Oligonucleotides In Solution Research Articles

Characterization of DNA hybridization on the optical fiber surface

Immobilized oligonucleotide has been utilized widely for the development of DNA biosensors. In this study we report the characterization of the oligonucleotide probe hybridization process on the optical fiber surface. Streptavidin was covalently linked to the core surface of a multimode optical fiber and used as a bridge for the immobilization of a thin layer of 5′-biotinylated oligonucleotide probes. Following hybridization to the 5′-fluorescein labeled target oligonucleotides in solution, the fluorescence signal generated on the optical fiber surface by laser excitation traveled back into the optical fiber core and was collected at the proximal end. With the evanescent wave excitation and detection method used, a very sharp discrimination of bulk fluorescence against surface excitation in combination with high excitation intensities could be achieved. The preliminary results showed that the hybridization process on the optical fiber surface was specific and it could identify a single base mismatch in the hybridized duplex under experimental conditions. Hybridization performance of surface immobilized oligonucleotides to various concentrations of target oligonucleotides in solution was studied. Regeneration of the optical fiber surface was possible without a significant loss of the hybridization ability.

A-form Conformational Motifs in Ligand-bound DNA Structures

Recognition and biochemical processing of DNA requires that proteins and other ligands are able to distinguish their DNA binding sites from other parts of the molecule. In addition to the direct recognition elements embedded in the linear sequence of bases (i.e. hydrogen bonding sites), these molecular agents seemingly sense and/or induce an “indirect” conformational response in the DNA base-pairs that facilitates close intermolecular fitting. As part of an effort to decipher this sequence-dependent structural code, we have analyzed the extent of B→ A conformational conversion at individual base-pair steps in protein and drug-bound DNA crystal complexes. We take advantage of a novel structural parameter, the position of the phosphorus atom in the dimer reference frame, as well as other documented measures of local helical structure, e.g. torsion angles, base-pair step parameters. Our analysis pinpoints ligand-induced conformational changes that are difficult to detect from the global perspective used in other studies of DNA structure. The collective data provide new structural details on the conformational pathway connecting A and B-form DNA and illustrate how both proteins and drugs take advantage of the intrinsic conformational mechanics of the double helix. Significantly, the base-pair steps which exhibit pure A-DNA conformations in the crystal complexes follow the scale of A-forming tendencies exhibited by synthetic oligonucleotides in solution and the known polymorphism of synthetic DNA fibers. Moreover, most crystallographic examples of complete B-to- A deformations occur in complexes of DNA with enzymes that perform cutting or sealing operations at the (O3′-P) phosphodiester linkage. The B→ A transformation selectively exposes sugar-phosphate atoms, such as the 3′-oxygen atom, ordinarily buried within the chain backbone for enzymatic attack. The forced remodeling of DNA to the A-form also provides a mechanism for smoothly bending the double helix, for controlling the widths of the major and minor grooves, and for accessing the minor groove edges of individual base-pairs.

Quantitative characterization of the interaction between purified human estrogen receptor alpha and DNA using fluorescence anisotropy.

In an effort to better define the molecular mechanisms of the functional specificity of human estrogen receptor alpha, we have carried out equilibrium binding assays to study the interaction of the receptor with a palindromic estrogen response element derived from the vitellogenin ERE. These assays are based on the observation of the fluorescence anisotropy of a fluorescein moiety covalently bound to the target oligonucleotide. The low anisotropy value due to the fast tumbling of the free oligonucleotide in solution increases substantially upon binding the receptor to the labeled ERE. The quality of our data are sufficient to ascertain that the binding is clearly cooperative in nature, ruling out a simple monomer interaction and implicating a dimerization energetically coupled to DNA binding in the nanomolar range. The salt concentration dependence of the affinity reveals formation of high stoichiometry, low specificity complexes at low salt concentration. Increasing the KCl concentration above 200 mM leads to specific binding of ER dimer. We interpret the lack of temperature dependence of the apparent affinity as indicative of an entropy driven interaction. Finally, binding assays using fluorescent target EREs bearing mutations of each of the base pairs in the palindromic ERE half-site indicate that the energy of interaction between ER and its target is relatively evenly distributed throughout the site.

