Voltammetric study of the interaction of ciprofloxacin-copper with nucleic acids and the determination of nucleic acids

The behavior of the ciprofloxacin (CPFX) complex with copper, Cu(II)L₂, at a mercury electrode has been investigated in borax–boric acid buffer. The adsorption phenomena were observed by linear sweep voltammetry. The mechanism of the electrode reaction was found to be reduction of Cu(II)L₂ adsorbed on the surface of the electrode by an irreversible charge transfer to metal amalgam, Cu(0)(Hg). In the presence of DNA, the formation of the electrochemically non-active complexes Cu(II)L₂–DNA results in the decrease of the equilibrium concentration of Cu(II)L₂ and its peak current. Under the optimum conditions, the decrease of the peak current is proportional to DNA concentration. The linear ranges are 6.67×10⁻⁸ to 1.20×10⁻⁵ g ml⁻¹ for calf thymus DNA (ctDNA), 3.30×10⁻⁸ to 2.33×10⁻⁶ g ml⁻¹ for fish sperm DNA (fsDNA) and 1.0×10⁻⁸ to 1.2×10⁻⁶ g ml⁻¹ for yeast RNA. The detection limits are 5.00×10⁻⁹, 3.00×10⁻⁹ and 2.50×10⁻⁹ g ml⁻¹, respectively. This method exhibits good recovery and high sensitivity.     

Alkylation of nucleic acids by the antitumor agent COMC

[reaction: see text]. Mass spectral data are presented indicating that the antitumor agent 2-crotonyloxymethyl-2-cyclohexenone (COMC) is capable of alkylating oligonucleotides via a mechanism involving an electrophilic exocyclic enone intermediate. Under physiological conditions, the exocyclic enone is likely the glutathionylated 2-exomethylenecyclohexenone. This supports a recent hypothesis that the antitumor activity of COMC arises from alkylation of nucleic acids and/or proteins critical to cell function and not from competitive inhibition of glyoxalase I by an adduct of COMC and glutathione.     

The heterogeneity of the glycosylation of alpha-1-acid glycoprotein between the sera and synovial fluid in rheumatoid arthritis

Alpha-1-acid glycoprotein (AGP) is a plasma glycoprotein produced by the liver that undergoes increased production and altered glycosylation in several physiological and pathological conditions including rheumatoid arthritis. To date, although present in the synovial fluid of rheumatoid arthritis patients, there has been no evidence for the separate extra-hepatic production of AGP. This study indicates that there could be a localized production of AGP in rheumatoid synovial fluid by demonstrating that the glycosylation patterns of AGP differed between the serum and synovial fluid in the same rheumatoid patient. Serum AGP was largely composed of fucosylated tri- and tetra-antennary oligosaccharide chains while the synovial fluid contained mainly bi-antennary chains that were fucosylated to a lesser extent. This structural heterogeneity of glycosylation resulted in functional diversity; serum but not synovial AGP is able to inhibit binding to the cell adhesion molecule E-selectin through expression of antigen sialyl Lewis X.     

Mass spectrometric proteome analyses of synovial fluids and plasmas from patients suffering from rheumatoid arthritis and comparison to reactive arthritis or osteoarthritis

Differential proteome analysis is used to study body fluids from patients suffering from rheumatoid arthritis (RA), reactive arthritis (reaA) or osteoarthritis (OA). Mass spectrometric structure characterization of gel-separated proteins provided a detailed view of the protein-processing events that lead to distinct protein species present in the respective body fluids. (i) Fibrin(ogen) beta-chain degradation products, presumably plasmin-derived, appeared solely in synovial fluids (SF) from both patient collectives, (ii) calgranulin B (MRP14) was exclusively identified in SF samples derived from 5 out of 6 patients suffering from RA. Calgranulin B was not observed in synovial fluids from OA patients, nor in plasmas from either patient group. In all cases where calgranulin B was detected, calgranulin C was identified as well. (iii) Serum amyloid A protein spots were determined in plasmas and synovial fluids from patients with RA, but not in patients with OA. In addition to disease-relevant differences, interindividual differences in haptoglobin patterns of the patients under investigation were observed. Hence, in-depth proteome analysis of body fluids has proven effective for identification of multiple molecular markers and determination of associated protein structure modifications, that are thought to play a role for specifically determining a defined pathological state of diseased joints.     

