Resonance light scattering spectroscopy study of interaction between norfloxacin and calf thymus DNA and its analytical application

The interaction between norfloxacin and calf thymus double-stranded DNA (dsDNA) has been studied by a resonance light scattering (RLS) technique with a common spectrofluorometer. The characteristics of RLS spectra, the effective factors and optimum conditions of the reaction have been investigated. In Britton-Robinson (BR) buffer (pH 5.87), norfloxacin has a maximum peak 405.5 nm and the RLS intensity is remarkably enhanced by trace amount of calf thymus dsDNA due to the interaction between norfloxacin and dsDNA. The binding of norfloxacin to DNA forms large particles, which were characterized by RLS spectrum, scanning electron microscopy (SEM), ultraviolet-visible (UV-vis) spectrum, and fluorescence spectrum. Based on the enhanced RLS intensity, a novel method for sensitive determination of calf thymus dsDNA concentration ranging from 0.02 to 2.3 microg ml(-1) was developed. The determination limit (3 sigma) was 1.2 ng ml(-1). The method is simple, rapid, practical and relatively free from interference generated by coexisting substance, as well as much more sensitive than most of the reported methods. Three synthetic samples of ctDNA were determined with satisfactory results.     

Comparison of dye (oxazine and thiazine) materials as a photosensitizer for use in photogalvanic cells based on molecular interaction with sodium dodecyl sulphate by spectral study

The photochemistry of dye is playing a significant role for understanding the mechanism of electron transfer reactions in photoelectrochemical devices such as photogalvanic cells, DSSC, semiconductor photo-catalysis, photoconductors, etc. Oxazines (Brilliant Cresyl Blue and Nile Blue O) and thiazines (Azur A, Azur B, Azur C, Methylene Blue and Toluidine Blue O) dyes have been used widely as a photosensitizer with and without surfactants in the photogalvanic cells for solar power conversion and storage. Since, the stability and solubility of photosensitizers (dyes) are increased in the presence of surfactant and these properties lead to enhance the electrical output of the photogalvanic cells. Therefore, here we have studied the extent of interaction of different dyes with sodium dodecyl sulphate (SDS), find out the order of stability of dye–SDS on the basis of magnitudes of shifting in λ_max of dye monomer and try to correlate order of dye–SDS interaction with already reported electrical output data of photogalvanic cells. Brilliant Cresyl Blue, Nile Blue O, Azur A and TB O have shown red shifting while Azur B, Azur C and MB have shown blue shifting in their λ_max value with SDS, which indicates formation of dye–surfactant complex. But, the extent of formation of complex for different dyes with SDS was different due to change in their alkyl groups. Dyes with red shifting have greater stability in excited state as well as higher electrical output data of the cell than dye with blue shifting. On the basis of both red and blue shifting, order of stability of dyes–SDS complex was found as: Brilliant Cresyl Blue?>?Toluidine Blue O?>?Azur A?>?Nile Blue?>?Azur B?>?Methylene Blue?>?Azur C. The order of electrical output values of these dyes in photogalvanic cells have also been supported by literature data in the presence of SDS. Hence, the dye–surfactant complex which would have greater stability in excited state might be more useful for improvement of conversion efficiency and storage capacity of photogalvanic cells in the future.     

Detection of DNA hybridization by various spectroscopic methods using the copper tetraphenylporphyrin complex as a probe

We are presenting new and highly sensitive hybridization assays. They are based on various spectroscopic methods including resonance light scattering, circular dichroism, ultraviolet spectra and fluorescence spectra, as well as atomic force microscopy, and relies on the interaction of the Cu(II), Ni(II), Mg(II), Co(II), Cd(II), and Zn(II) complexes, respectively, of tetraphenylporphyrin (TPP) with double-strand DNA (dsDNA) and single strand DNA (ssDNA). The interaction results in amplified resonance light scattering (RLS) signals and enables the detection of hybridization without the need for labeling DNA. The RLS signals are strongest in case of the Cu (II)-TPP complex which therefore was selected as the probe. The technique is simple, robust, accurate, and can be completed in less than one hour.

