Direct determination of single-to-double stranded DNA ratio in solution using steady-state fluorescence measurements

We report a simple and rapid method for quantitation of single-to-double stranded (ss : ds) DNA ratios in solution, using steady-state measurements of fluorescence from two simultaneously excited intercalated dyes; the ratio of fluorescence intensities from PicoGreen (525 nm) and ethidium bromide (610 nm) is directly proportional to the ss : ds DNA ratio.     

Spectral and Electrochemical Investigation of Intercalations of Adrenaline and CT－DNA

A strong interaction between double stranded calf-thymus DNA (ds-DNA) and adrenaline in solution, but no interaction between single stranded calf-thymus DNA (ss-DNA) and adrenaline was observed by the use of UV-visible spectroscopy and voltammetric techniques. It is suggested that the interaction leads to an intercalation of adrenaline molecules into the groove of ds-DNA and the formation of ds-DNA (adrenallne)n complex. The binding site size of the interaction of adrenaline with CT-DNA in nucleotide phosphate [ NP] has been determined as 25. The interaction of different concentration adrenaline with DNA modified GCE shows that the DNA modified GCE can be a good tool to detect lower concentration adrenaline.     

Type‐Dependent Identification of DNA Nucleobases by Using Diamondoids

The possibility of distinguishing between DNA nucleobases of different sizes is manifested here through quantum‐mechanical simulations. By using derivatives of small, modified diamond clusters, known as diamondoids, it is possible to separate the pyrimidines (cytosine and thymine) from the larger purines (adenine and guanine), according to the collective electronic and binding properties of these DNA nucleobases and the diamondoid. The latter acts as a probe with which these properties can be examined in detail. Short single‐stranded DNA is built up from single nucleobases to reveal the effect of each DNA unit on the sensing abilities of the diamondoid probe. Several ways of orienting the nucleobases, nucleosides, nucleotides, and short single‐stranded DNA are investigated; these lead to quite different electronic properties and may or may not enhance the possibility of separating the DNA nucleobases. For the optimum orientation, that is, one that promotes stronger hydrogen bonding of the diamondoid to the short DNA strand, it is found that the electronic band gaps of a purine strand lie in a completely different range to the band gaps of a pyrimidine strand. This difference can be over 1 eV, which is measurable and shows the potential of using diamondoids and their derivatives in biosensing devices.     

Cylindrical projection of electrostatic potential and image analysis tools for damaged DNA: the substitution of thymine with thymine glycol

Changes of electrostatic potential around the DNA molecule resulting from chemical modifications of nucleotides may play a role in enzymatic recognition of damaged sites. Effects of chemical modifications of nucleotides on the structure of DNA have been characterized through electronic structure computations. Quantum mechanical structural optimizations of fragments of five pairs of nucleotides with thymine or thymine glycol were performed at the density functional level of theory with a B3LYP exchange-correlation functional and 6-31G(d,p) basis sets. The electrostatic potential (EP) around DNA fragments was projected on a cylindrical surface around the double helix. The 2D maps of EP of intact and damaged DNA fragments were compared using image analysis methods to identify and measure modifications of the EP that result from the occurrence of thymine glycol. It was found that distortions of phosphate groups and displacements of the accompanying countercations by up to approximately 0.5 angstroms along the axis of DNA are clearly reflected in the EP maps. Modifications of the EP in the major groove of DNA near the damaged site are also reported.     

Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions

DNA/RNA chromatography presents a versatile platform for the analysis of nucleic acids. Although the mechanism of separation of double stranded (ds) DNA fragments is largely understood, the mechanism by which RNA is separated appears more complicated. To further understand the separation mechanisms of RNA using ion pair reverse phase liquid chromatography, we have analysed a number of dsRNA and single stranded (ss) RNA fragments. The high-resolution separation of dsRNA was observed, in a similar manner to dsDNA under non-denaturing conditions. Moreover, the high-resolution separation of ssRNA was observed at high temperatures (75 °C) in contrast to ssDNA. It is proposed that the presence of duplex regions/secondary structures within the RNA remain at such temperatures, resulting in high-resolution RNA separations. The retention time of the nucleic acids reflects the relative hydrophobicity, through contributions of the nucleic sequence and the degree of secondary structure present. In addition, the analysis of RNA using such approaches was extended to enable the discrimination of bacterial 16S rRNA fragments and as an aid to conformational analysis of RNA. RNA:RNA interactions of the human telomerase RNA component (hTR) were analysed in conjunction with the incorporation of Mg²⁺ during chromatography. This novel chromatographic procedure permits analysis of the temperature dependent formation of dimeric RNA species.     

