Induced cross-linking reactions to target genes using modified oligonucleotides

Synthetic oligonucleotides (ONs) are valuable tools that interfere with gene expression by specifically binding to target genes in a sequence-specific manner. Reactive ONs containing cross-linking agents are expected to induce efficient inhibition because they bind covalently to target genes. In recent years, researchers have reported several cross-linking reactions that target DNA induced by external stimuli. This short review highlights recently developed novel cross-linking reactions, focusing particularly on nucleoside derivatives developed by our group.     

Biochemical assays of immobilized oligonucleotides with mass spectrometry

This paper reports the use of mass spectrometry to characterize oligonucleotides immobilized to the surfaces of biochips. Biotinylated oligonucleotides were immobilized to self-assembled monolayers that present a streptavidin layer and then treated with a complementary strand to present short duplexes. Treatment of the surface with 5-methoxysalicylic acid and ammonium citrate matrix allows the individual oligonucleotides to be observed by matrix-assisted laser desorption/iozation and time-of-flight mass spectrometry (MALDI-TOF MS). Examples are shown wherein this method is applied to assays of hybridization, of cleavage by a deoxyribozyme, of a dephosphorylation reaction, and of the adducts formed on treatment of DNA with cis-platin. This work provides an early example of the application of mass spectrometry to DNA biochips and may substantially expand the applications of the now common oligonucleotide arrays.     

Fluorous affinity purification of oligonucleotides

[structure: see text] Nucleoside phosphoramidites bearing a fluorous dimethoxytrityl (FDMT) group were used to synthesize fluorous-tagged oligonucleotides, which were subjected to solid-phase extraction using a pH-stable fluorinated adsorbent. On-column detritylation afforded the purified oligonucleotides. The fluorous affinity purification method offers one-pass loading without ammonia removal, high selectivity for the removal of failure sequences, high recoveries (typically 70-100%), and the ability to purify long oligonucleotides (e.g., 50-100-mers).     

Amphiphilic copolymers with increased affinity for substrates

The copolymers of methyl quaternized 2-dimethylaminoethyl acrylate and styrene, 2-vinyl naphthalene, acrylic acid iso-octyl ester, or acrylic acid n-butyl ester have been prepared. Studies were made of the binding of a “binding probe,” methyl orange, by the copolymers in aqueous solution. The first binding constants and the thermodynamic parameters in the course of the binding were evaluated. Furthermore, the intensity of fluorescence of a hydrophobic fluorescent probe, 2-p-toluidinylnaphthalene-6-sulfonate, in the presence of these polymers was investigated. In addition, the fluorescence spectra of monomer and excimer emissions of the polymers with aromatic residues were measured. The excimer/monomer fluorescence intensity ratio was studied in the presence of various additives such as methyl orange, urea, methanol, and NaCl to gain an insight into the nature of microdomains in the polymer. The nature and phenomena of dye binding and hydrophobic fluorescent probe binding with the polymers are discussed. © 1993 John Wiley & Sons, Inc.     

Electron affinity of modified benzene

The electron affinities of organic molecules obeying Hückel's rule of aromaticity are vanishingly small, if not negative. For example, benzene, a classic example of an aromatic molecule, has an electron affinity of −1.15 eV. Using density functional theory, we have systematically calculated the electron affinities and vertical detachment energies of C₆H₆ by substituting H with halogen (F) and superhalogen (BO₂) moieties, as well as replacing one of the C atoms with B. The ground state geometries were obtained by examining about 330 isomers. The electron affinities are found to steadily increase with these substitutions/replacements, even surpassing that of Cl, the element with the highest electron affinity in the periodic table, in the case of C₅BH(BO₂)₅. In some special cases such as C₆H₅(BO₂) the electron affinity and vertical detachment energy differ by as much as 5 eV, indicating substantial changes in the geometry as the electron is removed from the anion. We hope that the ability to change the negative electron affinity of C₆H₆ to large positive values by substituting H and/or replacing C atom will motivate experimental studies.     

