Chemically induced hairpin formation in DNA monolayers

A naphthyridine dimer that binds specifically to G-G mismatches has been used to induce hairpin formation in oligonucleotides immobilized onto chemically modified gold surfaces. Surface plasmon resonance (SPR) imaging measurements of DNA microarrays were used to demonstrate that binding of the naphthyridine dimer to G-G mismatches within the stem portion of an immobilized 42-mer oligonucleotide could be used to induce hairpin formation that prevented hybridization of DNA complementary to the loop sequence. In addition, the selectivity of the naphthyridine dimer for G-G mismatches was verified through SPR imaging measurements of the hybridization adsorption of an 11-mer oligonucleotide to a four-component DNA array of zero- and single-base mismatch sequences.     

Ferrocenyl‐Modified DNA: Synthesis,Characterization and Integration with Semiconductor Electrodes

The ferrocenyl‐nucleoside, 5‐ethynylferrocenyl‐2′‐deoxycytidine ( 1 ) has been prepared by Pd‐catalyzed cross‐coupling between ethynylferrocene and 5‐iodo‐2′‐deoxycytidine and incorporated into oligonucleotides by using automated solid‐phase synthesis at both silica supports (CPG) and modified single‐crystal silicon electrodes. Analysis of DNA oligonucleotides prepared and cleaved from conventional solid supports confirms that the ferrocenyl‐nucleoside remains intact during synthesis and deprotection and that the resulting strands may be oxidised and reduced in a chemically reversible manner. Melting curve data show that the ferrocenyl‐modified oligonucleotides form duplex structures with native complementary strands. The redox potential of fully solvated ferrocenyl 12‐mers, 350 mV versus SCE, was shifted by +40 mV to a more positive potential upon treatment with the complement contrary to the anticipated negative shift based on a simple electrostatic basis. Automated solid‐phase methods were also used to synthesise 12‐mer ferrocenyl‐containing oligonucleotides directly at chemically modified silicon <111> electrodes. Hybridisation to the surface‐bound ferrocenyl‐DNA caused a shift in the reduction potential of +34 mV to more positive values, indicating that, even when a ferrocenyl nucleoside is contained in a film, the increased density of anions from the phosphate backbone of the complement is still dominated by other factors, for example, the hydrophobic environment of the ferrocene moiety in the duplex or changes in the ferrocene–phosphate distances. The reduction potential is shifted >100 mV after hybridisation when the aqueous electrolyte is replaced by THF/LiClO₄, a solvent of much lower dielectric constant; this is consistent with an explanation based on conformation‐induced changes in ferrocene–phosphate distances.     

Molecular dynamics simulation and binding energy calculation for estimation of oligonucleotide duplex thermostability in RNA-based therapeutics

For oligonucleotide-based therapeutics, a thorough understanding of the thermodynamic properties of duplex formation is critical to developing stable and potent drugs. For unmodified small interfering RNA (siRNA), DNA antisense oligonucleotide (AON) and locked nucleic acid (LNA), DNA/LNA modified oligonucleotides, nearest neighbor (NN) methods can be effectively used to quickly and accurately predict duplex thermodynamic properties such as melting point. Unfortunately, for chemically modified olignonucleotides, there has been no accurate prediction method available. Here we describe the potential of estimating melting temperature (T(m)) for nonstandard oligonucleotides by using the correlation of the experimental T(m) with the calculated duplex binding energy (BE) for oligonucleotides of a given length. This method has been automated into a standardized molecular dynamics (MD) protocol through Pipeline Pilot (PP) using the CHARMm component in Discovery Studio (DS). Results will be presented showing the correlation of the predicted data with experiment for both standard and chemically modified siRNA and AON.     

化学修饰的寡核苷酸: 合成、性质和应用

本文综述了近年来化学修饰的寡核苷酸研究的进展,介绍了化学修饰的寡核苷酸的种类, 化学合成方法, 生物作用原理及应用方面已达到的成継34This review deals with the progress in the research of chemically modified oligonucleotides: the synthesis, the chemical and biological properties and the potential applications as a new research tool and new therapeutic approach.     