Interaction of the mutagen ethidium bromide with DNA, using a carbon paste electrode and a hanging mercury drop electrode

The interaction of ethidium bromide (2,7-diamino-10-ethyl-9-phenylphenanthridinium bromide; EB) with double stranded (ds) calf thymus DNA and thermally denatured single stranded (ss) DNA was studied in solution and at the electrode surface by means of transfer voltammetry using a carbon paste electrode (CPE) as working electrode in 0.2 M acetate buffer, pH 5.0. As a result of intercalation of this dye between the base pairs of dsDNA, the characteristic peak of dsDNA, due to the oxidation of guanine residues, decreased and after a particular concentration of EB a new peak at +0.81 V appeared, probably due to the formation of a complex between dsDNA and EB. The non-intercalated EB gives another peak, but at an increased concentration of the dye. A similar behaviour was observed during the interaction of the dye with ssDNA.Furthermore, the interaction of EB with ds, ss and supercoiled (sc) DNA was studied at the hanging mercury drop electrode (HMDE) surface by means of alternating current voltammetry in 0.3 M NaCl and 50 mM sodium phosphate buffer (pH 8.5) as supporting electrolyte. dsDNA yields a smaller peak at −1.42 V (peak III) compared to the one yielded by ssDNA, since the latter is a relaxed and more accessible form. By addition of EB into the buffer solution an increase of peak III was observed in the dsDNA form as well as in ssDNA resulting from their interaction with EB. Furthermore, the appearance of peak III in covalently closed circular scDNA after exposure to increasing concentrations of EB is a result of the introduction of ‘free ends’ in DNA affecting its structural integrity.     

Simultaneous detection of purine and pyrimidine at highly boron-doped diamond electrodes by using liquid chromatography

Highly boron-doped diamond (BDD) electrode, have been examined for simultaneous detection of purine and pyrimidine bases in mild acidic media by using HPLC with amperometric detection. Cyclic voltammetry at as-deposited (AD) and anodically oxidized (AO) BDD were used to study the electrochemistry and to optimize the condition for HPLC applications. At AO BDD electrode, due to its higher overpotential of oxygen evolution reaction, well-defined anodic peaks were observed for the oxidation of purine and pyrimidine bases in acid medium, whereas at AD BDD the oxidation peak of thymine was overlapped with the anodic current of oxygen evolution. The chromatograms of adenine, guanine, cytosine, thymine and 5-methylcytosine mixture were well resolved by using a silica-based column and a solution of 5% acetonitrile in 100 mM ammonium acetate buffer (pH 4.25) as the mobile phase. The detection was carried out at AO BDD electrode at an applied potential of 1.6 V versus Ag/AgCl. Linear calibration curves were obtained within the concentration range from 0.1 to 10 μM with the limits of detection (S/N = 3) ranging from 26.3 to 162.1 nM, resulting in an order of magnitude higher sensitivities than those at conventional electrodes. HPLC analysis with diamond amperometric detector was successfully applied for determination of 5-methylcytosine in real DNA samples with high reproducibility. No deactivation of the electrode was found during cyclic voltammetric and HPLC measurements, indicating the high stability for analysis of biological samples.     

Synthesis and RNA-selective hybridization of α-l-ribo- and β-d-lyxo-configured oligonucleotides

Three α-l-ribofuranosyl analogues of RNA nucleotides (α-l-RNA analogues) have been synthesized and incorporated into oligonucleotides using the phosphoramide approach on an automated DNA synthesizer. The 4′-C-hydroxymethyl-α-l-ribofuranosyl thymine monomer was furthermore synthesized. Relative to the unmodified duplexes, incorporation of a single α-l-RNA monomer into a DNA strand leads to reduced thermal stability of duplexes with DNA complements but unchanged thermal stability of duplexes with RNA complements, whereas incorporation of more than one α-l-RNA monomer lead to moderately decreased thermal stability also of duplexes with RNA complements. Efficient hybridization with an RNA complement and no melting transition with a DNA complement were observed with stereoregular chimeric oligonucleotides composed of a mixture of α-l-RNA and affinity enhancing α-l-LNA monomers (α-l-ribo-configured locked nucleic acid). Furthermore, duplexes formed between oligodeoxynucleotides containing an α-l-RNA monomer and complementary RNA were good substrates for Escherichia coli RNase H. RNA-selective hybridization was also achieved by the incorporation of 1-(4-C-hydroxymethyl-β-d-lyxofuranosyl)thymine monomers into a DNA strand, whereas stable duplexes were formed with both complementary DNA and RNA when these monomers were incorporated into an RNA strand.     

