Synthesis of Oligonucleotides Containing the N6-(2-Deoxy-α,β-d-erythropentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy⋅dG) Oxidative Damage Product Derived from 2′-Deoxyguanosine

N⁶-(2-Deoxy-α,β-d -erythropentofuranosyl)-2,6-diamino-4-hydroxy-5-formamidopyrimidine (Fapy⋅dG) is a major DNA lesion produced from 2′-deoxyguanosine under oxidizing conditions. Fapy ⋅ dG is produced from a common intermediate that leads to 7,8-dihydro-8-oxo-2′-deoxyguanosine (8-OxodGuo), and in greater quantities in cells. The impact of Fapy ⋅ dG on DNA structure and function is much less well understood than that of 8-OxodGuo. This is largely due to the significantly greater difficulty in synthesizing oligonucleotides containing Fapy ⋅ dG than 8-OxodGuo. We describe a synthetic approach for preparing oligonucleotides containing Fapy ⋅ dG that will facilitate intensive studies of this lesion in DNA. A variety of oligonucleotides as long as 30 nucleotides are synthesized. We anticipate that the chemistry described herein will provide an impetus for a wide range of studies involving Fapy ⋅ dG.     

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.     

Nucleotides,Part LXIX,Synthesis of Phosphoramidite Building Blocks of Isoxanthopterin N8‐(2′‐Deoxy‐β‐D‐ribonucleosides): New Fluorescence Markers for Oligonucleotide Synthesis

The chemical synthesis of isoxanthopterin and 6‐phenylisoxanthopterin N⁸‐(2′‐deoxy‐β‐D ‐ribofuranosyl nucleosides) is described as well as their conversion into suitably protected 3′‐phosphoramidite building blocks to be used as marker molecules for DNA synthesis. Applying the npe/npeoc (=2‐(4‐nitrophenyl)ethyl/[2‐(4‐nitrophenyl)ethoxy]carbonyl) strategy, we used the new building blocks in the preparation of oligonucleotides by an automated solid‐support approach. The hybridization properties of a series of labelled oligomers were studied by UV‐melting techniques. It was found that the newly synthesized markers only slightly interfered with the abilities of the labelled oligomers to form stable duplexes with complementary oligonucleotides.     

Hairpin DNA‐Dependent Click Conjugation of Oligonucleotides for Electrochemical Monitoring of Copper(II)

A new electrochemical sensing platform was designed for sensitive detection of copper(II) (Cu²⁺) based on click conjugation of two short oligonucleotides by using methylene blue‐functionalized hairpin DNA as the template. The analyte (Cu²⁺) was in situ reduced to Cu⁺ by sodium ascorbate, which catalyzed the click conjugation between two single‐stranded oligonucleotides one was labelled with a 5′‐alkyne and the other with 3′‐azide group via the Cu⁺‐catalyzed azide‐alkyne cycloaddition. The newly formed long‐chain oligonucleotide induced the conformational change of hairpin DNA to open the hairpin, resulting in methylene blue far away from the electrode for the decrease of redox current. Under optimal conditions, the decrease in the electronic signal was directly proportional to target Cu²⁺ concentration, and allowed the detection of Cu²⁺ at a concentration as low as 1.23 nM. Our strategy also displayed high selectivity for Cu²⁺ against other metal ions owing to the highly specific Cu⁺‐catalyzed click chemistry reaction, and was applicable for monitoring of Cu²⁺ in drinking water with satisfactory results.     

Warum Pentose- und nicht Hexose-Nucleinsäuren??. Teil II. Oligonucleotide aus 2′,3′-Dideoxy-β-D-glucopyranosyl-Bausteinen (‘Homo-DNS’): Herstellung.