Assembly of DNA Nanostructures with Branched Tris‐DNA

Branched tris‐DNA, in which two oligonucleotides of the same sequence and one other oligonucleotide of a different sequence are connected with a rigid central linker, was prepared chemically by using a DNA synthesizer. Two branched tris‐DNA molecules with complementary DNA sequences form dimer and tetramer as well as linear and spherical oligomer complexes. The complex formation was studied by UV/thermal denaturation, enzyme digestion, gel electrophoresis, and AFM imaging.     

Covalent Chemical 5′‐Functionalization of RNA with Diazo Reagents

Functionalization of RNA at the 5′‐terminus is important for analytical and therapeutic purposes. Currently, these RNAs are synthesized de novo starting with a chemically functionalized 5′‐nucleotide, which is incorporated into RNA using chemical synthesis or biochemical techniques. Methods for direct chemical modification of native RNA would provide an attractive alternative but are currently underexplored. Herein, we report that diazo compounds can be used to selectively alkylate the 5′‐phosphate of ribo(oligo)nucleotides to give RNA labelled through a native phosphate ester bond. We applied this method to functionalize oligonucleotides with biotin and an orthosteric inhibitor of the eukaryotic initiation factor 4E (eIF4E), an enzyme involved in mRNA recognition. The modified RNA binds to eIF4E, demonstrating the utility of this labelling technique to modulate biological activity of RNA. This method complements existing techniques and may be used to chemically introduce a broad range of functional handles at the 5′‐end of RNA.     

Synthesis and Properties of Oligothymidylates Incorporating an Artificial Bend Motif

The uridylyl‐(3′→5′)‐thymidine dinucleotide block 14 (cUpdU), having a cyclic structure between the 2′‐hydroxy of the upstream uridine and the 5‐substituent of the downstream thymidine, was synthesized (Schemes 1 and 2). This cyclic structure is a stable mimic of the intraresidual H‐bonding found in the anticodon loop of an E. coli minor tRNA^Arg. The spectroscopic and molecular‐mechanics analyses of the cyclized dinucleotides predicted two major conformers, i.e., the turn and bent forms. The latter was expected to bend DNA oligomers when incorporated into them. This expectation was ascertained by incorporating the bent dimer motif into tetra‐, deca‐, or hexadecathymidylates by the conventional phosphoramidite method (see 18 – 20 in Scheme 4). The bending of oligonucleotides 18 – 20 was demonstrated by ³¹P‐NMR and CD spectra and gel‐electrophoretic studies. The duplex formation of these modified oligonucleotides with oligodeoxyadenylates was also studied. The decreased thermal stability of the duplexes when compared with unmodified ones indicates distorted structures of the modified duplexes. The 3D computer model of the duplexes showed a bend of ca. 30° with a `bulge‐out' at the position of an adenosine residue facing the cyclized dimer. The artificially bent DNAs might become a new tool for the study of the effect of DNA bending induced in DNA/DNA‐binding protein interactions.     

Introduction of structural diversity into oligonucleotides containing 6-thioguanine via on-column conjugation

A method is described for the introduction of structural diversity into the thiocarbonyl group of 6-thioguanine within support-bound, fully protected oligonucleotides via ‘on-column′ conjugation. 2′-Deoxy-6-thioguanosine with a chemically-labile trigger at its 6-thio function was incorporated at defined sites into chemically synthesized oligonucleotides. Following selective removal of the thio-protection group the support-immobilized oligonucleotides were conjugated with various groups on-column, and then deprotected and purified to produce a number of oligomers each containing a different modified base. Since the modification is accomplished on-column without affecting other functional and protecting groups in the oligomers this method is compatible with introducing structural diversity at multiple sites in DNA.     

