result of irradiation with energetic ions.

MATERIALS AND METHODS

Damage caused to DNA thin films as a result of exposure to 4 keV carbon ions beam was accessed by analyzing the infrared spectra, obtained in situ for different irradiation times, with both bi-dimensional (2D) correlation spectroscopy and independent component analysis (ICA).

RESULTS

Results indicated that deoxyribose, phosphate and base groups of the DNA molecule were being damaged and new reaction products as oxime and furfural groups are being formed.

CONCLUSIONS

Damage on DNA bases is consistent with the formation of oxime products which react with DNA deoxyribose products forming furfural groups and confirming that DNA damage is caused by direct and indirect processes.

Exploiting the interactions of PNA-DNA films with Ni2+ ions: detection of nucleobase mismatches and electrochemical genotyping of the single-nucleotide mismatch in apoE 4 related to Alzheimer's disease

The presence of Ni(2+) enables us to distinguish the presence of single-nucleotide mismatches in PNA (peptide nucleic acids)-DNA films on gold electrodes by electrochemical impedance spectroscopy (EIS). With the help of a modified Randles' equivalent circuit, differences in the charge transfer resistance (ΔR(CT)) before and after the addition of Ni(2+) are a diagnostic measure for the presence of single-nucleotide mismatch. The approach works under real-life conditions with concentrations of the DNA target strand down to 10 fM, and a PNA capture probe is used to genotype the single-nucleotide mismatch in apoE 4 related to Alzheimer's disease (AD).

Electrochemical impedance study of the interaction of metal ions with unlabeled PNA

The interactions of the metal ions Mg(2+), Zn(2+), Ni(2+), and Co(2+) with thin films of peptide nucleic acids (PNAs) were studied by electrochemical impedance spectroscopy (EIS), and the results show that Zn(2+), Ni(2+) and Co(2+) interacted favorably with the PNA film involving the backbone and the nucleobases with the exception of Mg(2+) for which the interaction with the backbone appears to be dominant.

Exploiting the interaction of metal ions and peptide nucleic acids-DNA duplexes for the detection of a single nucleotide mismatch by electrochemical impedance spectroscopy

The interaction of the metal ions Mg(2+), Zn(2+), Ni(2+), and Co(2+) with DNA-peptide nucleic acid (PNA) films on a gold surface is studied by electrochemical impedance spectroscopy in the presence of [Fe(CN)(6)](3-/4-) as the redox probe. Impedance data were analyzed with the help of a modified Randles' equivalent circuit. Changes in the charge-transfer resistance, R(CT), decreases in the order of Ni(2+) > Co(2+) > Zn(2+) > Mg(2+). We interpret these results in terms of stronger interactions for Ni(2+) with the DNA-PNA film compared to the other metal ions, potentially involving interactions with the nucleobases, presumably with the N7 of purines or the N3 of pyrimidines. On the basis of these observations, Ni(2+) was chosen to probe the detection of a C-T mismatch in 15-mer PNA-DNA films. Using Ni(2+), it is possible to detect a single C-T mismatch. The resulting DeltaR(CT) is larger for the PNA-DNA hybrid compared to that for the identical 15-mer DNA-DNA hybrid.

Interaction study of a lysozyme-binding aptamer with mono- and divalent cations by ACE

Binding between an aptamer and its target is highly dependent on the conformation of the aptamer molecule, this latter seeming to be affected by a variety of cations. As only a few studies have reported on the interactions of monovalent or divalent cations with aptamers, we describe herein the use of ACE in its mobility shift format for investigating interactions between various monovalent (Na+, K+, Cs+ or divalent (Mg2+, Ca2+, Ba2+) cations and a 30-mer lysozyme-binding aptamer. This study was performed in BGEs of different natures (phosphate and MOPS buffers) and ionic strengths. First, the effective charges of the aptamer in 30 mM ionic strength phosphate and MOPS (pH 7.0) were estimated to be 7.4 and 3.6, respectively. Then, corrections for ionic strength and counterion condensation effects were performed for all studies. The effective mobility shift was attributed not only to these effects, but also to a possible interaction with the buffer components (binary or ternary complexes) as well as possible conformational changes of the aptamer. Finally, apparent binding constants were calculated for divalent cations with mathematical linearization methods, and the influence of the nature of the BGE was evidenced.

