Atomic force microscopy and surface-enhanced Raman scattering detection of DNA based on DNA-nanoparticle complexes

We report a simple method for the label-free detection of double-stranded DNA using surface-enhanced Raman scattering (SERS). We prepared cetyltrimethylammonium bromide (CTAB)-capped silver nanoparticles and a DNA-nanoparticle complex by adding silver nanoparticles to lambda-DNA solutions. In the present study, the utilization of CTAB-capped silver nanoparticles facilitates the electrostatic interaction between DNA molecules and silver nanoparticles; at the same time, the introduction of DNA avoids adding aggregating agent for the formation of nanoparticle aggregates to obtain large enhancement of DNA, because the DNA acts as both the probe molecules and aggregating agent of Ag nanoparticles.

DNA based gold nanoparticles colorimetric sensors for sensitive and selective detection of Ag(I) ions

In this work, we reported both unlabeled and labeled sensing strategies for Ag(I) ions detection by using the DNA based gold nanoparticles (AuNPs) colorimetric method. In the unlabeled strategy, C-base riched single strand DNA (C-ssDNA) enwinded onto AuNPs to form AuNPs/C-ssDNA complex. In the labeled method, sulfhydryl group modified C-ssDNA (HS-C-ssDNA) was covalently labeled on AuNPs to produce AuNPs-S-C-ssDNA complex. In both strategies, C-ss DNA or HS-C-ssDNA could enhance the AuNPs stability against the salt-induced aggregation. However, the presence of Ag(I) ions in the obtained AuNPs/C-ssDNA or AuNPs-S-C-ssDNA complex would decrease such stability to display purple even blue colors due to the formation of Ag(I) ions mediated C-Ag(I)-C base pairs. Through this phenomenon, Ag(I) ions could be detected qualitatively and quantitatively using both unlabeled and labeled sensing strategies.

Anticancer Drug-DNA Interactions Measured Using a Photoinduced Electron-Transfer Mechanism Based on Luminescent Quantum Dots

A sensing system based on the photoinduced electron transfer of quantum dots (QDs) was designed to measure the interaction of anticancer drug and DNA, taking mitoxantrone (MTX) as a model drug. MTX adsorbed on the surface of QDs can quench the photoluminescence (PL) of QDs through the photoinduced electron-transfer process; and then the addition of DNA will bring the restoration of QDs PL intensity, as DNA can bind with MTX and remove it from QDs. Sensitive detection of MTX with the detection limit of 10 nmol L-1 and a linear detection range from 10 nmol L-1 to 4.5 mu mol L-1 was achieved. The dependence of PL intensity on DNA amount was successfully utilized to investigate the interactions between MTX and DNA. Both the binding constants and the sizes of binding site of MTX-DNA interactions were calculated based on the equations deduced for the PL recovery process. The binding constant obtained in our experiment was generally consistent with previous reports. The sensitive and speedy detection of MTX as well as the avoidance of modification or immobilization process made this system suitable and promising in the drug-DNA interaction studies.

Photoinduced DNA Cleavage by alpha-, beta-, and gamma-Cyclodextrin-Bicapped C-60 Supramolecular Complexes

Water-soluble supramolecular inclusion complexes of alpha-, beta-, and gamma-cyclodextrin-bicapped C-60 (CD/C-60) have been investigated for their photoinduced DNA cleavage activities, with the aim to assess the potential health risks of this class of compounds and to understand the effect of host cyclodextrins having different cavity dimensions. Factors such as incubation temperature, irradiation time, and concentration of NADH or CDs/C-60 supramolecular inclusion complexes have been examined. The results show that alpha-, beta-, and gamma-CDs/C-60 are all able to cleave double-stranded DNA under visible light irradiation in the presence of NADH. However, a difference in the photoinduced DNA cleavage efficiency is observed, where the cleavage efficiency increases in the order of alpha-, beta-, and gamma-CD/C-60. The difference is attributed to the different aggregation behavior of the inclusion complexes in aqueous solution, which is correlated to the cavity dimension of the host cyclodextrin molecules.

Enhanced catalytic DNAzyme for label-free colorimetric detection of DNA

A DNAzyme-based label-free method for the colorimetric detection of DNA is introduced, with a supramolecular hemin G-quartet complex as the sensing element and a 36-mer single-strand DNA as the analyte that is detected at 10 nM.