Why Pentose and Not Hexose Nucleic Acids? Part II . Preparation of Oligonucleotides Containing 2′,3′-Dideoxy-β-D -glucopyranosyl Building Blocks⁽⁷⁾ This paper describes the preparation of the 2′,3′-dideoxy-β-D -glucopyranosyl-( = 2′,3′-dideoxy-β-D -erythro-hexopyranosyl)-derived nucleosides of the five bases adenine, cytosine, guanine, thymine, and uracil ( = ‘homo-de-oxyribonucleosides’) as well as the synthesis of oligonucleotides derived from them. The methods used for both nucleoside and oligonucleotide synthesis closely follow the known methods of synthesis in the corresponding series of natural 2′-deoxyribonucleosides and oligonucleotides. The efficient methods of automated DNA synthesis proved to be fully applicable to the synthesis of homo-DNA oligonucleotides, the only change necessary for achieving satisfactory coupling yields being a slight lengthening of the coupling time. Homo-DNA oligonucleotides with chain lengths of up to twelve nucleoside units were assembled on solid support either manually or on a commercial DNA synthesizer in scales of 0.4 μmol to as much as 200 μmol and were purified by either reversed-phase or ion-exchange HPLC to single-peak purity according to both chromatographic systems (estimated purity > 95%). The choice of the specific base sequences to be synthesized was determined primarily by the constitutional problems of base pairing that emerged from experimental observations made in the course of systematic studies of the pairing properties of homo-DNA oligonucleotides. About 100 homo-DNA sequences were prepared for this purpose. Their pairing properties will be described in Part III of this series; the present paper is restricted to the characterization of the purity and constitutional integrity of a few selected (single-stranded) oligonucleotides by ¹H-, ³¹P-, and ¹³C-NMR spectroscopy as well as by FAB and time-of-flight mass spectroscopy. The English Footnotes to Schemes 1–9, Fig. 1–12, and Table 1 provide an extension of this summary.     

Targeting of Single‐Stranded Oligonucleotides through Metal‐Induced Cyclization of Short Complementary Strands

A new strategy to cyclize short synthetic oligonucleotides on DNA or RNA target strands is described. The approach is based on metal‐templated cyclization of short synthetic oligonucleotides conjugated with two chelating 2,2′ : 6′,2′′‐terpyridine (Tpy) moieties at their 3′‐ and 5′‐ends. Cyclization after metal addition (Zn²⁺, Fe²⁺) was demonstrated by means of thermal‐denaturation experiments, MALDI‐Q‐TOF‐MS, and gel electrophoresis (PAGE). 1D‐ and 2D‐NMR Experiments were performed to analyze the association of complementary strands after metal‐mediated cyclization. Our protocol allows the efficient circularization of synthetic oligonucleotides. Thereby, the hybridization on a complementary strand was more efficient with an RNA target strand and a 2′‐O‐methylated circularized oligomer.     

Inducement and stabilization of G-quadruplex DNA by a thiophene-containing dinuclear ruthenium(II) complex

G-quadruplex structures are attractive targets for the development of anticancer drugs, as their formation in human telomere could impair telomerase activity, thus inducing apoptosis in cancer cells. In this work, a thiophene-containing dinuclear ruthenium(II) complex, [Ru₂(bpy)₄(H₂bipt)]⁴⁺ {bpy = 2,2′-bipyridine, H₂bipt = 2,5-bis[1,10]phenanthrolin[4,5-f]-(imidazol-2-yl)thiophene}, was prepared and the interaction between the complex and human telomeric DNA oligomers 5′-G₃(T₂AG₃)₃-3′ (HTG21) has been investigated by UV-Vis, fluorescence and circular dichroism (CD) spectroscopy, fluorescence resonance energy transfer (FRET) melting assay, polymerase chain reaction (PCR) stop assay, fluorescent intercalator displacement (FID) titrations, Job plot and color reaction studies. The results indicate that the complex can well induce and stabilize the formation of antiparallel G-quadruplex of telomeric DNA in the presence or absence of metal cations, and the ΔT_m value of the G-quadruplex DNA treated with the complex was obtained to be 12.8 °C even at levels of 50-fold molar of duplex DNA (calf-thymus DNA), suggesting that the complex exhibits higher G-quadruplex DNA selectivity over duplex DNA. The complex shows high interaction ability with G-quadruplex DNA at (1.17 ± 0.12) × 10⁷ M^?1 binding affinity using a 2:1 [complex]/[quadruplex] binding mode ratio. A novel visual method has been developed here for making a distinction between G-quadruplex DNA and duplex DNA by our ruthenium complex binding hemin to form the hemin-G-quadruplex DNAzyme.     

