Site-directed cleavage of DNA by an oligonucleotide conjugate with o-bromobenzoic acid in the presence of copper ions

Site-directed cleavage of single- and double-stranded DNAs by an oligonucleotide conjugate with 5-[N-(3-aminopropyl)sulfamoyl]-2-bromobenzoic acid was investigated. When forming duplex complexes with a single-stranded DNA and triplex complexes with a double-stranded DNA, this conjugate cleaves DNA near the binding site in the presence of copper ions and free o-bromobenzoic acid. The efficacy and specificity of DNA cleavage by this conjugate and other oligonucleotide conjugates bearing tetracarboxyphthalocyanine Co^II and bleomycin A5 as reactive groups were compared.     

RNA–DNA Chimeras in the Context of an RNA World Transition to an RNA/DNA World

The RNA world hypothesis posits that DNA and proteins were later inventions of early life, or the chemistry that gave rise to life. Most scenarios put forth for the emergence of DNA assume a clean separation of RNA and DNA polymer, and a smooth transition between RNA and DNA. However, based on the reality of “clutter” and lack of sophisticated separation/discrimination mechanisms in a protobiological (and/or prebiological) world, heterogeneous RNA–DNA backbone containing chimeric sequences could have been common—and have not been fully considered in models transitioning from an RNA world to an RNA–DNA world. Herein we show that there is a significant decrease in Watson–Crick duplex stability of the heterogeneous backbone chimeric duplexes that would impede base‐pair mediated interactions (and functions). These results point to the difficulties for the transition from one homogeneous system (RNA) to another (RNA/DNA) in an RNA world with a heterogeneous mixture of ribo‐ and deoxyribonucleotides and sequences, while suggesting an alternative scenario of prebiological accumulation and co‐evolution of homogeneous systems (RNA and DNA).     

Electrochemical DNA sensor by the assembly of graphene and DNA-conjugated gold nanoparticles with silver enhancement strategy

Sensitive and selective detection of DNA is in urgent need due to its important role in human bodies. Many disorders, such as Alzheimer's disease and various cancers, are closely related with DNA damage. In this work, a novel electrochemical DNA biosensor was constructed on a DNA-assembling graphene platform which provided a robust, simple and biocompatible platform with large surface area for DNA immobilization. The as-designed DNA sensor was fabricated by directly assembling captured ssDNA on a graphene-modified electrode through the π-π stacking interaction between graphene and ssDNA bases. Then, the target DNA sequence and oligonucleotide probes-labeled AuNPs were able to hybridize in a sandwich assay format, following the AuNPs-catalyzed silver deposition. The deposited silver was further detected by differential pulse voltammetry. Owing to the high DNA loading ability of graphene and the distinct signal amplification by AuNPs-catalyzed silver staining, the resulting biosensor exhibited a good analytical performance with a wide detection linear range from 200 pM to 500 nM, and a low detection limit of 72 pM. Additionally, the biosensor was proved to be able to discriminate the complementary sequence from the single-base mismatch sequence. The simple biosensor is promising in developing electronic, on-chip assays in clinical diagnosis, environmental control, and drug discovery.     

Preparation and characterization of complexes of liposomes with gold nanoparticles

Gold nanoparticles (Au NPs), which are extremely useful materials for imaging and photothermal therapy, typically require a drug delivery system to transport them to the affected tissue and into the cells. Since liposomes are approved as drug carriers, complexes of liposomes with Au NPs were considered ideal solutions to deliver Au NPs to the target site in vivo. In this study, we prepared complexes of various liposomes with Au NPs via physical absorption and characterized them. The time dependency of the surface plasmon resonance of this complex, which is a unique property of Au NPs, shows that the liposomes promote the formation of stable dispersions of Au NPs under isotonic conditions, even though intact Au NPs aggregate immediately. From a release assay of calcein from liposomes and transmission electron microscopy analysis, the Au NPs were complexed with liposomes without membrane disruption. These complexes could be formed by using cationic liposomes and polyethylene glycol-modified liposomes, as well as by using phosphatidylcholine liposomes, which are useful for drug and gene delivery. We proposed this kind of complex as a nanomedicine with diagnostic and therapeutic ability.     