In silico targeting PAD4 for the treatment of rheumatoid arthritis

Structural Chemistry - Rheumatoid arthritis (RA) is an autoimmune disorder that causes chronic inflammation with periodic bursts of activity in multiple synovial joints which lead to irreversible...     

Analysis and purification of peptide nucleic acids by denaturing PAGE

A flexible and convenient protocol for the analysis and purification of peptide nucleic acid (PNA) oligomers and PNA-peptide chimeras by denaturing PAGE is described. Vertical slab gel electrophoresis, 26% in polyacrylamide and 8 M urea at pH 3, was suitable for analysis of oligomers ranging in size from tetramers (4-mers) to tetradodecamers (24-mers). Single-base resolution of oligomers was achieved and separations are generally superior to those given by standard RP-HPLC techniques. The separation of a related series of PNA oligomers showed the distance migrated was linearly dependent on the logarithm of the molecular weight. The migration of oligomers through the gel is dependent on the number of basic functional groups present, such as amino groups, and the A and C content of the oligomer. PNAs are amenable to detection by UV-shadowing technique illuminated at 260 nm or Coomassie blue staining, both with similar, sub-microgram per band detection limits.     

Study on the interaction between nucleic acids and cationic surfactants

The interactions of nucleic acids and cationic surfactants (cetylpyridine bromide (CPB) and cetyltrimethylammonium bromide (CTMAB)) in aqueous solution have been studied using the techniques of resonance light scattering (RLS) spectroscopy, the absorption spectroscopy, zeta potential assay and NMR assignment measurement. It is considered that CPB or CTMAB can assemble on the surface of nucleic acid via electrostatic and hydrophobic forces, which results in the formation of large associate of nucleic acid-cationic surfactant and RLS enhancement of nucleic acid. Besides these forces, the pi-pi stacking force between CPB and nucleic acid also exists in the associate. In comparison with CTMAB, CPB has larger enhancement on RLS of nucleic acid, which is attributed to that the enhancement of the former is only due to the absorption of the bases of nucleic acid, while the enhancement of the latter is own to the synergetic resonance caused by the absorption of both bases of nucleic acid and the pyridyl in CPB. These results have important implication for understanding the influence of surfactants on nucleic acid functionality in life science.     

UV- and visible-excited fluorescence of nucleic acids separated by capillary electrophoresis

UV- and visible-excited fluorescence detection strategies were compared for nucleic acids separated by capillary electrophoresis (CE). A dual-polymer sieving matrix consisting of hydroxypropylmethylcellulose and poly(vinylpyrrolidone) was used to separate DNA fragments from a 100-base pair ladder and RNA from individual cells. Two nucleic acid dyes, SYBR Gold and SYBR Green I, were evaluated for their performance at both UV (275 nm) and visible (488 nm) excitation wavelengths. While SYBR Gold-bound RNA from single cells yielded a substantially reduced UV-excited signal compared to that with visible excitation (as expected), the sensitivity of SYBR Gold-bound double-stranded DNA was comparable for UV and Vis excitation wavelengths. This study reveals the first demonstration of using SYBR Gold dyes for DNA detection following separation with CE and also the first example of SYBR-based detection of RNA sampled and separated from individual cells.     

Label-free detection of nucleic acids by turn-on and turn-off G-quadruplex-mediated fluorescence

In this study we have used two fluorescent probes, tetrakis(diisopropylguanidino)-zinc-phthalocyanine (Zn-DIGP) and N-methylmesoporphyrin IX (NMM), to monitor the reassembly of “split” G-quadruplex probes on hybridization with an arbitrary “target” DNA. According to this approach, each split probe is designed to contain half of a G-quadruplex-forming sequence fused to a variable sequence that is complementary to the target DNA. Upon mixing the individual components, both base-pairing interactions and G-quadruplex fragment reassembly result in a duplex–quadruplex three-way junction that can bind to fluorescent dyes in a G-quadruplex-specific way. The overall fluorescence intensities of the resulting complexes were dependent on the formation of proper base-pairing interactions in the duplex regions, and on the exact identity of the fluorescent probe. Compared with samples lacking any “target” DNA, the fluorescence intensities of Zn-DIGP-containing samples were lower, and the fluorescence intensities of NMM-containing samples were higher on addition of the target DNA. The resulting biosensors based on Zn-DIGP are therefore termed “turn-off” whereas the biosensors containing NMM are defined as “turn-on”. Both of these biosensors can detect target DNAs with a limit of detection in the nanomolar range, and can discriminate mismatched from perfectly matched target DNAs. In contrast with previous biosensors based on the peroxidase activity of heme-bound split G-quadruplex probes, the use of fluorescent dyes eliminates the need for unstable sensing components (H₂O₂, hemin, and ABTS). Our approach is direct, easy to conduct, and fully compatible with the detection of specific DNA sequences in biological fluids. Having two different types of probe was highly valuable in the context of applied studies, because Zn-DIGP was found to be compatible with samples containing both serum and urine whereas NMM was compatible with urine, but not with serum-containing samples.     