Photosensitized Generation of Singlet Oxygen from (Substituted Bipyridine)ruthenium(II) Complexes

Photophysical properties in dilute MeCN solution are reported for seven Ru^II complexes containing two 2,2′‐bipyridine (bpy) ligands and different third ligands, six of which contain a variety of 4,4′‐carboxamide‐disubstituted 2,2′‐bipyridines, for one complex containing no 2,2′‐bipyridine, but 2 of these different ligands, for three multinuclear Ru^II complexes containing 2 or 4 [Ru(bpy)₂] moieties and also coordinated via 4,4′‐carboxamide‐disubstituted 2,2′‐bipyridine ligands, and for the complex [(Ru(bpy)₂(L)]²⁺ where L is N,N′‐([2,2′‐bipyridine]‐4,4′‐diyl)bis[3‐methoxypropanamide]. Absorption maxima are red‐shifted with respect to [Ru(bpy)₃]²⁺, as are phosphorescence maxima which vary from 622 to 656 nm. The lifetimes of the lowest excited triplet metal‐to‐ligand charge transfer states ³MLCT in de‐aerated MeCN are equal to or longer than for [Ru(bpy)₃]²⁺ and vary considerably, i.e., from 0.86 to 1.71 μs. Rate constants k_q for quenching by O₂ of the ³MLCT states were measured and found to be well below diffusion‐controlled, ranging from 1.2 to 2.0⋅10⁹ dm³ mol⁻¹ s⁻¹. The efficiencies f of singlet‐oxygen formation during oxygen quenching of these ³MLCT states are relatively high, namely 0.53 – 0.89. The product of k_q and f gives the net rate constant k for quenching due to energy transfer to produce singlet oxygen, and k_q−k equals k, the net rate constant for quenching due to energy dissipation of the excited ³MLCT states without energy transfer. The quenching rate constants were both found to correlate with ΔG^CT, the free‐energy change for charge transfer from the excited Ru complex to oxygen, and the relative and absolute values of these rate constants are discussed.     

Nucleotides. Part XXXV. Synthesis of 3′-deoxyadenylyl-(2′–5′)-3′-deoxyadenyIyl-(2′–ω)-9-(ω-hydroxyalkyl)adenines

Via the phosphotriester approach, new structural analogs of (2′–5′)oligoadenyiates, namely 3′-deoxyadenylyl-(2′–5′)-3′-dcoxyadenylyl-(2′–ω)-9-(ω-hydroxyalkyl)adenines 18 – 21 , have been synthesized (see Scheme) which should preserve biological activity and show higher stability towards phosphodiesterases. The newly synthesized oligonucleotides 18 – 21 have been characterized by ¹H-NMR spectra, TLC, and HPLC analysis.     

Synthesis and Base Pairing Properties of 1′,5′‐Anhydro‐L‐Hexitol Nucleic Acids (L‐HNA)

Oligonucleotides composed of 1′,5′‐anhydro‐arabino‐hexitol nucleosides belonging to the L series (L ‐HNA) were prepared and preliminarily studied as a novel potential base‐pairing system. Synthesis of enantiopure L ‐hexitol nucleotide monomers equipped with a 2′‐(N⁶‐benzoyladenin‐9‐yl) or a 2′‐(thymin‐1‐yl) moiety was carried out by a de novo approach based on a domino reaction as key step. The L oligonucleotide analogues were evaluated in duplex formation with natural complements as well as with unnatural sugar‐modified oligonucleotides. In many cases stable homo‐ and heterochiral associations were found. Besides T_m measurements, detection of heterochiral complexes was unambiguously confirmed by LC‐MS studies. Interestingly, circular dichroism measurements of the most stable duplexes suggested that L ‐HNA form left‐handed helices with both D and L oligonucleotides.     

GenoMass software: a tool based on electrospray ionization tandem mass spectrometry for characterization and sequencing of oligonucleotide adducts

The analysis of DNA adducts is of importance in understanding DNA damage, and in the last few years mass spectrometry (MS) has emerged as the most comprehensive and versatile tool for routine characterization of modified oligonucleotides. The structural analysis of modified oligonucleotides, although routinely analyzed using mass spectrometry, is followed by a large amount of data, and a significant challenge is to locate the exact position of the adduct by computational spectral interpretation, which still is a bottleneck. In this report, we present an additional feature of the in‐house developed GenoMass software, which determines the exact location of an adduct in modified oligonucleotides by connecting tandem mass spectrometry (MS/MS) to a combinatorial isomer library generated in silico for nucleic acids. The performance of this MS/MS approach using GenoMass software was evaluated by MS/MS data interpretation for an unadducted and its corresponding N‐acetylaminofluorene (AAF) adducted 17‐mer (5'OH‐CCT ACC CCT TCC TTG TA‐3′OH) oligonucleotide. Further computational screening of this AAF adducted 17‐mer oligonucleotide (5′OH‐CCT ACC CCT TCC TTG TA‐3′OH) from a complex oligonucleotide mixture was performed using GenoMass. Finally, GenoMass was also used to identify the positional isomers of the AAF adducted 15‐mer oligonucleotide (5′OH‐ATGAACCGGAGGCCC‐3′OH). GenoMass is a simple, fast, data interpretation software that uses an in silico constructed library to relate the MS/MS sequencing approach to identify the exact location of adduct on oligonucleotides. Copyright © 2012 John Wiley & Sons, Ltd.     