Site-specific cleavage of RNA by a metal-free artificial nuclease attached to antisense oligonucleotides

RNA cleaving tris(2-aminobenzimidazoles) have been attached to DNA oligonucleotides via disulfide or amide bonds. The resulting conjugates are effective organocatalytic nucleases showing substrate and site selectivity as well as saturation kinetics. The benzimidazole conjugates also degrade enantiomeric RNA. This observation rules out contamination effects as an alternative explanation of RNA degradation. The pH dependency shows that the catalyst is most active in the deprotonated state. Typical half-lifes of RNA substrates are in the range of 12-17 h. Thus, conjugates of tris(2-aminobenzimidazoles) can compete with the majority of metal-dependent artificial nucleases.     

A label-free fluorescence sensor for probing the interaction of oligonucleotides with target molecules

This paper describes a universal, label-free fluorescence sensor that gauges the interaction of oligonucleotides with their targets. The sensor is based on supramolecular assemblies formed by oligonucleotides (polyanions) and small molecule cation surfactant in aqueous solution. The environmentally dependent dye pyrene, encapsulated in the apolar interiors of the assemblies via hydrophobic interactions works as the fluorescence probe. Target binding causes the conformational change of the oligonucleotides, which results in disorganization of supramolecular assemblies, release of pyrene into the aqueous solution and subsequent quenching of its fluorescence. The kinetic processes (including the formation of supramolecular assemblies and the release of pyrenes after adding the targets) were investigated. The fluorescence decreases of pyrenes are proportional to the concentrations of targets within the linear ranges. This label-free fluorescence system is simple, convenient, low cost, and can serve as an alternative tool for interaction studies of oligonucleotides with their targets, especially with small molecular targets.     

Electrochemical determination of melamine using oligonucleotides modified gold electrodes

A novel and simple electrochemical method for determination of melamine is developed based on oligonucleotides film modified gold electrodes. The electrochemical probe of ferricyanide was used to investigate the interactions between oligonucleotides and melamine. Results of cyclic voltammetries, differential pulse stripping voltammetries, electrochemical impedance spectrometry and atomic force microscope, proved that melamine might interact with oligonucleotides mainly through electrostatic and hydrogen-bonding interactions. The interactions between oligonucleotides and melamine lead to the increase in the peak currents of ferricyanide, which could be used for electrochemical sensing of melamine. The redox peak currents of ferricyanide were linear with the concentration of melamine in the range from 3.9 × 10⁻⁸ to 3.3 × 10⁻⁶ M with a linear coefficiency of 0.990. The detection limit was 9.6 × 10⁻⁹ M. The proposed electrochemical biosensor is rapid, convenient and low-cost for effective sensing of melamine. Particularly, the proposed method was applied successfully to the determination of melamine in milk products, and the recovery was 95%.     

A new method for the preparation of modified oligonucleotides

[reaction-see text] N-Nitrothymidine can be transformed into a phosphoramidite building block suitable for oligonucleotide synthesis using the standard phosphite triester solid-phase approach. The N-nitrothymidine residues remain stable during the elongation cycles and react smoothly with primary amines, furnishing oligonucleotides containing N3-modified thymidines. A number of N3-substituted oligonucleotides have been prepared using this methodology, some of them incorporating aminoalkyl or hydroxyalkyl groups.     

烯丙基作为保护基在修饰寡核苷酸合成中的应用

研究了烯丙基作为核苷糖环羟基保护基在寡核苷酸及其类似物的合成中应用的可能性。烯丙基保护基可用PdCl2在温和条件下脱除,适合应用于对碱不稳定的寡核苷酸的合成。应用烯丙基保护基成功地合成了三胸苷二碳酸酯和二胸苷亚硫酸酯。     

Microbead-based affinity chromatography chip using RNA aptamer modified with photocleavable linker