Muscle Differentiation Is Antagonized by SOX15, a New Member of the SOX Protein Family

SOX proteins belong to a multigenic family characterized by a unique DNA binding domain, known as the high mobility group box, that is related to that of the testis determining gene SRY. cDNA sequences for more than 30 SOX genes have been identified, and some are known to have diverse roles in vertebrate differentiation and development. Here, we report the isolation and characterization of mouse Sox15 that was uncovered during a screen for high mobility group box containing transcription factors that are expressed at different levels during skeletal muscle differentiation. Sox15 cDNAs were found at a much higher frequency in myoblasts prior to their differentiation into myotubes. Electrophoretic mobility shift assays indicated that recombinant SOX15 protein was capable of binding to a consensus DNA binding site for SOX proteins. When overexpressed in C2C12 myoblasts, wild type SOX15, but not a C-terminal truncated form or the related protein SOX11, specifically inhibited activation of muscle-specific genes and expression of the basic helix-loop-helix myogenic factors myogenin and MyoD, resulting in a failure of the cells to differentiate into myotubes. These results suggest a specific and repressive role for SOX15, requiring the C-terminal domain, during myogenesis.

Inhibition of inositol uptake in astrocytes by antisense oligonucleotides delivered by pH-sensitive liposomes.

An oligonucleotide of 20 bases, complementary to a region of the sodium/myo-inositol cotransporter (SMIT) mRNA, was used to investigate the uptake efficiency and activity of transferred antisense oligonucleotides with regard to substrate uptake. We compared the efficiency of oligonucleotide delivery after application of either free or liposome-encapsulated material. Delivery of liposome-encapsulated material (marker or oligonucleotides) into astrocytoma cells and primary astrocyte cultures was more effective with pH-sensitive liposomes [dioleoylphosphatidylethanolamine (DOPE)/cholesteryl hemisuccinate (CHEMS)] than with non-pH-sensitive liposomes (soy lecithin) or free material in solution. Antisense activity was evaluated by determination of myo-inositol uptake and detection of SMIT transcripts by RT-PCR. Encapsulation of oligonucleotides in pH-sensitive liposomes increased the inhibition of inositol uptake at least 50-fold compared with application of free oligonucleotides in solution.

Detection of Single-Base Substitutions in Amplified Fragments via Ligation of a Tandem of Short Oligonucleotides in Solution and on a Solid Carrier

Ligation of a tandem of short oligonucleotides was proposed for detecting single-base substitutions in amplified DNA fragments. An octamer–tetramer–octamer tandem was ligated on a 20-mer template with T4 DNA ligase. As shown with radiolabeled oligonucleotides, the efficiency and selectivity of ligation did not change with an octamer linked to a water-soluble carrier based on polyethylene glycol (MPEG), while ligation was somewhat lower with the octamer immobilized on methacrylate beads (DMEG). In both cases, polymer attachment improved the discrimination of 20-mer templates with single-base substitutions in the binding site for the tetramer or for the immobilized octamer. Tandems with a radiolabeled or biotinylated component were also efficiently ligated on amplified DNA fragments. The data obtained with DNA fragments of HIV-1 strains bru and rf demonstrate the possibility of reliable detection of single-base substitutions via ligation of a tandem and colorimetric detection of the immobilized ligation product with the streptavidin–alkaline phosphatase technique.

Interstrand cross-links of cisplatin induce striking distortions in DNA

In the reaction between cellular DNA and cisplatin, different bifunctional adducts are formed including intrastrand and interstrand cross-links. The respective role of these lesions in the cytotoxicity of the drug is not yet elucidated. This paper deals with the current knowledge on cisplatin interstrand cross-links and presents results on the formation, stability and structure of these adducts. A key step in the studies of these lesions is the recent determination of solution and crystallographic structures of double-stranded oligonucleotides containing a unique interstrand cross-link. The DNA distortions induced by this adduct exhibit unprecedented features such as the location of the platinum residue in the minor groove, the extrusion of the cytosines of the cross-linked d(GpC)·d(GpC) site, the bending of the helix axis towards the minor groove and a large DNA unwinding. In addition to a detailed determination of the distortions, the high resolution of the crystal structure allowed us to locate the water molecules surrounding the adduct. The possible implications of this structure for the chemical properties and the cellular processing of cisplatin interstrand cross-links are discussed.