The effect of spermine concentration on the solution structure of complexes formed in copper(II)/adenosine 5'-triphosphate/phosphoserine system

Quaternary systems of copper(II) complexes with adenosine 5'-triphosphate, O-phospho L-serine and with equimolar or excessive amount of spermine have been investigated. The studies have been performed in aqueous solution. Types of complexes and the overall stability constants have been determined using the potentiometric method with computer analysis of the data. On the basis of the results of spectroscopic studies (nuclear magnetic resonance, visible, circular dichroism, Raman, infrared and electron paramagnetic resonance spectroscopies) as well as equilibrium studies, the mode of interactions has been proposed. The reaction centers in the systems studied are the phosphate, carboxyl and amine groups from phosphorylated serine, heterocyclic nitrogen atom from purine ring and phosphate groups from adenosine 5'-triphosphate as well as amine groups from polyamine. The influence of change in the concentration of the polyamine (spermine) on the mode of coordination is discussed. It has been shown that in the physiological conditions an increase in the polyamine concentration changes the mode of metal bonding in the CuH(3)(ATP)(Ser-P)(Spm) complexes (isomer I - coordination {2N,O(x)}, isomer II - coordination {3N,O(x)} and significant differences in sites of interaction).

Interaction of metal ions and DNA films on gold surfaces: an electrochemical impedance study

Electrochemical impedance spectroscopy (EIS) has been used to investigate the effects of a number of metal ions with DNA films on gold surfaces exploiting [Fe(CN)6](3-/4-) as a solution-based redox probe. Alkaline earth metal ions Mg2+, Ca2+, trivalent Al3+, La3+ and divalent transition metal ions Ni2+, Cu2+, Cd2+ and Hg2+ have been selected in this study and the results are compared with previous studies on the effects of Zn2+ on the EIS of DNA films. All experimental results were evaluated with the help of equivalent circuits which allowed the extraction of resistive and capacitive components. For all metal ions studied here, addition of the metal ions causes a decrease in the charge transfer resistance. The difference of charge transfer resistance (DeltaR(ct)) of ds-DNA films in the presence and absence of the various metal ions is different and particular to any given metal ion. In addition, we studied the EIS of ds-DNA films containing a single A-C mismatch in the presence and absence of Ca2+, Zn2+, Cd2+ and Hg2+. DeltaR(ct) values for ds-DNA films with a single A-C mismatch is smaller than those of fully matched ds-DNA films.

Mechanistic study of protein phosphatase-1 (PP1), a catalytically promiscuous enzyme

The reaction catalyzed by the protein phosphatase-1 (PP1) has been examined by linear free energy relationships and kinetic isotope effects. With the substrate 4-nitrophenyl phosphate (4NPP), the reaction exhibits a bell-shaped pH-rate profile for kcat/KM indicative of catalysis by both acidic and basic residues, with kinetic pKa values of 6.0 and 7.2. The enzymatic hydrolysis of a series of aryl monoester substrates yields a Brønsted beta(lg) of -0.32, considerably less negative than that of the uncatalyzed hydrolysis of monoester dianions (-1.23). Kinetic isotope effects in the leaving group with the substrate 4NPP are (18)(V/K) bridge = 1.0170 and (15)(V/K) = 1.0010, which, compared against other enzymatic KIEs with and without general acid catalysis, are consistent with a loose transition state with partial neutralization of the leaving group. PP1 also efficiently catalyzes the hydrolysis of 4-nitrophenyl methylphosphonate (4NPMP). The enzymatic hydrolysis of a series of aryl methylphosphonate substrates yields a Brønsted beta(lg) of -0.30, smaller than the alkaline hydrolysis (-0.69) and similar to the beta(lg) measured for monoester substrates, indicative of similar transition states. The KIEs and the beta(lg) data point to a transition state for the alkaline hydrolysis of 4NPMP that is similar to that of diesters with the same leaving group. For the enzymatic reaction of 4NPMP, the KIEs are indicative of a transition state that is somewhat looser than the alkaline hydrolysis reaction and similar to the PP1-catalyzed monoester reaction. The data cumulatively point to enzymatic transition states for aryl phosphate monoester and aryl methylphosphonate hydrolysis reactions that are much more similar to one another than the nonenzymatic hydrolysis reactions of the two substrates.

Nucleic acid and nucleotide-mediated synthesis of inorganic nanoparticles

Since the advent of practical methods for achieving DNA metallization, the use of nucleic acids as templates for the synthesis of inorganic nanoparticles (NPs) has become an active area of study. It is now widely recognized that nucleic acids have the ability to control the growth and morphology of inorganic NPs. These biopolymers are particularly appealing as templating agents as their ease of synthesis in conjunction with the possibility of screening nucleotide composition, sequence and length, provides the means to modulate the physico-chemical properties of the resulting NPs. Several synthetic procedures leading to NPs with interesting photophysical properties as well as studies aimed at rationalizing the mechanism of nucleic acid-templated NP synthesis are now being reported. This progress article will outline the current understanding of the nucleic acid-templated process and provides an up to date reference in this nascent field.