Ultra‐performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) and UPLC/MSE analysis of RNA oligonucleotides

Fast and efficient ultra‐performance liquid chromatography/tandem mass spectrometry (UPLC/MS/MS) analysis of short interfering RNA oligonucleotides was used for identity confirmation of the target sequence‐related impurities. Multiple truncated oligonucleotides and metabolites were identified based on the accurate mass, and their presumed sequence was confirmed by MS/MS and MS^E (alternating low and elevated collision energy scanning modes) methods. Based on the resulting fragmentation of native and chemically modified oligonucleotides, it was found that the MS^E technique is as efficient as the traditional MS/MS method, yet MS^E is more general, faster, and capable of producing higher signal intensities of fragment ions. Fragmentation patterns of modified oligonucleotides were investigated using RNA 2′‐ribose substitutions, phosphorothioate RNA, and LNA modifications. The developed sequence confirmation method that uses the MS^E approach was applied to the analysis of in vitro hydrolyzed RNA oligonucleotide. The target RNA and metabolites, including the structural isomers, were resolved by UPLC, and their identity was confirmed by MS^E. Simultaneous RNA truncations from both termini were observed. The UPLC quadrupole time‐of‐flight (QTOF) MS/MS and MS^E methods were shown to be an effective tool for the analysis and sequence confirmation of complex oligonucleotide mixtures. Copyright © 2010 John Wiley & Sons, Ltd.     

De Novo Design of Functional Oligonucleotides with Acyclic Scaffolds

In this account, we demonstrate a new methodology for the de novo design of functional oligonucleotides with the acyclic scaffolds threoninol and serinol. Four functional motifs—wedge, interstrand‐wedge, dimer, and cluster—have been prepared from natural DNA or RNA and functional base surrogates prepared from d ‐threoninol. The following applications of these motifs are described: (1) photoregulation of formation and dissociation of a DNA duplex modified with azobenzene, (2) sequence‐specific detection of DNA using a fluorescent probe, (3) formation of fluorophore assemblies that mimic quantum dots, (4) improved strand selectivity of siRNA modified with a base surrogate, and (5) in vivo tracing of the RNAi pathway. Finally, we introduce artificial nucleic acids (XNAs) prepared from d ‐threoninol and serinol functionalized with each of the four nucleobases, which have unique properties compared with other acyclic XNAs. Functional oligonucleotides designed from acyclic scaffolds will be powerful tools for both DNA nanotechnology and biotechnology.     

Oligonucleotide‐Based Mimetics of Hepatocyte Growth Factor

Oligonucleotide‐based hepatocyte growth factor (HGF) mimetics are described. A DNA aptamer to Met, a cognate receptor for HGF, was shown to induce Met activation when used in dimer form. The most potent aptamer dimer, ss‐0, which was composed solely of 100‐mer single‐stranded DNA, exhibited nanomolar potency. Aptamer ss‐0 reproduced HGF‐induced cellular behaviors, including migration and proliferation. The present work sheds light on oligonucleotides as a novel chemical entity for the design of growth factor mimetics.     

Photo‐Tethers for the (Multi‐)Cyclic,Conformational Caging of Long Oligonucleotides

Intramolecular circularization of DNA oligonucleotides was accomplished by incorporation of alkyne‐modified photolabile nucleosides into DNA sequences, followed by a Cu^I‐catalyzed alkyne–azide cycloaddition with bis‐azido linker molecules. We determined a range of ring sizes, in which the caged circular oligonucleotides exhibit superior duplex destabilizing properties. Specific binding of a full‐length 90 nt C10 aptamer recognizing human Burkitt's lymphoma cells was then temporarily inhibited by locking the aptamer in a bicircularized structure. Irradiation restored the native aptamer conformation resulting in efficient cell binding and uptake. The photo‐tether strategy presented here provides a robust and versatile tool for the light‐activation of longer functional oligonucleotides, noteworthy without prior knowledge on the structure and the importance of specific nucleotides within a DNA aptamer.     

Photo‐Tethers for the (Multi‐)Cyclic,Conformational Caging of Long Oligonucleotides

Intramolecular circularization of DNA oligonucleotides was accomplished by incorporation of alkyne‐modified photolabile nucleosides into DNA sequences, followed by a Cu^I‐catalyzed alkyne–azide cycloaddition with bis‐azido linker molecules. We determined a range of ring sizes, in which the caged circular oligonucleotides exhibit superior duplex destabilizing properties. Specific binding of a full‐length 90 nt C10 aptamer recognizing human Burkitt's lymphoma cells was then temporarily inhibited by locking the aptamer in a bicircularized structure. Irradiation restored the native aptamer conformation resulting in efficient cell binding and uptake. The photo‐tether strategy presented here provides a robust and versatile tool for the light‐activation of longer functional oligonucleotides, noteworthy without prior knowledge on the structure and the importance of specific nucleotides within a DNA aptamer.     

