Chimeric oligonucleotides based on 2"-O-modified oligoribonucleotides with the terminal 3"—3" internucleotide linkage as potential inhibitors of MDR 1 gene expression

Chimeric constructs were synthesized based on oligoribonucleotides modified at the 2"-position of the ribose (2"-O-tetrahydropyranyl- or 2"-O-methyl-) and at the 3"-terminus of the oligonucleotide chain (terminal 3"—3" internucleotide linkage), which are complementary to a region of MDR 1 mRNA. A comparative study of the properties of these chimeric constructs was performed. The chimeric oligomers with the modified 3"-terminus are characterized by high stability with respect to 3"-exonucleases, form stable complementary complexes with RNA, and can activate RNase H in a duplex with RNA.     

Properties of the optimal environment inducing tautomerization of complementary base pairs

The optimal environment charge configurations are predicted for the tautomerization of complementary base pairs into their corresponding rare forms, and vice versa. Results indicate that cations approaching the N₃ guanine site may induce tautomerization of the normal guanine—cytosine (G---C) base pair into its rare form. The reverse process requires that the cation approach the O₂ thymine site of the rare adenine*—thymine* pair (A*---31T*) or the O₆ guanine site of rare guanine*—cytosine* base pair (G*---C*). Possible mutagenic and antimutagenic roles of metal cations approaching base pairs are also discussed.     

Applications of synthetic oligoribonucleotide analogues in studies of RNA structure and function

The study of RNA structure and function has been considerably aided by the development of methods for the chemical synthesis of oligoribonucleotides into which have been incorporated modified nucleosides carrying site-specific alterations. Such modifications are designed to eliminate or alter individual functional groups in the RNA which potentially can take part in hydrogen-bonding or other non-covalent interactions. Comparison of the properties of the modified RNA with unmodified RNA models allows conclusions to be drawn concerning the importance or otherwise of specific functional groups within the RNA. The methods have been applied to studies of RNA structure, RNA catalysis, and interactions of RNA with proteins.     

Synthesis, photophysical characterization, and enzymatic incorporation of a microenvironment-sensitive fluorescent uridine analog

The synthesis of a microenvironment-sensitive base-modified fluorescent ribonucleoside analog based on a 5-(benzo[b]thiophen-2-yl)pyrimidine core, enzymatic incorporation of its corresponding triphosphate into RNA oligonucleotides, and photophysical characterization of fluorescently modified oligoribonucleotides are described.     

Synthesis of Fluorobenzene and Benzimidazole Nucleic‐Acid Analogues and Their Influence on Stability of RNA Duplexes

Six different ribonucleoside phosphoramidites with fluorobenzenes or fluorobenzimidazoles as base analogues, one abasic site, and inosine were synthesized and incorporated into oligoribonucleotides. The oligomers were investigated by means of UV and CD spectroscopy to assess the contribution of H‐bonding, base stacking, and solvation to the stability of the RNA duplex. CD Spectra show that the incorporation of modified nucleosides does not lead to changes in the structure of RNA. The T_m differences determined are based on changes in base stacking and solvation. Individual contributions of base stacking and solvation of the modified nucleosides could be determined. In fluorobenzene⋅fluorobenzimidazole‐modified base pairs, a duplex‐stabilizing force was found that points to a weak F⋅⋅⋅H H‐bond.     

First evaluation of acyloxymethyl or acylthiomethyl groups as biolabile 2'-O-protections of RNA

[reaction: see text] Short oligo-U sequences containing 2'-O-acyloxymethyl or acylthiomethyl groups as biolabile 2'-O-protections of RNA have been synthesized. These modified homouridylates are deprotected upon cellular esterase activation to release the parent RNA. They exhibit exceptional resistance to nuclease degradation, and the evaluation of their pairing properties shows that the 2'-acyloxymethyl groups do not prevent the duplex dsRNA formation. These biolabile 2'-modifications overcome the first hurdle to turn oligoribonucleotides into candidates for RNA interference drugs.     

Synthesis and hybridization properties of 2'-O-methylated oligoribonucleotides incorporating 2'-O-naphthyluridines

2'-O-(1-Naphthyl)uridine and 2'-O-(2-naphthyl)uridine were synthesized by a microwave-mediated reaction of 2,2'-anhydrouridine with naphthols. Using the 3'-phosphoramidite building blocks, these 2'-O-aryluridine derivatives were incorporated into 2'-O-methylated oligoribonucleotides. Incorporation of five 2'-O-(2-naphthyl)uridines into a 2'-O-methylated RNA sense strand significantly increased the thermostability of the duplex with a 2'-O-methylated RNA antisense strand. Circular dichroism spectroscopy and molecular dynamic simulation of the duplexes formed between the modified RNAs and 2'-O-methyl RNAs suggested that there are π-π interactions between two neighboring naphthyl groups in a sequence of the five consecutively modified nucleosides.     

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.     