O6-Alkylguanine DNA Alkyltransferase Mediated Disassembly of a DNA Tetrahedron

Tetrahedron DNA structures were formed by the assembly of three-way junction ( TWJ ) oligonucleotides containing O⁶-2′-deoxyguanosine-alkylene-O⁶-2′-deoxyguanosine (butylene and heptylene linked) intrastrand cross-links (IaCLs) lacking a phosphodiester group between the 2′-deoxyribose residues. The DNA tetrahedra containing TWJs were shown to undergo an unhooking reaction by the human DNA repair protein O⁶-alkylguanine DNA alkyltransferase (hAGT) resulting in structure disassembly. The unhooking reaction of hAGT towards the DNA tetrahedra was observed to be moderate to virtually complete depending on the protein equivalents. DNA tetrahedron structures have been explored as drug delivery platforms that release their payload in response to triggers, such as light, chemical agents or hybridization of release strands. The dismantling of DNA tetrahedron structures by a DNA repair protein contributes to the armamentarium of approaches for drug release employing DNA nanostructures.     

9-(2′-Deoxy-β-D-xylofuranosyl)adenine Building Blocks for Solid-Phase Synthesis and Properties of Oligo(2′-deoxy-xylonucleotides)

The 9-(2′-deoxy-à-D -threo-pentofuranosyl)adenine (=9-(2′-deoxy-à-D -xylofuranosyl)adeninc, xA_d; 2) was protected at its 6-NH₂ group with cither a benzoyl ( 5a ) or a (dimethyfamino)methylidcnc ( 6a ) residue and with a dimethoxytntyl group at 5′-OH ( 5b, 6b ). Compounds 5b and 6b were then converted into the 3′-phosphonates 5c and 6c ; moreover, the 2-cyanoethyl phosphoramidite 6d was synthesized starting from fib. The DNA building blocks were used for solid-phase synthesis of d[(xA)₁₂2-A] ( 8 ). The latter was hybridized with d[(xT)12-T] (T_m = 35°); in contrast, with d(T₁₂), complex formation was not observed. Moreover, xAd and xTd were introduced into the self-complementary dodccamcr d(G-T-A-G-A-A-T-T-C-T-A-C) ( 12 ) at different positions lo give the oligomcrs 13 – 16 . All oligonucleotides were characterised by temperature-dependent CD and UV spectroscopy, and in addition, 14 by T-jump experiments. From concentration-dependent T_m measurements, the thermodynamic paraneters of the melting as well as the tendency of hairpin formation of the oligonucleotides were deduced. Oligemer 14 was hydrolyzed by snake-venom phosphodiesterase in a discontinuous way implying a fast hydrolysis of unmodified 3′- and 5′-flanks followed by a slow hydrolysis of the remaining modified tetramer. In contrast to this, oligonucleotide 16 was hydrolyzed in a continuous reaction. In both cases, calf-spleen phosphodiesterase hydrolyzed the oligomer only marginally.     

3′‐Deoxyribopyranose (4′→2′)‐Oligonucleotide Duplexes (=p‐DNA Duplexes) as Substitutes of RNA Hairpin Structures