Complexation of phthalate oxygens in poly(ethylene phthalate) with silver ions and its effect on the formation of silver nanoparticles

The interaction of a phthalate group in poly(ethylene phthalate) (PEP) with silver ion has been elaborated in detail to understand the reduction behavior of silver ions to silver nanoparticles. Previously, the polymer electrolytes consisting of silver ions dissolved in PEP have shown highly stable separation performance for propylene/propane mixtures primarily due to the retardation of the reduction reaction of silver ions to silver nanoparticles, which is possible by means of the chelating bonds between phthalate groups and silver ions. Thus, in this study, the interaction was systematically investigated by both the theoretical ab initio calculation and the experimental Fourier transform infrared spectroscopy and X‐ray photoelectron spectroscopy. The results show that the interaction of silver ion with phthalate group in PEP is approximately two times stronger than that with other functional groups such as amide, ketone, and ester in various polymers, in which the latter ones show the rapid reduction reaction and consequently lose their olefin carrier activity with time. Therefore, it is concluded that the reduction reaction of silver ions to silver nanoparticles is retarded remarkably in PEP/silver salts systems primarily because of the strong interaction between the phthalate group in PEP and silver ion, and consequently the formation of silver nanoparticles would be effectively prohibited, as confirmed by transmission electron microscopy and ultraviolet–visible spectroscopy. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3344–3350, 2004     

Switching Demethylation Activities between AlkB Family RNA/DNA Demethylases through Exchange of Active‐Site Residues

The AlkB family demethylases AlkB, FTO, and ALKBH5 recognize differentially methylated RNA/DNA substrates, which results in their distinct biological roles. Here we identify key active‐site residues that contribute to their substrate specificity. Swapping such active‐site residues between the demethylases leads to partially switched demethylation activities. Combined evidence from X‐ray structures and enzyme kinetics suggests a role of the active‐site residues in substrate recognition. Such a divergent active‐site sequence may aid the design of selective inhibitors that can discriminate these homologue RNA/DNA demethylases.     

Modification of Escherichia coli single-stranded DNA binding protein with gold nanoparticles for electrochemical detection of DNA hybridization

The unique binding event between Escherichia coli single-stranded DNA binding protein (SSB) and single-stranded oligonucleotides conjugated to gold (Au) nanoparticles is utilized for the electrochemical detection of DNA hybridization. SSB was attached onto a self-assembled monolayer (SAM) of single-stranded oligonucleotide modified Au nanoparticle, and the resulting Au-tagged SSB was used as the hybridization label. Changes in the Au oxidation signal was monitored upon binding of Au tagged SSB to probe and hybrid on the electrode surface. The amplified oxidation signal of Au nanoparticles provided a detection limit of 2.17 pM target DNA, which can be applied to genetic diagnosis applications. This work presented here has important implications with regard to combining a biological binding event between a protein and DNA with a solid transducer and metal nanoparticles.     

Insight into the Mechanism of the Initial Reaction of an OH Radical with DNA/RNA Nucleobases: A Computational Investigation of Radiation Damage

Earlier theoretical investigations of the mechanism of radiation damage to DNA/RNA nucleobases have claimed OH radical addition as the dominating pathway based solely on energetics. In this study we supplement calculations of energies with the kinetics of all possible reactions with the OH radical through hydrogen abstraction and OH radical addition onto carbon sites, using DFT at the ωB97X‐D/6‐311++G(2df,2pd) level with the Eckart tunneling correction. The overall rate constants for the reaction with adenine, guanine, thymine, and uracil are found to be 2.17×10^?12, 5.64×10^?11, 2.01×10^?11, and 5.03×10^?12 cm³ molecules^?1 s^?1, respectively, which agree exceptionally well with experimental values. We conclude that abstraction of the amine group hydrogen atoms competes with addition onto C₈ as the most important reaction pathway for the purine nucleobases, while for the pyrimidine nucleobases addition onto C₅ and C₆ competes with the abstraction of H₁. Thymine shows favourability against abstraction of methyl hydrogens as the dominating pathway based on rate constants. These mechanistic conclusions are partly explained by an analysis of the electrostatic potential together with HOMO and LUMO orbitals of the nucleobases.     