Butylacrylate‐nucleobase Conjugates as Targets for Two‐step Redox Labeling of DNA with an Osmium Tetroxide Complex

Modification of nucleic acids with osmium tetroxide reagents (Os,L, such as OsO₄,2,2′‐bipyridine, Os,bpy) has been applied in redox DNA labeling, in probing DNA structure as well as in studies of DNA interactions with other molecules. In natural DNA, primarily thymine residues form adducts with the Os,bpy in a structure selective manner. In this paper we introduce a new two‐step technique of DNA modification with the electroactive Os,bpy, consisting in enzymatic construction of DNA bearing butyl acrylate (BA) moieties attached to uracil at C5 or to 7‐deaza adenine at C7, followed by chemical modification of a reactive C=C double bond in the acrylate residue. We demonstrate a facile modification of the BA conjugates in both single‐ and double‐stranded (ds) DNA under conditions when modification within the nucleobase rings in ds DNA is hindered. Various DNA−Os,bpy adducts can easily be analyzed electrochemically and distinguished by different redox potentials. The two‐step procedure appears to be applicable in osmium redox labelling of ds DNA.     

COMPARATIVE STUDY OF OXIDATION OF NUCLEIC ACID COMPONENTS BY HYDROXYL RADICALS, SINGLET OXYGEN AND SUPEROXIDE ANION RADICALS

Abstract— Superoxide radicals, singlet oxygen and hydroxyl radicals are individually or in combination involved in radiation or photochemical processes and in various enzymatic reactions. The reactivity and the mechanism of reaction of these oxygen species with some biologically significant DNA components were investigated through the characterization of the final oxidation products.
Superoxide radicals appear to be unreactive with purine and pyrimidine 2'-deoxyribonucleosides. However, the autoxidation reaction of 6-hydroxydopamine leads to extensive degradation of thymine through the intermediary of hydroxyl radicals. Chemically and microwave-discharge generated singlet oxygen oxidation is specific to 2'-deoxyguanosine. The main oxidized products of these reactions were also characterized as well as an as yet unidentified nucleoside in the methylene-blue photooxydation of 2-deoxyguanosine. These results, in addition to specific deuterium effect experiments, lend support to the involvment of singlet oxygen (type II mechanism) in the methylene-blue photosentization. No singlet oxygen effect was observed in aqueous irradiated system.     

GAMMA RAY THERMOLUMINESCENCE IN NUCLEIC ACID CONSTITUENTS

Abstract— The phenomenon of gamma ray thermoluminescence has been studied in DNA, RNA, and their various constituents. Single peaks in the glow curves have been usually observed at 110–120°K except in cytosine which shows two peaks at 135°K and 180°K. Adenine and cytosine show very intense thermoluminescence whereas the intensity of light emitted from thymine, uracil and guanine is very small. The addition of sugar and sugar-phosphate groups to the base-molecules affects only the amount of light emitted. The thermoluminescence emission spectra lie in the same wavelength region as the u.v. induced phosphorescence, suggesting a triplet-singlet transition. The spectral content of DNA thermoluminescence seems to be superposition of contributions from its constituents. An attempt is made to explain the phenomenon as a result of electron-cation recombination.     

Electrochemical Quantitative Analysis of Nucleic Acids Using β‐Cyclodextrin Modified Gold Electrode

We present an electrochemical biosensor for the analysis of nucleic acids upon hybridization on the β‐cyclodextrin (β‐CD)‐modified gold electrode. The strategy is based on the following: The 5’‐ferrocene‐labeled single stranded capture probe DNA (5’‐fc‐ss‐DNA) was incorporated into the cavity of thiolated β‐CD which was immobilized on the surface of gold electrode. After hybridization of complementary target DNA, hybridized double stranded DNA (ds‐DNA) was released from the cavity of β‐CD. The difference of electrochemical properties on the modified gold electrode was characterized by cyclic voltametry and surface plasmon resonance. We successfully applied this method to the investigation of the sensor responses due to hybridization on various concentrations of applied target DNA. As a result, the label‐free electrochemical DNA sensor can detect the target DNA with a detection limit of 1.08 nM. Finally, our method does not require either hybridization indicators or other signalling molecules such as DNA intercalaters which most of electrochemical hybridization detection systems require.     