Disulfide‐Unit Conjugation Enables Ultrafast Cytosolic Internalization of Antisense DNA and siRNA

Development of intracellular delivery methods for antisense DNA and siRNA is important. Previously reported methods using liposomes or receptor‐ligands take several hours or more to deliver oligonucleotides to the cytoplasm due to their retention in endosomes. Oligonucleotides modified with low molecular weight disulfide units at a terminus reach the cytoplasm 10 minutes after administration to cultured cells. This rapid cytoplasmic internalization of disulfide‐modified oligonucleotides suggests the existence of an uptake pathway other than endocytosis. Mechanistic analysis revealed that the modified oligonucleotides are efficiently internalized into the cytoplasm through disulfide exchange reactions with the thiol groups on the cellular surface. This approach solves several critical problems with the currently available methods for enhancing cellular uptake of oligonucleotides and may be an effective approach in the medicinal application of antisense DNA and siRNA.     

Synthesis and Hybridization Properties of Sugar‐Modified Oligonucleotides

L ‐Threoninol‐derived acyclic nucleotide monomers were prepared and incorporated into oligonucleotides at preselected positions via phosphoramidite chemistry. Hybridization properties of these modified oligonucleotides with the corresponding natural oligomers were studied, and their vis‐à‐vis comparison with serinol‐modified oligonucleotides was made. Stability of the modified oligomers against nuclease in human serum and snake venom phosphodiesterase (SVPD) was examined.     

IMMUNOLOGICALLY ACTIVE LESIONS INDUCED ON DOUBLE-STRANDED DNA WITH ULTRAVIOLET

Abstract— Some immunochemical properties of double-stranded DNA irradiated with UV were studied, using a radioimmunoassay with irradiated [³H]-DNA and experimentally produced antibodies to DNA. Reactivity of antibodies revealed that irradiated DNA contained an immunologically active structure other than the irradiated DNA specific structure, resembling that of thermally denatured DNA. inhibition assay demonstrated that while DNA-antibody binding was effectively inhibited by mixed purine and pyrimidine oligonucleotides, thymine dimer containing pyrimidine oligonucleotides derived from the irradiated DNA showed no appreciable inhibition. The antigenic structure specific for irradiated DNA was found to be thermally labile in low salt medium. Cupric and ferrous ions and cysteine added to the DNA solution inhibited antigenicity formation during irradiation, but these substances exhibited no effect on dimer formation in irradiated frozen thymine solution. Calcium ions and histidine were inert for the former reaction but inhibited the latter effectively. This suggests that different mechanisms are involved in the 2 processes. The immunologically active UV-induced lesions appeared to depend mainly on a conformational structure change of the DNA strands rather than on a single modified base moiety.     

One‐Step Formation of “Chain‐Armor”‐Stabilized DNA Nanostructures

DNA‐based self‐assembled nanostructures are widely used to position organic and inorganic objects with nanoscale precision. A particular promising application of DNA structures is their usage as programmable carrier systems for targeted drug delivery. To provide DNA‐based templates that are robust against degradation at elevated temperatures, low ion concentrations, adverse pH conditions, and DNases, we built 6‐helix DNA tile tubes consisting of 24 oligonucleotides carrying alkyne groups on their 3′‐ends and azides on their 5′‐ends. By a mild click reaction, the two ends of selected oligonucleotides were covalently connected to form rings and interlocked DNA single strands, so‐called DNA catenanes. Strikingly, the structures stayed topologically intact in pure water and even after precipitation from EtOH. The structures even withstood a temperature of 95 °C when all of the 24 strands were chemically interlocked.     

pH-Responsive supramolecular DOX-dimer based on cucurbit[8]uril for selective drug release

A supramolecular dimer of doxorubicin (DOX) was constructed via ternary host-guest interactions between cucurbit[8]uril (CB[8]) and tryptophan modified DOX (DOX-Trp, connected with an acid-labile bond) and we demonstrate for the first time that a supramolecular dimer of DOX can be formed upon homo-dimerization by CB[8], which may act as a stimuli pH-responsive, supramolecular DOX dimer prodrug system. This supramolecular DOX dimer transported DOX efficiently and selectively to cancer cells, thereby exhibiting significantly minimized cytotoxicity against noncancerous cells while maintaining effective cytotoxicity against cancer cells. Under this strategy, many other anticancer drugs could be chemically modified and loaded as a dimeric “ammunition” into CB[8] as supramolecular dimer prodrug systems (or a “jet fighter”) for improved cancer therapy.     