Surface plasmon resonance and electrochemistry characterization of layer-by-layer self-assembled DNA and Zr4+ thin films, and their interaction with cytochrome c

Through electrostatic layer-by-layer (LbL) assembly, negatively charged calf thymus double stranded DNA (CTds-DNA), and positively charged Zr4+ ions were alternately deposited on gold substrate modified with chemisorbed cysteamine. Thus-prepared three-dimensional DNA networks were characterized by surface plasmon resonance (SPR) spectroscopy, X-ray photoelectron spectroscopy (XPS) and infrared reflection-absorption spectroscopy (IR-RAS). SPR spectroscopy indicates that the effective thickness of DNA monolayer in the (DNA/Zr4+), bilayer was 1.5 +/- 0.1 nm, which corresponds to the surface coverage of 79% of its full packed monolayer. At the same time, a linear increase of film thickness with increasing number of layers was also confirmed by SPR characterizations. The data of XPS and IR-RAS show that Zr4+ ions interact with both the phosphate groups and nitrogenous bases of DNA and load into the framework of DNA. Furthermore, the interactions between this composite film and heme protein cytochrome c (Cyt c) were investigated by SPR spectroscopy and electrochemistry.

Surface plasmon resonance and electrochemistry characterization of layer-by-layer self-assembled DNA and Zr4+ thin films, and their interaction with cytochrome c

Through electrostatic layer-by-layer (LbL) assembly, negatively charged calf thymus double stranded DNA (CTds-DNA), and positively charged Zr4+ ions were alternately deposited on gold substrate modified with chemisorbed cysteamine. Thus-prepared three-dimensional DNA networks were characterized by surface plasmon resonance (SPR) spectroscopy, X-ray photoelectron spectroscopy (XPS) and infrared reflection-absorption spectroscopy (IR-RAS). SPR spectroscopy indicates that the effective thickness of DNA monolayer in the (DNA/Zr4+), bilayer was 1.5 +/- 0.1 nm, which corresponds to the surface coverage of 79% of its full packed monolayer. At the same time, a linear increase of film thickness with increasing number of layers was also confirmed by SPR characterizations. The data of XPS and IR-RAS show that Zr4+ ions interact with both the phosphate groups and nitrogenous bases of DNA and load into the framework of DNA. Furthermore, the interactions between this composite film and heme protein cytochrome c (Cyt c) were investigated by SPR spectroscopy and electrochemistry. Compared with the adsorption of Cyt c on DNA monolayer, this composite multilayer film can obviously enhance the amount of immobilized Cyt c confirmed by SPR reflectivity-incident angle (R-theta) curves.

Enthalpy/entropy compensation: Influence of DNA flanking sequence on the binding of 7-amino actinomycin D to its primary binding site in short DNA duplexes

The effect of the context of the flanking sequence on ligand binding to DNA oligonucleotides that contain consensus binding sites was investigated for the binding of the intercalator 7-amino actinomycin D. Seven self-complementary DNA oligomers each containing a centrally located primary binding site, 5'-A-G-C-T-3', flanked on either side by the sequences (AT)(n) or (AA)(n) (with n = 2, 3, 4) and AA(AT)(2), were studied. For different flanking sequences, (AA)(n)-series or (AT)(n)-series, differential fluorescence enhancements of the ligand due to binding were observed. Thermodynamic studies indicated that the flanking sequences not only affected DNA stability and secondary structure but also modulated ligand binding to the primary binding site. The magnitude of the ligand binding affinity to the primary site was inversely related to the sequence dependent stability. The enthalpy of ligand binding was directly measured by isothermal titration calorimetry, and this made it possible to parse the binding free energy into its energetic and entropic terms.

Diluting thiol-derivatized oligonucleotide monolayers on Au(111) by mercaptohexanol replacement reaction

Surface replacement reaction of thiol-derivatized, single-stranded oligonucleotide (HS-ssDNA) by mercaptohexanol (MCH) is investigated in order to reduce surface density of the HS-ssDNA adsorbed to Au(111) surface. Cyclic voltammograms (CVs) and scanning tunneling microscopy (STM) are employed to assess the composition and state of these mixed monolayers. It is found that each CV of mixed self-assembled monolayers (SAMs) only shows a single reductive desorption peak, which suggests that the resulted, mixed SAMs do not form discernable phase-separated domains. The peak potential gradually shifts to negative direction and the peak area increases step by step over the whole replacement process. By analyzing these peak areas, it is concluded that two MCH molecules will replace one HS-ssDNA molecule and relative coverage can also be estimated as a function of exposing time. The possible mechanism of the replacement reaction is also proposed. The DNA surface density exponentially reduces with the exposing time increasing, in other words, the replacement reaction is very fast in the first several hours and then gradually slows down. Moreover, the morphological change in the process is also followed by STM.