Interaction of cetylpyridine bromide with nucleic acids and determination of nucleic acids at nanogram levels based on the enhancement of resonance Rayleigh light scattering

Resonance Rayleigh light scattering (RRLS) spectra of cetylpyridine bromide (CPB)-nucleic acid system and their analytical application have been first studied. The effective factors and optimum conditions of the reaction have been investigated. After CPB and nucleic acid are mixed together, a new absorption peak located at 300 nm appeared, which is due to the formation of new ion associate of CPB-nucleic acid. The new associate can result in two apparent RRLS peaks at 310-400 and 460-480 nm. The RRLS peak of the corrected spectra located at 290-350 nm, which indicate that the RRLS is originated from the absorption of CPB-nucleic acid associate. The peak at 460-480 nm disappears in the corrected RRLS spectra, which indicated that this peak is originated from the strong line emission of the Xe lamp. Under the optimum conditions, the enhanced intensity of RRLS is proportional to the concentration of nucleic acid in the range of 5.0 x 10(-9)-5.0 x 10(-5) g ml(-1) for calf thymus DNA (ctDNA), 1.0 x 10(-8)-4.0 x 10(-5) g ml(-1) for fish sperm DNA (fsDNA) and 1.0 x 10(-8)-5.0 x 10(-5) g ml(-1) for yeast RNA (yRNA). The detection limits (S/N = 3) are 4.3, 8.7 and 7.4 ng ml(-1), respectively. Synthetic samples were determined satisfactorily.     

Molecular orbital calculations on the conformation of nucleic acids and their constituents

The conformational properties of the furanose ring of purine- and pyrimidine--nucleosides and-nucleotides are studied quantum-mechanically with the help of the PCILO method, using the pseudorotational concept. The computations point to the existence of two stable conformational zones centered around the C(3)-endo and C(2)-endo conformations which in the isolated furanose ring are separated by barriers of the order of 4 kcal/mole. In nucleosides one of the barriers (the one running through the O(1)-exo-C(2)-exo path) becomes very high. A detailed study is made of the relation between the phase angle of pseudorotation, P, and the torsion angle about the glycosyl bond, _CN. A very satisfactory agreement with the available experimental data is observed.

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Zusammenfassung Die Konformationseigenschaften des Furanoserings in -Nucleosiden und Nucleotiden von Purin und Pyrimidin werden nach der PCILO-Methode unter Berücksichtigung der pseudorotatorischen Betrachtungsweise studiert. Die Rechnung läßt auf die Existenz zweier stabiler Konformationszonen schließen, die in der Umgebung der C(2)-endo und der C(3)-endo Konformationen liegen, und die im isolierten Furanosering durch Energiebarrieren der Größenordnung von 4 kcal/mol voneinander getrennt sind. In Nucleosiden wird eine der Barrieren (die durch den Weg O(1)-exo-C(2)-exo gekennzeichnete) sehr hoch. Die Relation zwischen dem Phasenwinkel der Pseudorotation, P, und dem Drehwinkel um die Glycosylbindung, _CN, wird einer eingehenden Untersuchung unterworfen. Man beobachtet eine sehr zufriedenstellende Übereinstimmung mit den verfügbaren experimentellen Daten.