By automated synthesis, we prepared hybrid oligonucleotides consisting of covalently linked RNA and p‐DNA sequences (p‐DNA=3′‐deoxyribopyranose (4′→2′)‐oligonucleotides) (see Table 1). The pairing properties of corresponding hybrid duplexes, formed from fully complementary single strands were investigated. An uninterrupted π‐π‐stacking at the p‐DNA/RNA interface and cooperative pairing between the two systems was achieved by connecting them via a 4′‐p‐DNA‐2′→5′‐RNA‐3′ and 5′‐RNA‐2′→4′‐p‐DNA‐2′ phosphodiester linkage, respectively (see Fig. 4). The RNA 2′‐phosphoramidites 9 – 12 , required for the formation of the RNA‐2′→4′‐p‐DNA phosphodiester linkage were synthesized from the corresponding, 3′‐O‐tom‐protected ribonucleosides (tom=[(triisopropylsilyl)oxy]methyl; Scheme 1). Analogues of the flavin mononucleotide (=FMN) binding aptamer 22 and the hammerhead ribozyme 25 were prepared. Each of these analogues consisted of two p‐DNA/RNA hybrid single strands with complementary p‐DNA sequences, designed to substitute stem/loop and stem motifs within the parent compounds. By comparative binding and cleavage studies, it was found that mixing of the two complementary p‐DNA/RNA hybrid sequences resulted in the formation of the fully functional analogues 23 ⋅ 24 and 27 ⋅ 28 of the FMN‐binding aptamer and of the hammerhead ribozyme, respectively.     

Nucleoside und Nucleotide. Teil 16. Verhalten von 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyrimidinon-5′-triphosphat, 1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)pyridinon-5′-triphosphat und 4-Amino-1-(2′-Desoxy-β-D-ribofuranosyl)-2(1 H)-pyridinon-5′-triphosphat gegenüber DNA-Polymerase

Nucleosides and Nucleotides. Part 16. The Behaviour of 1-(2′-Deoxy-β-D -ribofuranosyl)-2(1H)-pyrimidinone-5′-triphosphate, 1-(2′-Deoxy-β-D -ribofuranosyl-2(1H))-pyridinone-5′-triphosphate and 4-Amino-1-(2′-desoxy-β-D -ribofuranosyl)-2(1H)-pyridinone-5′-triphosphate towards DNA Polymerase The behaviour of nucleotide base analogs in the DNA synthesis in vitro was studied. The investigated nucleoside-5′-triphosphates 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyrimidinone-5′-triphosphate (pppM_d), 1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppII_d) and 4-amino-1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridinone-5′-triphosphate (pppZ_d) can be considered to be analogs of 2′-deoxy-cytidine-5′-triphosphate. However, their ability to undergo base pairing to the complementary guanine is decreased. When pppM_d, pppII_d or pppZ_d are substituted for pppC_d in the enzymatic synthesis of DNA by DNA polymerase no incorporation of these analogs is observed. They exhibit only a weak inhibition of the DNA synthesis. The mode of the inhibition is uncompetitive which shows that these nucleotide analogs cannot serve as substrates for the DNA polymerase.     

Thermochemistry of europium and dithiocarbamate complex Eu(C5H8NS2)3(C12H8N2)

A solid complex Eu(C₅H₈NS₂)₃(C₁₂H₈N₂) has been obtained from reaction of hydrous europium chloride with ammonium pyrrolidinedithiocarbamate (APDC) and 1,10-phenanthroline (o-phen⋅H₂O) in absolute ethanol. IR spectrum of the complex indicated that Eu³⁺ in the complex coordinated with sulfur atoms from the APDC and nitrogen atoms from the o-phen. TG-DTG investigation provided the evidence that the title complex was decomposed into EuS. The enthalpy change of the reaction of formation of the complex in ethanol, Δ_r H _m ^θ(l), as –22.214±0.081 kJ mol^–1, and the molar heat capacity of the complex, c _m, as 61.676±0.651 J mol^–1 K^–1, at 298.15 K were determined by an RD-496 III type microcalorimeter. The enthalpy change of the reaction of formation of the complex in solid, Δ_r H _m ^θ(s), was calculated as 54.527±0.314 kJ mol^–1 through a thermochemistry cycle. Based on the thermodynamics and kinetics on the reaction of formation of the complex in ethanol at different temperatures, fundamental parameters, including the activation enthalpy (ΔH _≠ ^θ), the activation entropy (ΔS _≠ ^θ), the activation free energy (ΔG _≠ ^θ), the apparent reaction rate constant (k), the apparent activation energy (E), the pre-exponential constant (A) and the reaction order (n), were obtained. The constant-volume combustion energy of the complex, Δ_c U, was determined as –16937.88±9.79 kJ mol^–1 by an RBC-II type rotating-bomb calorimeter at 298.15 K. Its standard enthalpy of combustion, Δ_c H _m ^θ, and standard enthalpy of formation, Δ_f H _m ^θ, were calculated to be –16953.37±9.79 and –1708.23±10.69 kJ mol^–1, respectively.     