Influence of low concentration silver nanoparticles on the electrical and electro-optical parameters of nematic liquid crystals

Thermodynamical, optical, dielectric and electro-optical characterisation of nematic liquid crystals (LCs) and silver nanoparticle (NP) composites have been carried out. Transition temperatures of pure and composites systems have been measured. Thermodynamical studies suggest increase of clearing temperature of the composite material as compared to the pure material. Threshold voltage for switching from bright to dark state and splay elastic constant of the pure and composite materials have been determined. From frequency dependence of dielectric measurements, permittivity, loss, relaxation frequency and dielectric strength of flip-flop mechanism of LC molecules in the nematic phase have been calculated. Dielectric properties of composites have been explained in reference of Maier and Meier theory. The effects of doping of NPs on dielectric and electro-optic properties of LC-NP composites have been discussed.     

Synthesis of Naphthyridine Dimers with Conformational Restriction and Binding to DNA and RNA

One of the important determinants in the efficiency of a molecular interaction is the necessity for conformational changes in host and/or guest molecules upon binding. In small‐molecule interactions with nucleic acids, conformational changes on both molecules are often involved, especially in intercalating binding. Mismatch binding ligands (MBLs) we described here consist of two heterocycles that predominantly exist in one conformation, so it is of interest to determine if such molecules can bind to any DNA and RNA structures. One molecule, 1 ‐NHR, which predominantly exists as the unstacked conformation in aqueous solvent, has been successfully synthesized and characterized. Compound 1 ‐NHR did not efficiently bind to GX/Y DNA and RNA sequences, but the binding pattern is different from that of authentic MBL naphthyridine carbamate dimer. In vitro selection of RNA that specifically binds to 1 ‐NHR was performed from pre‐miR‐29a loop library RNA, and one RNA, to which 1 ‐NHR bound with high affinity, has been successfully identified. Although it was anticipated that 1 ‐NHR, with a predominantly unstacked conformation, would show entropy‐driven binding, isothermal titration calorimetry analysis suggested that the binding of 1 ‐NHR to RNA was enthalpy driven with an apparent K _d of about 100 nm .     

RNA is more UV resistant than DNA: the formation of UV-induced DNA lesions is strongly sequence and conformation dependent

DNA and RNA hairpins, which represent well-folded oligonucleotide structures, were irradiated and the amount of damaged hairpins was directly quantified by using ion-exchange HPLC. The types of photoproducts formed in the hairpins were determined by ESI-HPLC-MS/MS experiments. Irradiation of hairpins with systematically varied sequences and conformations (A versus B) revealed remarkable differences regarding the amount of photolesions formed. UV-damage formation is, therefore, a strongly sequence and conformation dependent process.     

Mechanism of mercury detection based on interaction of single-strand DNA and hybridized DNA with gold nanoparticles

Mechanisms of interaction of single-strand DNA and hybridized DNA on gold nanoparticles in the presence of Hg²⁺ was studied in this work. Recently the detection of Hg²⁺ using unmodified gold nanoparticles (AuNPs) combined with DNA is becoming a promising technique with the advantages of simplicity, cost-effectiveness and high sensitivity. However, few studies focused on the interaction of ssDNA and hybridized DNA on AuNPs to date. In the present work, we compared the interactions of different DNA probes on AuNPs using both absorption and fluorescence detection. It was found that there were only small partial dsDNA dissociated from the surface of AuNPs after hybridization in the presence of Hg²⁺. Moreover, we found that the aggregated AuNPs/DNA system tended to be dispersed again with increasing Hg²⁺ concentration up to 250 μM. Based on these results, the mechanisms of mercury detection based on interaction between DNA-conjugated gold nanoparticles were investigated. Positively charged dsDNA could bind to the surface of AuNPs and dominate the electrostatic interactions and consequently aggregation of the AuNPs/DNA system.     