Direct electrochemistry and surface plasmon resonance characterization of alternate layer-by-layer self-assembled DNA-myoglobin thin films on chemically modified gold surfaces

Alternate layer-by-layer (L-by-L) polyion adsorption onto gold electrodes coated with chemisorbed cysteamine gave stable, electroactive multilayer films containing calf thymus double stranded DNA (CT ds-DNA) and myoglobin (Mb). Direct, quasi-reversible electron exchange between gold electrodes and proteins involved the Mb heme Fe2+/Fe3+ redox couple. The formation of L-by-L (DNA/Mb), films was characterized by both in situ surface plasmon resonance (SPR) monitoring and cyclic voltammetry (CV). The effective thickness of DNA and Mb monolayers in the (DNA/Mb)l bilayer were 1.0 +/- 0.1 and 2.5 +/- 0.1 mn, corresponding to the surface coverage of similar to65% and similar to89% of its full packed monolayer, respectively. A linear increase of film thickness with increasing number of layers was confirmed by SPR characterizations. At pH 5.5, the electroactive Mb in films are those closest to the electrode surface; additional protein layers did not communicate with the electrode. CV studies showed that electrical communication might occur through hopping conduction via the electrode/base pair/Mb channel, thanks to the DNA-Mb interaction. After the uptake of Zn2+, a special electrochemical behavior, where MbFe(2+) acts as a DNA-binding reduction catalyst in the Zn2+-DNA/Mb assembly, takes place.

Conformational transition of DNA induced by cationic lipid vesicle in acidic solution: spectroscopy investigation

The conformational transition of DNA induced by the interaction between DNA and a cationic lipid vesicle, didodecyidimethylammonium bromide (DDAB), had been investigated by circular dichroism (CD) and UV spectroscopy methods. We used singular value decomposition least squares method (SVDLS) to analyze the experimental CD spectra. Although pH value influenced the conformation of DNA in solution, the results showed that upon binding to double helical DNA, positively charged liposomes induced a conformational transition of DNA molecules from the native B-form to more compact conformations. At the same time, no obvious conformational changes occurred at single-strand DNA (ssDNA). While the cationic lipid vesicles and double-strand DNA (dsDNA) were mixed at a high molar ratio of DDAB vesicles to dsDNA, the conformation of dsDNA transformed from the B-form to the C-form resulting in an increase in duplex stability (DeltaT(m) = 8 +/- 0.4 degreesC). An increasing in T-m was also observed while the cationic lipid vesicles interacted with ssDNA.

Assembly of alternating polycation and DNA multilayer films by electrostatic layer-by-layer adsorption

The assembly of alternating DNA and positively charged poly(dimethyldiallylammonium chloride) (PDDA) multilayer films by electrostatic layer-by-layer adsorption has been studied. The real-time surface plasmon resonance (BIAcore) technique was used to characterize and monitor the formation of multilayer films in solution in real time continuously. Electrochemical impedance spectroscopy (EIS) and UV-vis absorbance measurements were also used to study the film assembly, and linear film growth was observed. All the results indicate that the uniform multilayer can be obtained on the poly(ethylenimine)- (PEI-) coated substrate surface. The kinetics of the adsorption of DNA on PDDA surface was also studied by the real-time BIAcore technique; the observed rate constant was calculated using a Langmuir model (k(obs) = (1.28 +/- 0.08) x 10(-2) s(-1).

Lanthanide binuclear macrocyclic complexes as synthetic enzymes for the cleavage of DNA

Lanthanide binuclear complexes can accelerate the cleavage of pUC19 plasmid DNA, yielding predominantly linear form. The saturation kinetics of the cleavage of pUC19 was studied. The observed rates with lanthanide binuclear complexes showed the expected increase with the catalyst concentration. The rate of cleavage is greater than that of lanthanide ions alone. (C) 1998 Elsevier Science B.V. All rights reserved.

Electrochemical study of interactions between DNA and viologen-thiol self-assembled monolayers

We investigated the binding characteristics of double-stranded DNA to self-assembled monolayers (SAMs) containing viologen groups formed on the surface of gold electrodes via Au-S bonds. The positive charged and hydrophobic surfaces of the viologen SAMs modified gold electrodes are suitable to bind strongly dth DNA, whose interactions to solution DNA and adsorbed DNA both lead to positive shifts (22.5 mV and 65 mV, respectively) in the first redox potential ci viologen centers, indicating that the main interaction is from a hydrophobic interaction. Meanwhile, the binding of DNA strongly affects the kinetics of electron transfer of the viologen group so that the separation of anodic and cathodic peak potentials becomes larger and the heterogeneous electron transfer constant becomes smaller.

The topological configuration and conformational analysis of mRNA in translation

The theoretical model construction of mRNA hairpin structure and single-stranded structure as well as the simulation studies on RNA structure determined by the X-ray crystal diffraction and nuclear magnetic resonance revealed that in translation, after mRNA being unfolded into single-stranded structure, its topological configuration was closely correlative with the original hairpin structure. The conformational features of single-stranded mRNA appeared as helical regions alternating with curly regions to different extents, which might exert the influence on the folding of nascent polypeptide by various regulating effects including different translational rates.