Use of Mercury Film Glassy Carbon Electrode Modified with Multiwalled Carbon Nanotubes in Electrochemical Analysis of DNA

Mercury film plated on a glassy carbon electrode modified with multiwalled carbon nanotubes (MF/MWNTs/GCE) was used for the analysis of single (ss) and double stranded (ds) DNA, as well as for Jurkat genomic DNAs methylated to different degrees. The results indicated that the DNA molecules adsorbed quite strongly on the MF/MWNTs/GCE surface allowing ex situ adsorption and produce well developed peaks (due to cytosine and adenine) by using adsorptive stripping (Ads, ex situ) square wave voltammetry (SWV). Also, SWV of Jurkat DNA mixtures methylated to different degrees revealed a linear decrease of the peak height with increasing methylation indicating an increase of structural rigidity.     

Interaction Between DNA and Some Salicylic Acid Derivatives and Characterization of Their DNA Targets

A nanofiber polypyrrole (PPy) film was electrochemically deposited on a Pt electrode and used for immobilization of single‐stranded DNA (ssDNA) and investigation of hybridization events. Then, the interaction of DNA with four salicylic acid (SA) derivatives was studied with electrochemical methods. The oxidation peak of guanine was decreased by increasing the concentrations of salicylic acid derivatives. The binding constants of these compounds with four different sequences of DNA including different percentages of guanine‐cytosine and adenine‐thymine bases were calculated and it was clarified that sequences with higher percentage of adenine‐thymine bases have a higher binding constant in their interaction with SA derivatives.     

Electrocatalytic oxidation of nucleobases by TiO2 nanobelts

Two kinds of TiO(2) nanobelts were prepared from commercial P-25 powders via an alkaline hydrothermal method with and without an acid etching process. The uncauterized nanobelts (TNs) exhibited a smooth surface, and mixed phases of anatase and TiO(2) (B), whereas the cauterized ones (CTNs) displayed a rough surface and a pure anatase structure. TNs and CTNs were then deposited onto a glassy carbon electrode (GCE) surface with a conductive adhesive (CA), and the resulting chemically modified electrodes exhibited electrocatalytic activities in the oxidation of nucleobases in a 0.1 M phosphate buffer solution (PBS) at pH 7.4. For guanine and adenine, well-defined oxidation peaks were observed in voltammetric measurements at about +0.62 and +0.89 V, respectively, at a potential sweep rate of 100 mV s(-1), whereas for cytosine, uracil and thymine, the voltammetric features were not obvious. The average surface coverages (Γ) of guanine and adenine on the CTNs/CA/GCE electrode were estimated to be 4.75 × 10(-10) and 7.44 × 10(-10) mol cm(-2), respectively, which were about twice those at the TNs/CA/GCE electrode. The enhanced activity of the CTN-based electrode towards purine nucleobase oxidation was ascribed to the large specific surface area and anatase structures with enhanced (001) facets of the CTN that facilitated adsorption of the analytes onto the electrode surface and charge transport through the electrode surface layer.     

Ultrasensitive and Signal‐on Electrochemiluminescence Aptasensor Using the Multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin Complexes

An ultrasensitive and signal‐on electrochemiluminescence (ECL) aptasensor to detect target protein (thrombin or lysozyme) was developed using the host‐guest recognition between a metallocyclodextrin complex and single‐stranded DNA (ss‐DNA). The aptasensor uses both the photoactive properties of the metallocyclodextrins named multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin complexes and their specific recognition with ss‐DNA, which amplified the ECL signal without luminophore labeling. After investigating the ECL performance of different multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin (multi‐Ru‐β‐CD) complexes, tris‐tris(bipyridine)‐ruthenium(II)‐β‐cyclodextrin (tris(bpyRu)‐β‐CD) was selected as a suitable host molecule to construct an atasensor. First, double‐stranded DNA (ds‐DNA) formed by hybridization of the aptamer and its target DNA was attached to a glassy carbon electrode via coupling interaction, which showed low ECL intensity with 2‐(dibutylamino) ethanol (DBAE) as coreactant, because of the weak recognition between ds‐DNA and tris(bpyRu)‐β‐CD. Upon addition of the corresponding protein, the ECL intensity increased when target ss‐DNA was released because of the higher stability of the aptamer‐protein complex than the aptamer‐DNA one. A linear relationship was observed in the range of 0.01 pmol/L to 100 pmol/L between ECL intensity and the logarithm of thrombin concentrations with a limited detection of 8.5 fmol/L (S/N=3). Meanwhile, the measured concentration of lysozyme was from 0.05 pmol/L to 500 pmol/L and the detection limit was 33 fmol/L (S/N=3). The investigations of proteins in human serum samples were also performed to demonstrate the validity of detection in real clinical samples. The simplicity, high sensitivity and specificity of this aptasensor show great promise for practical applications in protein monitoring and disease diagnosis.     