D 2 dopamine receptor but not AMPA and kainate glutamate receptor genes show altered expression in response to long term treatment with trans- and cis-flupenthixol in the rat brain

Glutamate receptor function has been hypothesized as an important factor in both the aetiology and treatment of schizophrenia. We have used a multiprobe oligonucleotide solution hybridization (MOSH) technique to examine the regulation of gene expression of the GluR1–7, KA1, and KA2 glutamate receptor subunits in the left rat brain following treatment with the optical isomers of flupenthixol at a dose of 0.2 mg kg −1 day −1 over a period of 4, 12, 24 weeks in order to understand how specific glutamate receptor genes are involved in the treatment of schizophrenia. The GluR2/3 and GluR6/7 subunit immunoreactivity in the right brain following 4 and 24 weeks of drug treatment was also examined by Western blotting. Neither trans- nor cis-flupenthixol was found to alter the gene expression of any of the 9 non-NMDA glutamate receptor subunits. On the other hand, we found a nearly two-fold increase in gene expression of the D 2 dopamine receptor in specific brain regions. These results suggest that non-NMDA types of glutamate receptor subunits, in contrast to NMDA receptors, are less likely to have a role in the action of antipsychotic drugs.

Structure of a binary complex of HhaI methyltransferase with S-adnosyl-l-methionine formed in the presence of a short non-specific DNA oligonucleotide

We have determined a structure for a complex formed between HhaI methyltransferase (M.HhaI) and S-adenosyl-l-methionine (AdoMet) in the presence of a non-specific short oligonucleotide. M.HhaI binds to the non-specific short oligonucleotides in solution. Although no DNA is incorporated in the crystal, AdoMet binds in a primed orientation, identical with that observed in the ternary complex of the enzyme, cognate DNA, and AdoMet or S-adenosyl-l-homocysteine (AdoHcy). This orientation differs from the previously observed unprimed orientation in the M.HhaI-AdoMet binary complex, where the S+-CH3 unit of AdoMet is protected by a favorable cation-π interaction with Trp41. The structure suggests that the presence of DNA can guide AdoMet into the primed orientation. These results shed new light on the proposed ordered mechanism of binding and explains the stable association between AdoMet and M.HhaI.

Chemistry of Oligonucleotide-Gold Nanoparticle Conjugates

Conjugates prepared by immobilizing thiol-terminated oligonucleotides onto gold nanoparticles form stable colloidal solutions in aqueous media. The oligonucleotides can serve as linkers to organize the gold particles reversibly into three dimensional assemblies, and the gold particles can function as colorimetric reporters for hybridization of the bound oligomers with target oligonucleotides in solution.

Synthesis of antisense oligonucleotides

It is demonstrated that mixed-sequence phosphorothioate oligodeoxyribonucleotides can be synthesized on scales up to 80 mmol without using chlorinated solvents like dichloromethane, while preserving both high yield and purity of the product. A solution of dichloroacetic acid in toluene cleanly and efficiently removes 4,4′-dimethoxytrityl groups from the 5′-terminus of the growing oligonucleotide chain during synthesis on solid support. Ammonium hydroxide treatment at room temperature at atmospheric pressure furnishes deprotected oligonucleotides reducing the risk that pressurized reaction glass vessels pose. To ensure facile separation of polymer beads (Primer HL 30) and oligonucleotide solution, minimum agitation of the reaction mixture is applied.

Tryptophan metabolism in male Sardinian alcohol-preferring (sP) and -non-preferring (sNP) rats.

Parameters of tryptophan (Trp) and related metabolism were compared in male Sardinian alcohol-preferring (sP) and -non-preferring (sNP) rats. Liver Trp pyrrolase activity was 38-58% higher in sP than in sNP rats, and this was associated with a greater expression of the enzyme mRNA as measured by multiprobe oligonucleotide solution hybridization. Moderately (about 10-19%), but significantly, lower concentrations of free serum, total serum, and brain Trp were also observed in sP compared with sNP rats. Concentrations of whole brain 5-hydroxytryptamine (5-HT) and its major metabolite 5-hydroxyindol-3-yl-acetic acid (5-HIAA) were, however, 14-21% higher in sP rats. Serum corticosterone concentration was 18% higher in sP rats. We conclude that alcohol preference in Sardinian rats is associated with increased liver Trp pyrrolase activity and mRNA expression leading to a decrease in Trp availability to the brain. Although a simple serotonin deficiency could not be demonstrated in the whole brain, the possibility could not be ruled out that a deficiency may be present in discrete areas of the brain of the sP rat.