An abnormal resonance light scattering arising from ionic-liquid/DNA/ethidium interactions

In the aqueous phase, ethidium bromide (EB) intercalates into the double helix structure of dsDNA (ds=double-stranded) with a notable enhancement in fluorescence and resonance light scattering (RLS). However, when dsDNA was extracted into an ionic liquid (IL), 1-butyl-3-methylimidazolium hexafluorophosphate (BmimPF(6)), an abnormal RLS arising from the interactions of IL-DNA-EB was observed, with a substantial decrease of the recorded RLS. The cationic Bmim(+) groups of BmimPF(6) intercalate into the DNA helix structure, in which they interact with the P-O bonds of phosphate groups in DNA strands and result in a reduction of the base-pair interstice along with transformation of DNA conformations that consequently prohibits the intercalation of EB with DNA. Thus, in the IL phase, the interactions between ethidium and DNA were dominated by electrostatic interactions and hydrogen bonding, leading to a congregation of EB entities around the DNA strands that results in an increase of absorption by ethidium, and consequently the inner filter effect leads to a reduction of the RLS. The present observation has been applied to the direct quantification of DNA in an ionic-liquid phase after DNA from human whole blood was extracted into BmimPF(6).     

Study of the interaction of Azur B with DNA and the determination of DNA based on resonance light scattering measurements

Based on the measurements of molecular absorption and resonance light scattering (RLS), the aggregation of Azur B (AB) was in a medium of pH ranging from 1.98 to 2.56 and ionic strength <0.12 M. The presence of double stranded DNA prompts the aggregation, resulting in enhanced RLS signals. Linear relationships were achieved between the enhanced RLS intensity at 359.7 nm and DNA concentration in the range of 0-4.5 μg ml⁻¹ for both calf thymus DNA (ctDNA) and fish sperm DNA (fsDNA) if 3.0×10⁻⁵ M AB was employed. The 3σ limits of detection were 9.3 and 8.9 ng ml⁻¹ for ctDNA and fsDNA, respectively. Five synthetic samples were analysed satisfactorily.     

Selective interactions of a few acridinium derivatives with single strand DNA: study of photophysical and DNA binding interactions

Novel acridinium derivatives 1-3, wherein steric factors have been varied systematically through substitution at the ninth position of the acridinium ring, were synthesized and their interactions with single strand and double strand DNA have been investigated through photophysical, biophysical, and microscopic techniques. The acridinium derivative 1 exhibited quantitative fluorescence yields (phi f approximately =1) and high lifetime of 35 ns, while significantly lower fluorescence yields of 0.11 and 0.02 and lifetimes of 3.5 and 1.2 ns were observed for 2 and 3, respectively. The derivatives 1 and 2 having 2-methylphenyl and 2,4-dimethylphenyl substituents at the ninth position of the acridinium ring showed selective interactions with single strand DNA (ssDNA) with association constants of KssDNA = 6.3-6.6 x 10(4) M(-1), while negligible interactions were observed with double strand DNA (dsDNA). In contrast, the derivative 3 with 2,6-dimethylphenyl substitution showed negligible interactions with both ssDNA and dsDNA. Studies with a series of 19-mer oligonucleotides indicate that these derivatives exhibit significant selectivity for the sequences rich in guanosine (ca. 3-fold) as compared to the cytosine-rich sequences. These derivatives with high water solubility and the ability to distinguish between ssDNA and dsDNA through changes in fluorescence emission can be used as fluorescent probes for understanding the role of ssDNA in various biological processes and to study various DNA-ligand interactions.     