A microbead-based affinity chromatography chip (micro-BACC) controlling hundreds of nanoliters of reaction volume was developed to separate and analyze hepatitis C virus (HCV) RNA polymerase protein by immobilization of an RNA aptamer on beads. A photocleavable linker was conjugated in between the beads and the aptamer to elute the bound RNA polymerase from the RNA aptamer in one step by UV irradiation, resulting in an efficient method to elute and identify the target molecule bound on RNA using a mass spectrometer. This linker showed a cleavage activity over 70% upon UV irradiation at 1050 mW/cm2 for more than 5 min. The photoelution method could prevent the target molecule from contaminations in affinity chromatography caused by elution solutions of high salt concentration, extreme pH and detergent, respectively. In this chip, sample reagents up to 800 nL could be metered quantitatively into the bead chamber using a nanoliter dispenser working, based on surface-guided flow control and pneumatic control by external air pressure on the chip. RNA polymerase eluted after UV irradiation was successfully analyzed by trypsin treatment without additional purification. As a result, using the aptamer, we could detect RNA polymerase from 800 nL hepatitis C patient serum containing 96 fmol HCV RNA polymerase. The detection limit of this system was estimated to be 9.6 fmol HCV RNA polymerase.     

Synthesis and properties of novel l-isonucleoside modified oligonucleotides and siRNAs

Antisense oligonucleotides and siRNAs are potential therapeutic agents and their chemical modifications play an important role to improve the properties and activities of oligonucleotides. Isonucleoside is a type of nucleoside analogue, in which the nucleobase is moved from C-1 to other positions of ribose. In this report, a novel isonucleoside containing a 5'-CH(2)-extended chain at the sugar moiety was synthesized, thus isoadenosine and isothymidine were incorporated into a DNA single strand and siRNA. It was found that isonucleoside modified oligonucleotides can form stable double helical structures with their complementary DNA and RNA and the stability towards nuclease and ability to activate RNase H are more promising compared with the unmodified, natural analogues. In siRNA, passenger strand modified with isonucleoside () at 3' or 5' terminal can retain the silencing activity and minimize the passenger strand specific off-target effect.     

Capillary electrophoresis for capture and concentrating of target nucleic acids by affinity gels modified to contain single-stranded nucleic acid probes

Selective capture and pre-concentration of target nucleic acids from relatively complicated samples may provide a method to facilitate introduction to a microfluidic-based detection system to improve detection limits. An acrylamide polymer gel modified with Acrydite^™ that contained 20mer oligonucleotide probe was prepared and loaded into a capillary column. The results indicated that the amount of probe DNA that was captured into the acrylamide was about 40% of the starting monomer, and different quantities of probe could therefore be coupled into the gel. The gel was passivated by pre-treatment with non-complementary DNA oligonucleotide to block non-selective adsorption sites, and the gel was determined to be stable for multiple cycles of use. The probe could hybridize with target sequences that were introduced by electrokinetic injection from a sample solution. The target could be freed from the polymer gel by use of a combination of heating, chaotropic salt and voltage conditions. Target capture efficiency was up to 90% when using samples that did not saturate probe sites in the columns, and recovery of target from the gel could be as high as 95%.     

Circular permutation of the starch-binding domain: inversion of ligand selectivity with increased affinity

Proteins containing starch-binding domains (SBDs) are used in a variety of scientific and technological applications. A circularly permutated SBD (CP90) with improved affinity and selectivity toward longer-chain carbohydrates was synthesized, suggesting that a new starch-binding protein may be developed for specific scientific and industrial applications.     