Gene expression studies of mRNAs encoding the NMDA receptor subunits NMDAR1, NMDAR2A, NMDAR2B, NMDAR2C, and NMDAR2D following long-term treatment with cis- and trans-flupenthixol as a model for understanding the mode of action of schizophrenia drug treatment

It has been hypothesized that glutamate receptor function is important in both the aetiology and treatment of schizophrenia. In order to understand how specific glutamate receptor genes are involved in the treatment of schizophrenia we have used a multiprobe oligonucleotide solution hybridization (MOSH) technique to examine the regulation of gene expression of the NMDAR1, 2A, 2B, 2C, 2D receptor subunits in the left rat brain following treatment with the optical isomers of flupenthixol. cis- and trans-flupenthixol are both present in the commonly used oral and depot treatments for schizophrenia and a controlled trial showed that cis-flupenthxiol had a significantly superior ability to ameliorate the positive symptoms of schizophrenia compared to its trans-isomer. At a dose of 0.2 mg/kg/day over a period of 1, 2, 4, 8, 12 and 24 weeks, we found that both isomers down regulated the expression of NMDAR1 mRNA in most regions of the brain. NMDAR2A, 2B and 2C receptor subunits showed a significantly decreased expression from 12 to 24 weeks but after 2 weeks NMDAR2B, 2C, 2D expression was increased in several brain regions. The NMDAR1 receptor subunit immunoreactivity in the right brain following 4 and 24 weeks of drug treatment was also examined by Western blotting. Both trans- and cis-flupenthixol significantly decreased the NR1 immunoreactivity in the right cerebellum after 24 weeks of treatment. These results suggest that NMDA receptor subunits may have a role in the action of antipsychotic drugs. If we assume that the NMDA receptor expression changes reflect a beneficial and significant mechanism in the treatment of schizophrenia, it could be argued that NMDA receptor changes are more related to the negative or non-specific symptoms of schizophrenia.

Water and monovalent ions in the minor groove of B-DNA oligonucleotides as seen by NMR.

During the past 8 years, two complementary nmr techniques-magnetic relaxation dispersion and nuclear Overhauser effect spectroscopy-have been applied extensively to the study of water and monovalent ions in the minor groove of B-DNA oligonucleotides in solution. In this review, the possibilities and limitations of the two methods are outlined, with emphasis on the interpretational steps whereby molecular-level information is extracted from the primary data. The results on sequence-dependent hydration and ion-DNA interactions obtained so far by these methods is summarized and critically assessed. The nmr results are also compared with structural data from x-ray crystallography.

1H‐NMR determination of the thermodynamics of drug complexation with single‐stranded and double‐stranded oligonucleotides in solution: Ethidium bromide complexation with the deoxytetranucleotides 5′‐d(ApCpGpT), 5′‐d(ApGpCpT), and 5′‐d(TpGpCpA)

1H‐NMR determination of the thermodynamics of drug complexation with single‐stranded and double‐stranded oligonucleotides in solution: Ethidium bromide complexation with the deoxytetranucleotides 5′‐d(ApCpGpT), 5′‐d(ApGpCpT), and 5′‐d(TpGpCpA)

1H-NMR determination of the thermodynamics of drug complexation with single-stranded and double-stranded oligonucleotides in solution: ethidium bromide complexation with the deoxytetranucleotides 5'-d(ApCpGpT), 5'-d(ApGpCpT), and 5'-d(TpGpCpA).