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Résumé Les propriétés conformationnelles du noyau furanose des -nucleosides et nucleotides des purines et pyrimidines sont étudiées par la méthode PCILO en faisant appel au concept de la pseudorotation. Les calculs indiquent l'existence de deux zones de conformations stables, centrées autour des conformations C(2)-endo et C(3)-endo, qui sont dans le sucre isolé séparées par des barrières de l'ordre de 4 kcal/mole. Dans les nucleosides, l'une de ces barrières (celle qui passe par le chemin O(1)-exo-C(2)-exo) devient très élevée. Une étude détaillée est effectuée sur la relation entre l'angle de phase de la pseudorotation P et l'angle de torsion autour de la liaison glycosylique, _CN. Un excellent accord avec les données expérimentales disponibles est observé.

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This research was supported by the R.C.P. 173 and the A.T.P. A 655-2303 of the C.N.R.S.     

The point-of-care-testing of nucleic acids by chip,cartridge and paper sensors

Point-of-care nucleic acid testing (POCNAT) has played an important role in the outbreak of infectious diseases (e.g., COVID-19) over recent years. POCNAT aims to realize the rapid, simple and automatic detection of nucleic acid. Thanks to the development of manufacturing technology, electronic information technology, artificial intelligence technology, and biological information technology in recent years, the development of the POCNAT device has led to significant advancement. Instead of the normal nucleic acid detection methods used in the laboratory, some novel experimental carriers have been applied, such as chips, cartridges and papers. The application of these experimental carriers has realized the automation and integration of nucleic acid detection. The entire process of nucleic acid detection is normally divided into three steps (nucleic acid extraction, target amplification and signal detection). All of the reagents required by the process can be pre-stored on these experimental carriers, without unnecessary manual operation. Furthermore, all of the processes are carried out in this experimental carrier, with the assistance of a specific control device. Although they are complicated to manufacture and precise in design, their application provides a significant step forwards in nucleic acid detection and realizes the integration of nucleic acid detection. This technology has great potential in the field of point-of-care molecular diagnostics in the future. This paper focuses on the relevant content of these experimental carriers.     

Electrophoretic separation of nucleic acids: evaluation by video and photographic densitometry

The separation of DNA by gel electrophoresis provides a rapid method for determining size distributions of DNA in solution. Densitometric scanning of photographs of gels has been the standard method of analysis of agarose gels. However, analysis of photographs is complicated by the non-linear response of photographic film. Charged-coupled device video cameras have become popular for quantitative densitometry and we have used a charge-coupled device camera to image agarose gels to quantitate DNA damage. We compare video and photographic densitometry for quantitation of ultraviolet radiation (UV)-induced DNA damage and find that the two methods give equivalent results.     

Control of the photocatalytic activity of bimetallic complexes of pyropheophorbide-a by nucleic acids

Photocatalytic activity of a photosensitizer (PS) in an oligodeoxyribonucleotide duplex 5'-PS~ODN1/ODN2~Q-3' is inhibited because of close proximity of a quencher Q. The ODN2 in this duplex is selected to be longer than the ODN1. Therefore, in the presence of a nucleic acid (analyte), which is fully complementary to the ODN2 strand, the duplex is decomposed with formation of an analyte/ODN2~Q duplex and a catalytically active, single stranded PS~ODN1. In this way the catalytic activity of the PS can be controlled by the specific nucleic acids. We applied this reaction earlier for the amplified detection of ribonucleic acids in live cells (Arian, D.; Cló, E.; Gothelf, K.; Mokhir, A. Chem.-Eur. J.2010, 16(1), 288). As a photosensitizer (PS) we used In(3+)(pyropheophorbide-a)chloride and as a quencher (Q)--Black-Hole-Quencher-3 (BHQ-3). The In(3+) complex is a highly active photocatalyst in aqueous solution. However, it can coordinate additional ligands containing thiols (e.g., proteins, peptides, and aminoacids), that modulate properties of the complex itself and of the corresponding bio- molecules. These possible interactions can lead to undesired side effects of nucleic acid controlled photocatalysts (PS~ODN1/ODN2～Q) in live cells. In this work we explored the possibility to substitute the In(3+) complex for those ones of divalent metal ions, Zn(2+) and Pd(2+), which exhibit lower or no tendency to coordinate the fifth ligand. We found that one of the compounds tested (Pd(pyropheophorbide-a) is as potent and as stable photosensitizer as its In(3+) analogue, but does not coordinate additional ligands that makes it more suitable for cellular applications. When the Pd complex was introduced in the duplex PS~ODN1/ODN2~Q as a PS, its photocatalytic activity could be controlled by nucleic acids as efficiently as that of the corresponding In(3+) complex.     