A resonance light scattering sensor based on methylene blue–sodium dodecyl benzene sulfonate for ultrasensitive detection of guanine base associated mutations

A resonance light scattering (RLS) sensor for guanine base associated mutations has been developed on the basis of the high selectivity of methylene blue (MB) for guanine bases in the presence of sodium dodecyl benzene sulfonate (SDBS). MB, when bound to SDBS, underwent a dramatic enhancement of its RLS intensity. However, the addition of double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) caused the strong RLS intensity of MB-SDBS to decrease, and the RLS intensity of MB-SDBS-ssDNA was much lower than that of MB-SDBS-dsDNA. Consequently, it can be concluded that the binding abilities of MB-SDBS with ssDNA and dsDNA were different. Besides, the experimental results showed that MB-SDBS could bind specifically to oligonucleotides rich in guanine bases. Short DNA targets with sequences related to β-thalassaemia, thrombophilia and psoriasis, all of which are guanine base relevant mutations, were synthesized. It was found that MB-SDBS could recognize the single-base mismatches in the mutational DNA, followed by different RLS signal changes between MB-SDBS-normal DNA systems and MB-SDBS-mutational DNA systems. The ultrasensitive sensor allows simple, rapid, sensitive and selective detection of guanine base associated mutations, indicating its potential application in the medical field.     

Spectral assignments to the light emissions of fluorescent organic small molecules in aqueous medium

Spectrofluorometric identifications of artificial organic dyes have important environmental significance, but both scattered light signals and the fluorescence signals were twins in fluorospectroscopy, and the light scattering signals are always the interference sources of spectrofluorometry. In order to investigate the relationship between the light scattering and fluorescence in the spectrofluorometric measurements, herein we discuss the scattered light and fluorescence emission properties of organic small molecules (OSMs) using Lignin Pink (LP) in neutral medium as an example. With the help of UV-vis measurements, and starting from three-dimensional light emission measurements, scattered light and fluorescence emissions could be assigned. Investigations by increasing LP concentration showed that the light emission at 282.0 and 344.0 nm could be attributed to the resonance light scattering (RLS) signals and that at 420.0 and 570.0 nm are composed of both RLS and fluorescence emissions, respectively. UV-vis measurements showed that LP does not have the tendency of aggregation, and the strong RLS signals should be ascribed to the large hydrodynamic diameter of LP itself in aqueous medium, supported by dynamic light scattering (DLS) measurements.     

Monitoring human telomere DNA hybridization and G-quadruplex formation using gold nanorods

A facile and multi-response strategy for studying the transformations of human telomere DNA from single strand (ss) to double strand (ds) and G-quadruplex has been established by using positively charged gold nanorod (AuNR) as an optical label. The conformation change information of the telomere DNA was transferred into multiple optical signals, including changes in fluorescence emission, near infrared (NIR) absorption, plasma resonance light scattering (PRLS) and dynamic light scattering (DLS) response. The formations of dsDNA and G-quadruplex DNA induced fluorescence quenching of dye on DNA, and were accompanied by the intensity decrease and blue shift of the longitudinal absorption peak of AuNRs. Meanwhile, PRLS and DLS results revealed slightly increased AuNR aggregation due to increased charge density of dsDNA and G-quadruplex DNA as compared to ssDNA. Control experiment suggests that the AuNR-based assay is highly sequence specific; and the high sensitivity allows the study of human telomere DNA at a concentration as low as 58 nM.     

Positive ion electrospray ionization mass spectrometry of double-stranded DNA/drug complexes.

Positive ion electrospray ionization mass spectra of 16 base-pair double-stranded (ds)DNA have been obtained with essentially no ions from single-stranded DNA present. Single-stranded DNA was minimized by: (1) careful choice of DNA sequences; (2) the use of a relatively high salt concentration (0.1 M ammonium acetate, pH 8.5), and, (3) a low desolvation temperature (40 degrees C). Similarly, ESI-MS complexes of dsDNA with cisplatin, daunomycin and distamycin were obtained that contained only negligible amounts of single-stranded DNA. The complexes with daunomycin and distamycin were more stable to strand separation in the gas phase than dsDNA alone. This is in agreement with solution studies and with other recent gas phase results. These data contrast with many earlier ESI-MS studies of dsDNA and DNA/drug complexes in which ions from ssDNA are also normally observed.     