Cross-linked polyvinylpyrrolidones with increased affinity and specificity for methyl orange and its homologs

Polyvinylpyrrolidones of various degrees of cross-linkage have been prepared by radical polymerization of N-vinylpyrrolidone with methylenebisacrylamide to regulate the fraction of cross-linkage. The insoluble polymers obtained were examined for their ability to bind methyl orange and its homologs, methyl orange, ethyl orange, propyl orange, and butyl orange at 5, 15, 25, and 35°C, respectively, in an aqueous solution. The first binding constants and the thermodynamic parameters that accompanied the binding were calculated. For any particular dye the extent of binding, the absolute magnitude of ΔF°, and the value of ΔS° increased as the degree of cross-linkage increased, starting with water-soluble polyvinylpyrrolidone (zero cross-linkage) and proceeding to the polymer with high cross-linking density. This behavior can be accounted for in terms of more extensive hydrophobic domains in the cross-linked polymeric matrix that enhances hydrophobic interactions in the binding process. Moreover, the cross-linked macromolecule polymerized in the presence of methyl orange and then stripped of the bound methyl orange shows substantially stronger binding for this small molecule than the polymer cross-linked in the absence of methyl orange. In contrast, the cross-linked polymer prepared similarly in the presence of the larger molecule, butyl orange, exhibits decreased affinity toward the smaller consolute, methyl orange, than either of the other polymers described. It seems, therefore, that the polymeric matrix provides favorable binding sites or pockets that can accommodate a specific small molecule. The preparative procedure, which uses a small-molecule template, molds into the polymer some structural specificity in the binding of small molecules.     

Synthesis and RNA binding selectivity of oligonucleotides modified with five-atom thioacetamido nucleic acid backbone structures

Convenient chemical synthesis and incorporation of dithymidine and thymidine-cytidine dimer blocks connected with a five-atom amide linker N3'-CO-CH2-S-CH2 into oligonucleotides (ONs) are reported. The UV-Tm experiments for binding affinities of these mixed backbone ONs with complementary DNA and RNA sequences revealed important results such as significantly higher RNA-binding selectivity as compared with complementary DNA. NMR studies of the dimer blocks suggested a marginal increase in the N-type sugar conformations over that of the native DNA.     

Synthesis of oligonucleotides with a 2'-cap at the 3'-terminus via reversed phosphoramidites

[reaction: see text] A method is presented for the synthesis of single compounds or small combinatorial libraries of oligonucleotides with 2'-acylamido-2'-deoxyuridine residues at the 3'-terminus. Selection experiments identified the residue of anthraquinone-2-carboxylic acid as a "molecular cap" that increases the UV melting point of the duplex (5'-ACGCGU-3')(2) by up to 28 degrees C compared to the unmodified control duplex.     

A novel route for immobilization of oligonucleotides onto modified silica nanoparticles

A novel approach for immobilization of probe oligonucleotides that uses zirconium phosphate modified silica nanoparticles is proposed. The surface modification of nanoparticles was carried out in two stages. Initially binding of Zr4+ to the surface of silica nanoparticles and later treated with phosphoric acid for terminal phosphate groups. Oligonucleotide probes modified with amine group at 5'-end were strongly binds to the phosphate terminated silica nanoparticles with imidazole in presence of 0.1 mol L(-1) EDC [N-ethyl-N'-(3-dimethylaminopropyl) carbodiimide], as phosphate groups are more reactive towards amine group. Various studies, i.e., synthesis of silica nanoparticles, their surface modification, probe immobilization, measurement of hybridization and effect of bovine serum albumin (BSA) were carried out during optimization of reaction conditions. The significant reduction in the background signal was observed by treating the probe modified silica nanoparticles with bovine serum albumin prior to hybridization. The probe modified silica nanoparticles were retained their properties and the hybridization was induced by exposure of single-stranded DNA (ssDNA) containing silica nanoparticles to the complementary DNA in solution. The decrease in the fluorescence signal for one mismatch and three mismatch was observed upon hybridization of probe with target DNAs, while there was no response for the random target ssDNA under the same experimental conditions. The intensity of fluorescence signal was linear to the concentration of target DNA ranging from 3.9 x 10(-9) to 3.0 x 10(-6)mol L(-1). A detection limit of 1.22 x 10(-9) mol L(-1) of oligonucleotides can be estimated. The proposed hybridization assay is simple and possesses good analytical characteristics and it can provide an effective and efficient route in the development of DNA biosensors and biochips.