Efficient Automated Solid‐Phase Synthesis of DNA and RNA 5′‐Triphosphates

A fast, high‐yielding and reliable method for the synthesis of DNA‐ and RNA 5′‐triphosphates is reported. After synthesizing DNA or RNA oligonucleotides by automated oligonucleotide synthesis, 5‐chloro‐saligenyl‐N,N‐diisopropylphosphoramidite was coupled to the 5′‐end. Oxidation of the formed 5′‐phosphite using the same oxidizing reagent used in standard oligonucleotide synthesis led to 5′‐cycloSal‐oligonucleotides. Reaction of the support‐bonded 5′‐cycloSal‐oligonucleotide with pyrophosphate yielded the corresponding 5′‐triphosphates. The 5′‐triphosphorylated DNA and RNA oligonucleotides were obtained after cleavage from the support in high purity and excellent yields. The whole reaction sequence was adapted to be used on a standard oligonucleotide synthesizer.     

Synthesis of oligonucleotides containing 7-(2-deoxy-β-d-erythro-pentofuranosyl)guanine and 8-amino-2′-deoxyguanosine

The synthesis of oligonucleotides containing 7-(2-deoxy-β-D-erythro-pentofuranosyl)guanine and 8-amino-2′-deoxyguanosine was accomplished. The viable intermediate N²-isobutyryl-7-(2-deoxy-β-D-erythro-pentofuranosyl)guanine ( 6 ) was prepared via a four step deoxygenation procedure from 7-β-D-ribofuranosylguanine ( 1 ). The 5′-hydroxyl group of 6 was protected as 4,4′-dimethoxytrityl ether and then converted to the target phosphoramidite ( 8 ) via conventional phosphitylation procedure. The amino groups of 8-amino-2′-deoxyguanosine ( 9 ) were protected in the form of N-(dimethylainino)methylene functions to give the protected nucleoside 10 , which was subsequently converted to the target phosphoramidite 12 via dimethoxytritylation followed by phosphitylation. The phosphoramidites 8 and 12 were incorporated into a 26-mer and a 31-mer G-rich oligonucleotide using solid-support, phosphoramidite methodology. Analysis of antiparallel triplex formation by the oligonucleotides containing 7-(2-deoxy-β-D-erythro-pentofura-nosyl)guanine in place of 2′-deoxyguanosine showed no enhancement in triple helix formation.     

DNA Interactions of the Functionalized (Mixed Polypyridine)ruthenium(II) Complex Bis(2,2′‐bipyridine‐κN1,κN1′)(methyl dipyrido[3,2‐a : 2′,3′‐c]phenazine‐11‐carboxylate‐κN4,κN5)ruthenium(2+) ([Ru(bpy)2(dppz‐11‐CO2Me)]2+)

A novel polypyridine ligand, dipyrido[3,2‐a:2′,3′‐c]phenazine‐11‐carboxylic acid methyl ester (=dppz‐11‐CO₂Me), and its ruthenium(II) complex, [Ru(bpy)₂(dppz‐11‐CO₂Me)]²⁺ ( 1 ), were synthesized and characterized. The binding properties of this complex to calf‐thymus DNA (CT‐DNA) were investigated by different spectrophotometric methods and viscosity measurements. The results suggest that the complex binds to DNA in an intercalative mode and serves as a molecular ‘light switch’ for DNA. When irradiated at 365 nm, the complex 1 promoted the photocleavage of plasmid pBR‐322 DNA.     

A Practical Synthesis of 3′-Thioguanosine and of Its 3′-Phosphoramidothioite (a Thiophosphoramidite)

Starting from guanosine, an efficient method for the synthesis of 3′-thioguanosine (see 13 ) and of its 3′-phosphoramidothioite (see 23 ), suitable for automated incorporation into oligonucleotides, was developed. Reaction of 5′-N²-protected guanosine with 2-acetoxyisobutyryl bromide afforded stereoselectively the 2′-O-acetyl-3′-bromo-β-D -xylofuranosyl derivative 3 , which was converted to a 7 : 3 mixture of the S-acyl ribofuranosyl intermediates 5 or 6 and the 3′,4′-unsaturated by-product 4 . The S-acylated nucleosides 5 and 6 were then converted in three steps to 5′-O-(4,4′-dimethoxytrityl)-3′-S-(pyridin-2-ylthio)-3′-thioguanosine ( 11 ), which served as a common intermediate for the preparation of free 3′-thionucleoside 13 and 3′-thionucleoside 3′-phosphoramidothioite 23 .