A DFT study of reactions of methyldiazonium ion with DNA/RNA nucleosides: Investigating effect of sugar moiety on methylation pattern of bases

Methyldiazonium ion ( ) is an ultimate carcinogen that can methylate multiple sites in DNA/RNA. In present contribution, density functional theory calculations using the B3LYP and M06‐2X functionals and the 6‐31G(d,p) and aug‐cc‐pVDZ basis sets are carried out to study methylation reactions of at the different nucleophilic sites of DNA/RNA bases and their nucleosides. Total 12 nucleophilic sites, that is, the N2, N3, N7, and O6 sites of guanine; the N1, N3, N6, and N7 sites of adenine; O2 and N3 sites of cytosine and the O2 and O4 sites of thymine and uracil have been considered for study. Thus, a total of 30 reactions have been studied here. The polarizable continuum model is used for solvation calculations. The N7 site of guanine, N7(G), is found to be most reactive in all the reactions studied here, which is in agreement with experiment. However, the calculated reactivity of toward the N7(G) site in aqueous media follows the order: guanine > deoxyguanosine > guanosine. The reactivities of many other sites including the O6(G), O2(C), and N3(A) sites are also modified in going from DNA/RNA bases to their nucleosides and from DNA to RNA nucleosides. Thus, we note that the presence of sugar moiety significantly modifies the methylation pattern of bases caused by . © 2014 Wiley Periodicals, Inc.     

Templated Formation of Discrete RNA and DNA:RNA Hybrid G‐Quadruplexes and Their Interactions with Targeting Ligands

G‐rich RNA and DNA oligonucleotides derived from the human telomeric sequence were assembled onto addressable cyclopeptide platforms through oxime ligations and copper‐catalyzed azide‐alkyne cycloaddition (CuAAc) reactions. The resulting conjugates were able to fold into highly stable RNA and DNA:RNA hybrid G‐quadruplex (G4) architectures as demonstrated by UV, circular dichroism (CD), and NMR spectroscopic analysis. Whereas rationally designed parallel RNA and DNA:RNA hybrid G4 topologies could be obtained, we could not force the formation of an antiparallel RNA G4 structure, thus supporting the idea that this topology is strongly disfavored. The binding affinities of four representative G4 ligands toward the discrete RNA and DNA:RNA hybrid G4 topologies were compared to the one obtained with the corresponding DNA G4 structure. Surface plasmon resonance (SPR) binding analysis suggests that the accessibility to G4 recognition elements is different among the three structures and supports the idea that G4 ligands might be shaped to achieve structure selectivity in a biological context.     

Facile preparation of Kaolin supported silver nanoparticles mediated by Thymbra spicata extract and investigation of the anti-human lung cancer properties

The present work demonstrates the synthesis of kaolin supported Ag nanoparticles (AgNPs@Kaolin) by using an aqueous extract of Thymbra spicata as a green reductant and capping agent. Physicochemical characteristics of the synthesized nanocomposite were studied by field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), energy-dispersive X-ray spectroscopy (EDS), elemental mapping, X-ray diffraction (XRD) and inductively coupled plasma (ICP) techniques. The biogenic AgNPs are uniformly globular. Owing to the surface modification by the plant derived phytochemicals, the NPs are found to be distributed evenly on the kaolin surface. The AgNPs@Kaolin nanocomposite has been explored biologically in the anticancer and antioxidant assays. In the cellular and molecular part of the recent study, the treated cells with AgNPs@Kaolin nanocomposite were assessed by MTT assay for 48 h about the cytotoxicity and anti-human lung adenocarcinoma properties on normal (HUVEC) and lung adenocarcinoma cell lines i.e. lung well-differentiated bronchogenic adenocarcinoma (HLC-1), lung moderately differentiated adenocarcinoma (LC-2/ad), and lung poorly differentiated adenocarcinoma (PC-14). The viability of malignant lung cell line reduced dose-dependently in the presence of AgNPs@Kaolin nanocomposite. The IC50 of AgNPs@Kaolin nanocomposite were 509, 315, and 189 µg/mL against HLC-1, LC-2/ad, and PC-14 cell lines, respectively. In the antioxidant test, the IC50 of AgNPs@Kaolin nanocomposite and BHT against DPPH free radicals were 125 and 161 µg/mL, respectively. After the clinical study, AgNPs@Kaolin nanocomposite containing T. spicata leaf aqueous extract may be used to formulate a new chemotherapeutic drug or supplement to treat the several types of human lung adenocarcinoma.     