Interaction of morin-cetyltrimethylammonium bromide with nucleic acids and determination of nucleic acids at nanograms per milliliter levels based on the enhancement of preresonance light scattering

A new preresonance light scattering (PRLS) assay of nucleic acids is presented. At pH 7.30, the weak PRLS of morin-cetyltrimethylammonium bromide (CTMAB) can be greatly enhanced by the addition of nucleic acids, owing to the interaction between the nucleic acid and morin-CTMAB. After the addition of morin and CTMAB to DNA, the zeta potential of DNA decreases and changes from negative to positive, which is due to the formation of an associate, the aggregation of morin on nucleic acids and the electric neutralization between DNA and the cationic surfactant CTMAB. Mechanism studies showed that the enhanced PRLS comes from the aggregation of morin in the presence of nucleic acids and CTMAB. The enhanced intensity of PRLS is in proportion to the concentration of nucleic acids in the range 7.5 x 10(-9)-1.0 x 10(-5) g ml(-1) for calf thymus DNA, 7.5 x 10(-9)-1.0 x 10(-6) g ml(-1) for salmon sperm DNA and 1.0 x 10(-8)-1.0 x 10(-6) g ml(-1) for yeast RNA. The detection limits are 3.4, 6.2 and 4.1 ng ml(-1) for calf thymus DNA, salmon sperm DNA and yeast RNA, respectively. Synthetic samples were analyzed satisfactorily.     

The interaction of poly(ethylenimine) with nucleic acids and its use in determination of nucleic acids based on light scattering

For the first time, poly(ethylenimine) (PEI) was used to determine nucleic acids with a light scattering technique using a common spectrofluorometer. The interaction of PEI with DNA results in greatly enhanced intensity of light scattering at 300 nm, which is caused by the formation of the big particles between DNA and PEI. Based on this, a new quantitative method for nucleic acid determination in aqueous solutions has been developed. Under the optimum conditions, the enhanced intensity of light scattering is proportional to the concentration of nucleic acid in the range of 0.01-10.0 microg ml(-1) for herring sperm DNA (hsDNA), 0.02-10.0 microg ml(-1) for calf thymus DNA (ctDNA), 0.02-20.0 microg ml(-1) for yeast RNA (yRNA). The detection limits are 5.3, 9.9, and 13.7 ng ml(-1), respectively. Synthetic samples were determined satisfactorily. At the same time, the light scattering technique has been successfully used to obtain the information on the effects of pH and ionic strength on the formation and the stability of the DNA/PEI complex, which is important in some fields such as genetic engineering and gene transfer. Using ethidium bromide (EB) as a fluorescent probe, the binding of PEI with hsDNA was studied. Both the binding constant of EB with DNA and the number of binding sites per nucleotide decrease with increasing concentration of PEI, indicating noncompetitive inhibition of EB binding to DNA in the presence of PEI. And the association constant of PEI to DNA obtained is 1.2 x 10(5) M(-1). IR-spectra show that PEI interacts with DNA through both the phosphate groups and the bases of DNA and the formation of DNA/PEI complex may cause the change of the conformation of the DNA secondary structure, which is also proved by UV-spectra.     

Cyclic voltammetry of nucleic acids and determination of submicrogram quantities of deoxyribonucleic acids by adsorptive stripping voltammetry

In cyclic voltammetry (at a mercury drop electrode) guanine residues in the polynucleotide chain give a characteristic anodic peak at potentials close to ?0.3 V (vs. saturated calomel electrode). At low concentrations of polynucleotide, this peak can be enhanced substantially if the potential scan is preceded by adsorptive preconcentration of the polynucleotide at the hanging mercury drop electrode. With accumulation times shorter than 10 min at pH 6.8, the limit of detection of a single-stranded polynucleotide is < 0.1 μg ml^?1. The peak of double-helical deoxyribonucleic acid (DNA) is considerably lower than that of single-stranded DNA under the same conditions, which can be exploited to determine low concentrations of single-stranded DNA in the presence of double-stranded DNA.