The thermodynamical parameters (free energy, enthalpy, and entropy) of complex formation between ethidium bromide and single-stranded and double-stranded tetranucleotides of different base sequence [5-d(TpGpCpA), 5-d(ApCpGpT), and 5-d(ApGpCpT) have been determined from the temperature dependencies of 500 MHz proton nmr chemical shifts. The analysis enables the contributions to be differentiated for the formation of different types of complexes (1:1, 2:1, 1.2 and 2:2) in aqueous solution. The results have been interpreted in terms of the main types of intermolecular interactions responsible for formation of the different complexes; van der Waals and electrostatic interactions are important for formation of complexes of ethidium bromide with single-stranded tetranucleotides, whereas van der Waals and hydrophobic interactions play a significant role in the binding of the dye to the tetramer duplexes.

A novel solid support for synthesis of 3′-phosphorylated chimeric oligonucleotides containing internucleosidic methyl phosphotriester and methylphosphonate linkages

A novel solid phase synthesis of 3′-phosphorylated oligonucleotides is described. The chain assembly is carried out by phosphoramidite strategy on solid support 2, which allows a mild and fast release of the oligonucleotide in solution. The applicability of the method is demonstrated by preparation of 3′-phosphorylated chimeric oligonucleotides containing methyl phosphotriester and methyl phosphonate internucleosidic linkages.

Detection of Oligonucleotide Hybridization on a Single Microparticle by Time-Resolved Fluorometry: Hybridization Assays on Polymer Particles Obtained by Direct Solid Phase Assembly of the Oligonucleotide Probes

Oligodeoxyribonucleotides were assembled by conventional phosphoramidite chemistry on uniformly sized (50 microns) porous glycidyl methacrylate/ethylene dimethacrylate (SINTEF) and compact polystyrene (Dynosphere) particles, the aminoalkyl side chains of which were further derivatized with DMTrO-acetyl groups. The linker was completely resistant toward ammonolytic deprotection of the base moieties. The quality of oligonucleotides was assessed by repeating the synthesis on the same particles derivatized with a cleavable ester linker. The ability of the oligonucleotide-coated particles to bind complementary sequences via hybridization was examined by following the attachment of oligonucleotides bearing a photoluminescent europium(III) chelate to the particles. The fluorescence emission was measured directly on a single particle. The effects of the following factors on the kinetics and efficiency of hybridization were studied: number of particles in a given volume of the assay solution, loading of oligonucleotide on the particle, concentration of the target oligonucleotide in solution, length of the hybridizing sequence, presence of noncomplementary sequences, and ionic strength. The fluorescence signal measured on a single particle after hybridization was observed to be proportional to the concentration of the target oligonucleotide in solution over a concentration range of 5 orders of magnitude.

The Phenylacetyl Group—The First Amino Protecting Group That Can Be Removed Enzymatically from Oligonucleotides in Solution and on a Solid Support

Penicillin G acylase from E. coli was used to cleave the phenylacetyl group—the first enzyme‐labile protecting group for the amino function of nucleobases. Now protected oligonucleotides can be unmasked both in solution and on solid supports with this versatile enyzme under mild conditions (pH 7, room temperature). These results may lead to the development of new enzymatic reactions in oligonucleotide and solid‐phase chemistry as well as in combinatorial chemistry.

Fluorometric detection of HIV-1 genome through use of an internal control, inosine-substituted primers, and microtiter plate format

We describe a PCR-based fluorometric assay for the detection of the HIV-1 genome. This technique consists of a reverse hybridization with oligonucleotide probes covalently coated onto a microtiter plate as a solid support. Several improvements to the PCR amplification and detection steps gave greater sensitivity and specificity for HIV-1 screening and resulted in a convenient and rapid technique. False-positive results were avoided by using uracyl DNA glycosylase. False-negative results from the presence of PCR inhibitors were detected by coamplifying an internal control with the viral sequence. False-negative results from viral genome variability were limited by using two pairs of primers and by incorporating inosine at the primer positions corresponding to viral polymorphic nucleotides. Furthermore, the hybridization buffer and enzymatic reaction were optimized to increase the assay's sensitivity. The sensitivity and specificity of the fluorometric detection were similar to those of radioisotopic oligonucleotide solution hybridization; however, hands-on time was reduced, and the use of radioactivity was eliminated. We have used this technique routinely on 115 samples and obtained 100% specificity and high sensitivity (only one false-negative result) according to viral culture and (or) serological status of the patients.