Oxidative amination of cuprated pyrimidine and purine derivatives

Using regioselective cuprations (via magnesiations), various primary, secondary and tertiary aminated pyrimidine and purine derivatives were prepared by the oxidative coupling of lithium amidocuprates using chloranil. DNA and RNA units such as aminated uracil or thymine, and adenine, as well as a CDK inhibitor, purvalanol A, were all obtained under mild conditions and satisfactory yields.     

Thermodynamics for the Formation of Double‐Stranded DNA–Single‐Walled Carbon Nanotube Hybrids

For the first time, the thermodynamics are described for the formation of double‐stranded DNA (ds‐DNA)–single‐walled carbon nanotube (SWNT) hybrids. This treatment is applied to the exchange reaction of sodium cholate (SC) molecules on SWNTs and the ds‐DNAs d(A)₂₀–d(T)₂₀ and nuclear factor (NF)‐κB decoy. UV/Vis/near‐IR spectroscopy with temperature variations was used for analyzing the exchange reaction on the SWNTs with four different chiralities: (n,m)=(8,3), (6,5), (7,5), and (8,6). Single‐stranded DNAs (ss‐DNAs), including d(A)₂₀ and d(T)₂₀, are also used for comparison. The d(A)₂₀–d(T)₂₀ shows a drastic change in its thermodynamic parameters around the melting temperature (T_m) of the DNA oligomer. No such T_m dependency was measured, owing to high T_m in the NF‐κB decoy DNA and no T_m in the ss‐DNA.     

Electrospray tandem mass spectrometry of mixed-sequence RNA/DNA oligonucleotides

The fragmentation of electrospray-generated multiply deprotonated RNA and mixed-sequence RNA/DNA pentanucleotides upon low-energy collision-induced dissociation (CID) in a hybrid quadrupole time-of-flight mass spectrometer was investigated. The goal of unambiguous sequence identification of mixed-sequence RNA/DNA oligonucleotides requires detailed understanding of the gas-phase dissociation of this class of compounds. The two major dissociation events, base loss and backbone fragmentation, are discussed and the unique fragmentation behavior of oligoribonucleotides is demonstrated. Backbone fragmentation of the all-RNA pentanucleotides is characterized by abundant c-ions and their complementary y-ions as the major sequence-defining fragment ion series. In contrast to the dissociation of oligodeoxyribonucleotides, where backbone fragmentation is initiated by the loss of a nucleobase which subsequently leads to the formation of the w- and [a-base]-ions, backbone dissociation of oligoribonucleotides is essentially decoupled from base loss. The different behavior of RNA and DNA oligonucleotides is related to the presence of the 2'-hydroxyl substituent, which is the only structural alteration between the DNA and RNA pentanucleotides studied. CID of mixed-sequence RNA/DNA pentanucleotides results in a combination of the nucleotide-typical backbone fragmentation products, with abundant w-fragment ions generated by cleavage of the phosphodiester backbone adjacent to the deoxy building blocks, whereas backbone cleavage adjacent to ribonucleotides induces the formation of c- and y-ions.     

RNA analysis by MEKC with LIF detection

We have developed and validated a procedure of high sensitivity for the analysis of RNA. The procedure is based on the separation and detection of the 5'-monophosphates of ribonucleosides selectively conjugated with 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-propionyl ethylene diamine hydrochloride (BODIPY FL EDA) at the 5'-phosphate group using CE with LIF. BODIPY conjugates of the four common ribonucleoside-5'-monophosphates were prepared and subjected to CE-LIF to serve as standard compounds for peak assignment and to develop separation conditions. After digestion of RNA or oligoribonucleotides to 5'-monophosphates by nuclease P1 and fluorescence labeling BODIPY conjugates were detected and resolved by CE-LIF without further purification steps. Comparative CE-LIF analyses with DNA digested to deoxyribonucleoside-5'-monophosphates showed that the assay is equally efficient and sensitive for RNA analysis. Conditions to determine the modified ribonucleosides inosine, xanthosine, pseudouridine and 2'-O-methyladenosine were also established. The limits of detection were in the range of 80-200 pM. After calibrating the assay with oligoribonucleotides, pseudouridine was quantified in total RNA of Drosophila, human liver, human kidney and t-RNA of Saccharomyces cerevisiae. These studies demonstrate good potential of fluorescence labeling of ribonucleoside-5'-monophosphates with BODIPY FL EDA and detection by CE-LIF to determine RNA composition with high accuracy and sensitivity.