Study on the resonance light-scattering spectrum of anionic dye xylenol orange-cetyltrimethylammonium-nucleic acids system and determination of nucleic acids at nanogram levels

The interaction of xylenol orange (XO) and nucleic acids in the presence of cetyltrimethylammonium bromide (CTMAB) in aqueous solution has been studied by a resonance light-scattering (RLS) technique with a common spectrofluorometer. In hexamethylenetetramine (HMTA) buffer (pH7.30), XO and nucleic acids react with cetyltrimethylammonium bromide to form large particles of three-component complex, which results in strong enhanced RLS signals characterized by three peaks at 295.9, 335.5 and 542 nm, Mechanistic studies showed that the enhanced RLS stems from the aggregation of XO on DNA through the bridged and synergistic effect of CTMAB. With the enhanced RLS signals at the three wavelengths, the enhanced RLS intensity is proportional to the concentration of nucleic acids in an appropriate range. The lowest limit of determination was 5.31 ng ml(-1), three synthetic samples of yDNA were analyzed satisfactorily.     

Selective enzymatic labeling to detect packing-induced denaturation of double-stranded DNA at interfaces

The adsorption of DNA on surfaces is a widespread procedure and is a common way for fabrication of biosensors, DNA chips, and nanoelectronic devices. Although the biologically relevant and prevailing in vivo structure of DNA is its double-stranded (dsDNA) conformation, the characterization of DNA on surfaces has mainly focused on single-stranded DNA (ssDNA). Studying the structure of dsDNA on surfaces is of invaluable importance to microarray performance since their effectiveness relies on the ability of two DNA molecules to hybridize and remain stable. In addition, many of the enzymatic transactions performed on DNA require dsDNA, rather than ssDNA, as a substrate. However, it is not established that adsorbed dsDNA remains in its structure and does not denature. Here, two methodologies have been developed for distinguishing between surface-adsorbed single- and double-stranded DNA. We demonstrate that, upon formation of a dense monolayer, the nonthiolated strand comprising the dsDNA is released and the monolayer consists of mostly ssDNA. The fraction of dsDNA within the ssDNA monolayer depends on the length of the oligomers. A likely mechanism leading to this rearrangement is discussed.     

Resonance light scattering and derived techniques in analytical chemistry: past, present, and future

From 1993 to 1995, with a conventional fluorescence spectrophotometer (CFS) (convenient) and working in a synchronous scan model (easy-to-use), Pasternack et al. proposed the resonance light-scattering (RLS) technique, to efficiently characterize self-assemblies or self-aggregations of chromophores with good electronic coupling. Incident wavelengths were specially considered within their absorption envelopes (rather unorthodox), and their amplified signals were observed (good sensitivity and selectivity). Due to these absorbing benefits, RLS technique, as a novel readout method, commenced on its exciting analytical tours soon after Liu et al. and especially Li et al., separately, set out their corresponding pioneering investigations from 1995 to 1997. From then on, it has received an increasing attention by analysts, as a consequence exhibiting more and more fascinating analytical applications. Moreover, various attractive RLS-derived techniques have been developed successively to improve it or to enlarge its possibilities. Later on, Liu et al. and Li et al., Tabak et al., Yguerabide et al., Huang et al., Lakowicz et al. and Fernández Band et al. have made their outstanding contributions. In this review, we concentrate on major achievements of RLS in analytical chemistry for over a decade, involving the developments and analytical applications of RLS derived techniques treated as an impacting progress of RLS technique in analytical chemistry. Finally, an indication of future directions of RLS technique in analytical chemistry is provided.     

The structure of a mixed LNA/DNA:RNA duplex is driven by conformational coupling between LNA and deoxyribose residues as determined from 13C relaxation measurements

A study of the internal dynamics of an LNA/DNA:RNA duplex has been performed to further characterize the conformational changes associated with the incorporation of locked nucleic acid (LNA) nucleotides in a DNA:RNA duplex. In general, it was demonstrated that the LNA/DNA:RNA duplex has a very high degree of order compared to dsDNA and dsRNA duplexes. The order parameters of the aromatic carbon atoms in the LNA/DNA strand are uniformly high, whereas a sharp drop in the degree of order was seen in the RNA strand in the beginning of the AUAU stretch in the middle of the strand. This can be related to a return to normal dsRNA dynamics for the central A:U base pair. The high order of the heteroduplex is consistent with preorganization of the chimera strand for an A-form duplex conformation. These results partly explain the dramatic increase in T(m) of the chimeric heteroduplex over dsDNA and DNA:RNA hybrids of the same sequence.     