Unwinding DNA and RNA with Synthetic Complexes: On the Way to Artificial Helicases

Synthetic helicases can be designed on the basis of ligands that bind more strongly to single‐stranded nucleic acids than to double‐stranded nucleic acids. This can be achieved with ligands containing phenyl groups, which intercalate into single strands, but due to their small size not into double strands. Moreover, two phenyl rings are combined with a distance that allows bis‐intercalation with only single strands and not double strands. In this respect, such ligands also mimic single‐strand binding (SSB) proteins. Exploration with more than 23 ligands, mostly newly synthesised, shows that the distance between the phenyl rings and between those and the linker influence the DNA unwinding efficiency, which can reach a melting point decrease of almost ΔT_m=50 °C at much lower concentrations than that with any other known artificial helicases. Conformational pre‐organisation of the ligand plays a decisive role in optimal efficiency. Substituents at the phenyl rings have a large effect, and increase, for example, in the order of H<F<Cl<Br, which illustrates the strong role of dispersive interactions in intercalation. Studies with homopolymers revealed significant selectivity: for example, with a ligand concentration of 40 μM at 35 °C, only GC double strands melt (ΔT_m=48 °C), whereas the AT strand remains untouched, and with poly(rA)–poly(rU) as an RNA model one observes unfolding at 29 °C with a concentration of only 30 μM .     

DNA and RNA binding properties of an arginine-based ‘Extended Chiral Box’ Peptide Nucleic Acid

Lys-based ‘chiral box’ Peptide Nucleic Acids (PNAs with three adjacent 2D-Lys-based chiral monomers) have shown unsurpassed specificity in DNA recognition. In this Letter, the binding performances of arginine-based chiral PNAs were evaluated for PNAs containing in the middle part of the strand either a 2D,5L-Arg monomer or three adjacent 2D-; 2D,5L-; 5L-Arg monomers (‘Extended Chiral Box’), a combination never studied before. The binding performances of the PNAs were studied by evaluating the melting temperatures of fullmatch and mismatch PNA-DNA and PNA-RNA hybrids and by studying their structure by circular dichroism (CD). The data indicated that the arginine side chains inserted in the PNA structure are perfectly equivalent to lysine side chains as far as oligonucleotide recognition is concerned. The insertion of an ‘Extended Chiral Box’ into PNA differently influences the binding properties to DNA and RNA: the additional side chains had no observable effect on binding affinity and selectivity toward DNA, whereas, seemed to slightly disturb the binding affinity to RNA but at the same time highly enhancing the recognition selectivity.     

Interaction of zanamivir with DNA and RNA: Models for drug–DNA and drug–RNA bindings

Zanamivir (ZAN) is the first of a new generation of influenza virus-specific drugs known as neuraminidase inhibitors, which acts by interfering with life cycles of influenza viruses A and B. It prevents the virus spreading infection to other cells by blocking the neuraminidase enzyme present on the surface of the virus. The aim of this study was to examine the stability and structural features of calf thymus DNA and yeast RNA complexes with zanamivir in aqueous solution, using constant DNA or RNA concentration (12.5 mM) and various zanamivir/polynucleotide (P) ratios of 1/20, 1/10, 1/4, and 1/2. FTIR and UV–visible spectroscopy are used to determine the drug external binding modes, the binding constant and the stability of zanamivir–DNA and RNA complexes in aqueous solution. Structural analysis showed major interaction of zanamivir with G-C (major groove) and A-T (minor groove) base pairs and minor perturbations of the backbone PO₂ group with overall binding constants of K_{zanamivir–DNA} = 1.30 × 10⁴ M⁻¹ and K_{zanamivir–RNA} = 1.38 × 10⁴ M⁻¹. The drug interaction induces a partial B to A-DNA transition, while RNA remains in A-conformation.