Synthesis and biological activity of phosphonoacetate- and thiophosphonoacetate-modified 2'-O-methyl oligoribonucleotides

Chimeric 2'-O-methyl oligoribonucleotides (2'-OMe ORNs) containing internucleotide linkages which were modified with phosphonoacetate (PACE) or thiophosphonoacetate (thioPACE) were prepared by solid-phase synthesis. The modified 2'-OMe ORNs contained a central phosphate or phosphorothioate sequence with up to 4 PACE or thioPACE modifications, respectively, at either end of the ORN in a "gapmer" motif. Both PACE and thioPACE 2'-OMe ORNs formed stable duplexes with complementary RNA. The majority of these duplexes had higher thermal melting temperatures than an unmodified RNA:RNA duplex. The modified 2'-OMe ORNs were effective passenger strands with complementary, unmodified siRNAs, for inducing siRNA activity in a dual luciferase assay in the presence of a lipid transfecting agent. As single strands, thioPACE 2'-OMe ORNs were efficiently taken up by HeLa cells in the absence of a lipid transfecting agent. Furthermore, thioPACE modifications greatly improved the potency of a 2'-OMe phosphorothioate ORN as an inhibitor of microRNA-122 in Huh7 cells, without lipid transfection.     

Ultrafast internal conversion of excited cytosine via the lowest pipi electronic singlet state

Computational evidence at the CASPT2 level supports that the lowest excited state pipi* contributes to the S1/S0 crossing responsible for the ultrafast decay of singlet excited cytosine. The computed radiative lifetime, 33 ns, is consistent with the experimentally derived value, 40 ns. The nOpi* state does not play a direct role in the rapid repopulation of the ground state; it is involved in a S2/S1 crossing. Alternative mechanisms through excited states pisigma* or nNpi* are not competitive in cytosine.     

A general method for the synthesis of 2'-O-cyanoethylated oligoribonucleotides having promising hybridization affinity for DNA and RNA and enhanced nuclease resistance

[reaction: see text] An effective method for the synthesis of 2'-O-cyanoethylated oligoribonucleotides as a new class of 2'-O-modified RNAs was developed. The reaction of appropriately protected ribonucleoside derivatives with acrylonitrile in t-BuOH in the presence of Cs2CO3 gave 2'-O-cyanoethylated ribonucleoside derivatives in excellent yields, which were converted by a successive selective deprotection/protection strategy to 2'-O-cyanoethylated 5'-O-dimethoxytritylribonucleoside 3'-phosphoramidite derivatives in high yields. Fully 2'-O-cyanoethylated oligoribonucleotides, (Uce)12 and (GceAceCceUce)3, were successfully synthesized in the phosphoramidite approach by use of the phosphoramidite building blocks. It was also found that oligoribonucleotides having a 2'-O-cyanoethylated ribonucleoside (Uce, Cce, Ace, or Gce) could be obtained by the selective removal of the TBDMS group from fully protected oligoribonucleotide intermediates without loss of the cyanoethyl group by use of NEt3 x 3HF as a desilylating reagent. The detailed T(m) experiments revealed that oligoribonucleotides containing 2'-O-cyanoethylated ribonucleosides have higher hybridization affinity for both DNA and RNA than the corresponding unmodified and 2'-O-methylated oligoribonucleotides. In addition, introduction of a cyanoethyl group into the 2'-position of RNA resulted in significant increase of nuclease resistance toward snake venom and bovine spleen phosphodiesterases compared with that of the methyl group.     

Expanding the Scope of 2′‐SCF3 Modified RNA

The 2′‐trifluoromethylthio (2′‐SCF₃) modification endows ribonucleic acids with exceptional properties and has attracted considerable interest as a reporter group for NMR spectroscopic applications. However, only modified pyrimidine nucleosides have been generated so far. Here, the syntheses of 2′‐SCF₃ adenosine and guanosine phosphoramidites of which the latter was obtained in highly efficient manner by an unconventional Boc‐protecting group strategy, are reported. RNA solid‐phase synthesis provided site‐specifically 2′‐SCF₃‐modified oligoribonucleotides that were investigated intensively. Their excellent behavior in ¹⁹F NMR spectroscopic probing of RNA ligand binding was exemplified for a noncovalent small molecule–RNA interaction. Moreover, comparably to the 2′‐SCF₃ pyrimidine nucleosides, the purine counterparts were also found to cause a significant thermodynamic destabilization when located in double helical regions. This property was considered beneficial for siRNA design under the aspect to minimize off‐target effects and their performance in silencing of the BASP1 gene was demonstrated.     

Synthesis and properties of oligodeoxyribonucleotides containing 2’-<Emphasis Type="Italic">O</Emphasis>-(2,3-dihydroxypropyl)- and 2’-<Emphasis Type="Italic">O</Emphasis>-(2-oxoethyl)arabinouridine residues

2’-O-(2,3-Dihydroxypropyl)arabinouridine-containing oligodeoxyribonucleotides were synthesized starting from a new modified nucleoside, viz., 2’-O-(2,3-dihydroxypropyl)arabinouridine, and the corresponding 3’-phosphoramidite. Oxidation of these oligodeoxyribonucleotides with sodium periodate afforded oligonucleotides containing 2’-O-(2-oxoethyl)arabinouridine residues. Subsequent modification of the aldehyde-containing oligonucleotides involved the reactions with 9-hydrazinoacridine and N-aminooxyacetyl peptide and reductive amination by 4-(1-pyrenyl)butyrohydrazide and biotin hydrazide. Thermal stabilities of duplexes of modified oligodeoxyribonucleotides with complementary oligodeoxyribonucleotides are slightly lower than those of natural duplexes. Duplexes with complementary oligoribonucleotides are substantially destabilized.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 233–241, January, 2005.     