Ferrocenyl-modified DNA: synthesis, characterization and integration with semiconductor electrodes

The ferrocenyl-nucleoside, 5-ethynylferrocenyl-2'-deoxycytidine (1) has been prepared by Pd-catalyzed cross-coupling between ethynylferrocene and 5-iodo-2'-deoxycytidine and incorporated into oligonucleotides by using automated solid-phase synthesis at both silica supports (CPG) and modified single-crystal silicon electrodes. Analysis of DNA oligonucleotides prepared and cleaved from conventional solid supports confirms that the ferrocenyl-nucleoside remains intact during synthesis and deprotection and that the resulting strands may be oxidised and reduced in a chemically reversible manner. Melting curve data show that the ferrocenyl-modified oligonucleotides form duplex structures with native complementary strands. The redox potential of fully solvated ferrocenyl 12-mers, 350 mV versus SCE, was shifted by +40 mV to a more positive potential upon treatment with the complement contrary to the anticipated negative shift based on a simple electrostatic basis. Automated solid-phase methods were also used to synthesise 12-mer ferrocenyl-containing oligonucleotides directly at chemically modified silicon <111> electrodes. Hybridisation to the surface-bound ferrocenyl-DNA caused a shift in the reduction potential of +34 mV to more positive values, indicating that, even when a ferrocenyl nucleoside is contained in a film, the increased density of anions from the phosphate backbone of the complement is still dominated by other factors, for example, the hydrophobic environment of the ferrocene moiety in the duplex or changes in the ferrocene-phosphate distances. The reduction potential is shifted >100 mV after hybridisation when the aqueous electrolyte is replaced by THF/LiClO(4), a solvent of much lower dielectric constant; this is consistent with an explanation based on conformation-induced changes in ferrocene-phosphate distances.     

The use of strong anion-exchange (SAX) magnetic particles for the extraction of therapeutic siRNA and their analysis by liquid chromatography/mass spectrometry

Traditional methods for extracting oligonucleotides from serum and other biological fluids are often time-consuming and require multiple steps. Magnetic particle based separation of oligonucleotides has gained importance recently due to the advantages of simplicity and high efficiency. Here we report the development and optimization of commercially available strong anion-exchange (SAX) magnetic beads for the extraction of siRNA from human serum. The beads allowed for rapid extraction of siRNA from human serum in 100-200 μL of liquid chromatography/mass spectrometry (LC/MS)-compatible buffer in less than 1 h for a 96-well plate with no further drying steps. Due to the strong cation-binding properties of oligonucleotides, volatile ammonium salts such as triethylammonium bicarbonate (TEAB), ammonium bicarbonate, and NH(4) Cl were used to elute the siRNA from the beads. For more hydrophobic siRNA sequences, the addition of 5-10% organic solvent was required for elution. The recovery of chemically modified siRNA from human serum was around 80% for two types of beads examined; however, the recovery for highly modified sequences differed greatly between the two types of beads. In addition to extracting highly modified oligonucleotides, the SAX beads were also able to extract liposomal formulated siRNAs from serum with no interference from the lipid formulation. The extraction of siRNA from human serum was linear over the tested range of 50 ng/mL to 10 μg/mL. Using this extraction methodology, we have created a workflow to monitor siRNA serum stability by LC/MS. Initial observations confirm that RNase A type degradation with strand cleavage on the 3' side of uridine or cytosine is the dominant cleavage pattern in serum. This finding has implications for the selection and modification of therapeutic siRNAs and demonstrates the utility of magnetic beads as a simple and rapid extraction technique for siRNA.