Detection of short oligonucleotide sequences using an electrochemical DNA hybridization biosensor

An electrochemical DNA hybridization biosensor was developed for the detection of DNA hybridization using MDB and proflavine as electrochemical labels. The biosensor was based on the interaction of 7-dimethyl-amino-1,2-benzophenoxazi-nium Meldola’s Blue (MDB) and proflavine with double stranded DNA (dsDNA) The electrochemical behaviour of MDB and proflavine as well as its interaction with double stranded (dsDNA) were investigated by cyclic (CV) and square wave voltammetry (SWV) and screen printed electrodes (ScPE). Furthermore, DNA-hybridization biosensors were developed for the detection of hybridization between oligonucleotides, which was detected by studying changes in the voltammetric peaks of MDB (reduction peak at −0.251 V) and proflavine (reduction peak at 0.075 V). MDB and proflavine were found to intercalate between the base pairs of dsDNA and oligonucleotides. Several factors affecting the dsDNA or oligonucleotides immobilization, hybridization and indicator preconcentration and interaction time, were investigated. As a result of the interaction of MDB with dsDNA and hybridized oligonucleotides, the voltammetric signals of MDB increased. Furthermore, guanine’s oxidation peak (at 0.901 V) was decreased as MDB’s concentration was increased. As a result of the interaction of proflavine with dsDNA and hybridized oligonucleotides, the voltammetric signals of proflavine decreased. These results were similar for carbon paste and screen printed electrodes. A comparison of the performance between CPE and ScPE was done. Our results showed that lower concentrations of MDB and proflavine were detected using screen printed electrodes. Moreover, reproducibility was better using screen printed electrodes and the detection was faster (regarding the experimental steps), but they are more cost effective.      

Fluorescence study of DNA binding and bending by EcoRI DNA methyltransferase

We have applied fluorescence anisotropy and fluorescence resonance energy transfer (FRET) techniques to study the interaction between EcoRI DNA methyltransferase (M.EcoRI) and its target DNA in solution. Upon binding with M.EcoRI, the dsDNA containing GAATTC bends to flip out the second adenine for methylation. The binding affinity of M.EcoRI to two dsDNA fragments (20 and 38 bp) was studied with fluorescence anisotropy. Their binding constants at different temperatures from 20 to 40 degrees C were obtained, and the thermodynamic parameters of binding were derived. The results showed that M.EcoRI had a higher binding affinity to the short dsDNA strand than to the long one, and its binding to DNA was primarily entropy-driven. By labeling the 5' ends of the 20-bp dsDNA with two fluorescent dyes, fluorescein (FAM) and tetramethylrhodamine (TMR), we were able to monitor the enhanced TMR fluorescence in the presence of M.EcoRI. The end-to-end distance of the dsDNA determined from the FRET efficiency was changed from 72.4 to 63.4 A, and the DNA bending angle was estimated as 57.8 degrees .     