Structure and Transformations of 1-Alkyladamantane Radical-Cations

The structure of the radical-cations of 1-alkyladamantanes (alkyl = Me, Et, i-Pr, t-Bu) was investigated by computational methods (BLYP and MP2) in 6-316* basis set. It was shown that the adiabatic ionization potentials decrease significantly in this series. The competition between C—H and C—C fragmentation of the radical-cations was investigated both theoretically and experimentally in the presence of outer-sphere and electrophilic oxidants.     

Nonenzymatic recombination of RNA by means of transesterification

Coupled nonenzymatic cleavage/ligation of oligoribonucleotides catalyzed by magnesium ions afforded longer RNA molecules with a new sequence. The efficiency of formation of ligation products reaches 6%. The possible role of this reaction in the evolution of the RNA world is discussed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2413–2419, December, 2007.     

Site-specific modification of the 5"-terminal fragment of PGY1/MDR1 gene mRNA by reactive conjugates of antisense oligonucleotides

The site-specific modification of the 5"-terminal fragment of PGY1/MDR1 mRNA by oligodeoxyribonucleotide conjugates bearing residues of bleomycin A₅ (Blm), cobalt(ii) tetracarboxyphthalocyanine (Phcn), 4-[N-(2-chloroethyl)-N-methylamino]benzylamine (RCl), or perfluoroarylazide (Az) was studied. Conjugates of oligonucleotides complementary to the RNA sequences 123—138 and 155—166 selectively modify RNA in the vicinity of these regions. The highest efficacy (up to 50%) was achieved in reactions with alkylating and perfluoroarylazide conjugates of oligonucleotides. Conjugates of perfluoroarylazide with 2"-O-modified oligonucleotides are much more efficient than analogous conjugates with oligodeoxyribonucleotides (extents of RNA modification are 40—50% and 20%, respectively).     

Synthesis and spectroscopic properties of soluble aza analogs of phthalocyanine and naphthalocyanine

The syntheses of aryl-substituted octaaza analogs of phthalocyanine — tetra-2,3-(4,5-diphenylpyrazino)porphyrazin and its vanadyl complex — and also of the vanadyl complex of tetra-2,3-(4-phenylquinolino)porphyrazin — a tetraaza analog of naphthalocyanine — are described. A modified singlestage method for the synthesis of the previously reported tetra-2,3-(5-tert-butylpyrazino)porphyrazin is put forward. The electronic absorption spectra of the compounds synthesized have been studied in organic solvents and acid media — in sulfuric acid solution and in organic solvents with the addition of phenol or trichloroacetic acid.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 1, pp. 58–63, January, 1993.     

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.     

Permselectivities and ion-exchange properties of organically modified sol—gel electrodes

Sol—gel films prepared from organosilanes containing acidic/basic sites have been investigated as permselective and ion-exchange coatings for electroanalytical and bioanalytical investigations. When a glassy carbon electrode was modified with a sol—gel film fabricated from 3-aminopropyl-methyl-diethoxysilane (silane—NH₂), excellent permselectivity and anion-exchange properties were obtained. For a pH 7.4, 1 mM potassium ferricyanide solution, an eight-fold increase in current was observed after the electrode was immersed in solution for 10min whereas complete suppression of the electrochemical response for ruthenium hexaamine and methyl viologen was observed. Sol—gel films fabricated from trimethoxysilylpropyl ethylenediamine triacetic acid (silane—(COOH)₃) exhibited nearly complementary behavior. An approximately 10-fold increase in current was observed for pH 7.4, 1 mM ruthenium hexaammine solutions and complete suppression of the potassium ferricyanide response was observed. These ion-exchange properties can be attributed to the strong electrostatic interactions between the acid/basic functional group in the matrix and the highly charged analyte molecules. When glassy carbon electrodes were modified with diethyl-(triethoxysilypropyl) malonate (silane—(COOEt)₂), the films did not exhibit distinct ion-exchange properties but rather suppressed the reduction of potassium ferricyanide. The observed permselectivity results from the electron dense carbonyl group and/or hydrolyzed ester functionalities in the film.     

RNA synthesis via dimer and trimer phosphoramidite block coupling

The solid-phase synthesis of oligoribonucleotides using dimer and trimer phosphoramidite blocks is described. This method significantly reduces the total number of steps required in the synthesis of a target RNA sequence, provides more material, and simplifies separation of the product from shorter failure sequences. The procedure is illustrated by the synthesis of UpU, ApA, and UpUpU phosphoramidite blocks and their use in the rapid synthesis of oligoribonucleotides on a solid support. Dimer and trimer amidite blocks will likely find use in the large scale solution (or solid)-phase synthesis of siRNA drugs.