In situ evaluation of heavy metal-DNA interactions using an electrochemical DNA biosensor

Heavy metal ions, lead, cadmium and nickel, are well known carcinogens with natural different origins and their direct mode of action is still not fully understood. A dsDNA-electrochemical biosensor, employing differential pulse voltammetry, was used for the in situ evaluation of Pb2+, Cd2+ and Ni2+ interaction with dsDNA. The results confirm that Pb2+, Cd2+ and Ni2+ bind to dsDNA, and that this interaction leads to different modifications in the dsDNA structure. These modifications were electrochemically recognized as changes in the oxidation peaks of guanosine and adenosine bases. Using homopolynucleotides of guanine and adenine it has been proved that the interaction between Pb2+ and DNA causes oxidative damage and preferentially takes place at adenine-containing segments, with the formation of 2,8-dihydroxyadenine, the oxidation product of adenine residues and a biomarker of DNA oxidative damage. The Pb2+ bound to dsDNA can still undergo oxidation. The interaction of Cd2+ and Ni2+ causes conformational changes, destabilizing the double helix, which can enable the action of other oxidative agents on DNA.

Kinetic isotope effects for alkaline phosphatase reactions: implications for the role of active-site metal ions in catalysis

Enzyme-catalyzed phosphoryl transfer reactions have frequently been suggested to proceed through transition states that are altered from their solution counterparts, with the alterations presumably arising from interactions with active-site functional groups. In particular, the phosphate monoester hydrolysis reaction catalyzed by Escherichia coli alkaline phosphatase (AP) has been the subject of intensive scrutiny. Recent linear free energy relationship (LFER) studies suggest that AP catalyzes phosphate monoester hydrolysis through a loose transition state, similar to that in solution. To gain further insight into the nature of the transition state and active-site interactions, we have determined kinetic isotope effects (KIEs) for AP-catalyzed hydrolysis reactions with several phosphate monoester substrates. The LFER and KIE data together provide a consistent picture for the nature of the transition state for AP-catalyzed phosphate monoester hydrolysis and support previous models suggesting that the enzymatic transition state is similar to that in solution. Moreover, the KIE data provides unique information regarding specific interactions between the transition state and the active-site Zn2+ ions. These results provide strong support for a model in which electrostatic interactions between the bimetallo Zn2+ site and a nonbridging phosphate ester oxygen atom make a significant contribution to the large rate enhancement observed for AP-catalyzed phosphate monoester hydrolysis.

The role of metal ion binding in generating 8-hydroxy-2'-deoxyguanosine from the nucleoside 2'-deoxyguanosine and the nucleotide 2'-deoxyguanosine-5'-monophosphate

The metal ions Cu(II), Fe(II), and Cr(III) were allowed to react with H(2)O(2) in the presence of either the mononucleoside 2'-deoxyguanosine (dG) or the mononucleotide 2'-deoxyguanosine-5'-monophosphate (dGMP). The percentage of reacted dG or dGMP that formed the oxidative damage marker 8-hydroxy-2'-deoxyguanosine (8-OH-dG) was monitored. Oxidative damage from reactions involving Cu(II) appear dependent on an interaction between copper and N7 on the guanine base. Any interactions involving the phosphate group have little additional effect on overall oxidative damage or 8-OH-dG production. Reactions involving Fe(II) seem very dependent on an interaction that may involve both N7 on the guanine base and the phosphate group. This interaction may slow oxidation of Fe(II) to Fe(III) in solution, keeping iron in a readily available form to undergo the Fenton reaction. Chromium(III) appears to interact with the phosphate group of dGMP, resulting in significant overall oxidative damage. However, production of 8-OH-dG appears to be very dependent on the ability of Cr(III) to interact with N7 on the guanine base, an interaction that seems to be weak for both the mononucleoside and mononucleotide.

Quantification of single-stranded nucleic acid and oligonucleotide interactions with metal ions by affinity capillary electrophoresis: part I

The interactions between oligonucleotides and inorganic cations have been measured by capillary zone electrophoresis. With increasing concentrations of divalent cations (Ca(2+), Mg(2+), Mn(2+) and Ni(2+)) in the running buffer, the migration behavior was evaluated by calculation of the binding constants. Besides these fundamental studies of binding equilibria, different buffer components, tris(hydroxymethyl)aminomethane and 3-(N-morpholino)propanesulfonic acid, have been investigated and their effects on metal ion binding quantified.