Characterization of single- and double-stranded DNA on gold surfaces

Single- and double-stranded deoxy ribonucleic acid (DNA) molecules attached to self-assembled monolayers (SAMs) on gold surfaces were characterized by a number of optical and electronic spectroscopic techniques. The DNA-modified gold surfaces were prepared through the self-assembly of 6-mercapto-1-hexanol and 5'-C(6)H(12)SH -modified single-stranded DNA (ssDNA). Upon hybridization of the surface-bound probe ssDNA with its complimentary target, formation of double-stranded DNA (dsDNA) on the gold surface is observed and in a competing process, probe ssDNA is desorbed from the gold surface. The competition between hybridization of ssDNA with its complimentary target and ssDNA probe desorption from the gold surface has been investigated in this paper using X-ray photoelectron spectroscopy, chronocoulometry, fluorescence, and polarization modulation-infrared reflection absorption spectroscopy (PM-IRRAS). The formation of dsDNA on the surface was identified by PM-IRRAS by a dsDNA IR signature at approximately 1678 cm(-)(1) that was confirmed by density functional theory calculations of the nucleotides and the nucleotides' base pairs. The presence of dsDNA through the specific DNA hybridization was additionally confirmed by atomic force microscopy through colloidal gold nanoparticle labeling of the target ssDNA. Using these methods, strand loss was observed even for DNA hybridization performed at 25 degrees C for the DNA monolayers studied here consisting of attachment to the gold surfaces by single Au-S bonds. This finding has significant consequence for the application of SAM technology in the detection of oligonucleotide hybridization on gold surfaces.     

A resonance light-scattering off–on system for studies of the selective interaction between adriamycin and DNA

On the basis of the resonance light scattering (RLS) of Ag nanoparticles (AgNPs), an RLS off–on system was developed for studies of the selective interaction between adriamycin (ADM) and DNA. In this strategy, addition of ADM could induce a proportional decrease in the RLS intensity of AgNPs; this could be used to detect trace amounts of ADM with a detection limit of 12.75 ng mL⁻¹ in the range 0.021–10.0 μg mL⁻¹. Subsequently, by investigating the ability of different DNA sequences to restore the RLS intensity of the analytical systems, we found that ADM was selective to dsDNA and had an obvious preference for sequences that were rich in guanine and cytosine bases. In order to validate the results of the RLS assay, fluorescence quenching was used, and binding constants and binding numbers of each system were calculated. Compared with other methods, this RLS off–on strategy was more sensitive, fast, and reliable. It has also supplied a novel method for studying the sequence selectivity of DNA-targeted anticancer drugs and is a novel application of the RLS technique in analytical chemistry.     

Massively parallel display of genomic DNA fragments by rolling-circle amplification and strand displacement amplification on chip

Massively parallel genomic DNA fragments display on chip plays a key role in the new generation DNA sequencing. Here, we developed a new technology to display the parallel genomic DNA fragment massively based on two-step reaction with Ф29 DNA polymerase. The genomic DNA fragments were firstly amplified by rolling-circle amplification (RCA) reaction in liquid phase, and then amplified further on the chip by the strand displacement of Ф29 DNA polymerase. In our experiments, through DNA colonies produced by two-step amplification reaction T7 genomic DNA fragments are displayed massively and parallely on the chip, which has been verified through hybridizing the probe labeled with fluorescence or extension reaction with fluorescent-dNTP. The significant difference of fluourescence signals between background and displayed DNA fragments could be obtained. Our results show that the method has good reproducibility in experiments, which may be hopeful to serve the high-throughput sequencing.     

Carbon nanotubes/(pLys/dsDNA) n layer-by-layer multilayer films for electrochemical studies of DNA damage

Carboxylic group-functionalized carbon nanotubes (c-CNT) were modified on the surface of carbon paste electrode to obtain a conducting precursor film. Positively charged poly-l-lysine (pLys) and negatively charged double-stranded DNA (dsDNA) were alternately adsorbed on the c-CNT-modified electrode, forming (pLys/dsDNA) _n layer-by-layer (LBL) films. Cyclic voltammetry and electrochemical impedance spectroscopy of the electroactive probe [Fe(CN)₆]^3−/4− could give the valuable dynamic information of multilayer films growth. The oxidative DNA damage induced by cadmium ion (Cd²⁺) in the LBL multilayer films was studied by differential pulse voltammetry (DPV) with methylene violet (MV) as the intercalation redox probe. The electrochemical signals of MV on the multilayer films were effectively amplified via LBL technology. The specific intercalation of MV into dsDNA base pairs and the amplified electrochemical response of MV, combined with the unique feature of loading reversibility of MV in the DNA layer-by-layer films, made the difference in DPV response between the intact, and damaged dsDNA films become pronounced. This biosensor exhibited that the (pLys/dsDNA) _n films could be utilized for investigations of DNA damage.