Oligonucleotides Containing Disaccharide Nucleosides

Disaccharide nucleosides with 2′‐O‐(D ‐arabinofuranosyl), 2′‐O‐(L ‐arabinofuranosyl), 2′‐O‐(D ‐ribopyranosyl), 2′‐O‐(D ‐erythrofuranosyl), and 2′‐O‐(5‐azido‐5‐deoxy‐D ‐ribofuranosyl) substituents were synthesized. These modified nucleosides were incorporated into oligonucleotides (see Table). Single substitution resulted in a ΔT_m of +0.5 to −1.4° for DNA/RNA and a ΔT_m of −0.8 to −4.7° for DNA/DNA duplexes. These disaccharide nucleosides can be well accommodated in RNA/DNA duplexes, and the presence of a NH₂−C(5″) group has a beneficial effect on duplex stability.     

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.     

2′‐Ethynyl‐DNA: Synthesis and Pairing Properties

2‐Ethynyl‐DNA was developed as a potential DNA‐selective oligonucleotide analog. The synthesis of 2′‐arabino‐ethynyl‐modified nucleosides was achieved starting from properly protected 2′‐ketonucleosides by addition of lithium (trimethylsilyl)acetylide followed by reduction of the tertiary alcohol. After a series of protecting‐group manipulations, phosphoramidite building blocks suitable for solid‐phase synthesis were obtained. The synthesis of oligonucleotides from these building blocks was successful when a fast deprotection scheme was used. The pairing properties of 2′‐arabino‐ethynyl‐modified oligonucleotides can be summarized as follows: 1) The 2′‐arabino‐ethynyl modification of pyrimidine nucleosides leads to a strong destabilization in duplexes with DNA as well as with RNA. The likely reason is that the ethynyl group sterically influences the torsional preferences around the glycosidic bond leading to a conformation not suitable for duplex formation. 2) If the modification is introduced in purine nucleosides, no such influence is observed. The pairing properties are not or only slightly changed, and, in some cases (deoxyadenosine homo‐polymers), the desired stabilization of the pairing with a DNA complementary strand and destabilization with an RNA complement is observed. 3) In oligonucleotides of alternating deoxycytidine‐deoxyguanosine sequence, the incorporation of 2′‐arabino‐ethynyl deoxyguanosine surprisingly leads to the formation of a left‐handed double helix, irrespective of salt concentration. The rationalization for this behavior is that the ethynyl group locks such duplexes in a left‐handed conformation through steric blockade.     

A Nucleobase‐Discriminating Pyrrolo‐dC Click Adduct Designed for DNA Fluorescence Mismatch Sensing

New pyrrolo‐dC click adducts ( 4 and 5 ) tethered with a 1,2,3‐triazole skeleton were synthesized and oligonucleotides were prepared. The triazole system was either directly linked to the pyrrolo moiety ( 5 ) or connected via an n‐butyl linker ( 4 ). The quantum yield of nucleoside 5 (Φ=0.32), which is 10 times higher than those of 8‐methylpyrrolo‐dC ( 1 b , Φ=0.026) or the long linker derivative 4 (Φ=0.03), is maintained in oligonucleotides. Compound 5 was used as a nucleobase‐discriminating fluorescence sensor in duplex DNA. Excellent mismatch discrimination was observed when 5 was positioned opposite the four canonical nucleosides. Compound 5 has the potential to be used for SNP detection in long DNA targets when conventional techniques such as high resolution melt analysis fail.     

Solid‐Phase Synthesis of Dipeptide‐Conjugated Nucleosides and Their Interaction with RNA

Dipeptide‐conjugated nucleosides were efficiently synthesized from the intermediates of 3′‐amino‐3′‐deoxy‐nucleosides by using the solid‐phase synthetic strategy with HOBt/HBTU (1‐hydroxy‐1H‐benzotriazole/2‐(1H‐benzotriazol‐1‐yl)‐1,1,3,3‐tetramethyluronium hexafluoroborate) as the coupling reagents (Schemes 1–3). CD Spectra and thermal melting studies showed that the synthesized hydrophobic dipeptide? thymidine and ? uridine derivatives 8a – 8d, 13a – d , and 18 had a mild affinity with the polyA?polyU duplex and could induce the change of RNA conformation. The results also implied that the interaction of conjugates with RNA might be related to the sugar pucker conformation of the nucleoside.     

Synthesis and antimicrobial activity of new C‐furyl glycosides bearing substituted 1,3,4‐oxadiazoles

New 2,5‐disubstituted 1,3,4‐oxadiazole derivatives bearing C‐furyl glycoside moieties and their sugar hydrazone as well as their per‐O‐acetyl derivatives were synthesized starting from ethyl 2‐[5‐(3,4‐dihydroxytetrahydrofuran‐2‐yl)‐2‐methylfuran‐3‐yl]‐2‐oxoacetate. Heterocyclization of the sugar hydrazones using acetic anhydride afforded the corresponding oxadiazoline acyclic C‐nucleosides. The antimicrobial activity evaluation showed that many of the synthesized compounds revealed moderate to high antimicrobial activity. J. Heterocyclic Chem., (2011)     

Synthesis,Base Pairing,and Fluorescence Properties of Oligonucleotides Containing 1H‐Pyrazolo[3,4‐d]pyrimidin‐6‐amine (8‐Aza‐7‐deazapurin‐2‐amine) as an Analogue of Purin‐2‐amine

The synthesis of the N⁹‐ and N⁸‐(β‐D ‐2′‐deoxyribonucleosides) 2 and 10 , respectively, of 8‐aza‐7‐deazapurin‐2‐amine (=1H‐pyrazolo[3,4‐d]pyrimidin‐6‐amine) is described. The fluorescence properties and the stability of the N‐glycosylic bond of 2 were determined and compared with those of the 2′‐deoxyribonucleosides 1 and 3 of purin‐2‐amine and 7‐deazapurin‐2‐amine respectively. From the nucleoside 2 , the phosphoramidite 14 was prepared, and oligonucleotides were synthesized. Duplexes containing compound 1 or 2 are slightly less stable than those containing 2′‐deoxyadenosine, while their CD spectra are rather different. The fluorescence of the nucleosides is strongly quenched (>95%) in single‐stranded as well as in duplex DNA. The residual fluorescence was used to determine the melting profiles, which gave T_m values similar to those determined from the UV melting curves.     

Pentopyranosyl Oligonucleotide Systems,Communication No.12, The β‐D‐Xylopyranosyl‐(4′→2′‐oligonucleotide System

β‐D ‐Xylopyranosyl‐(4′→2′)‐oligonucleotides containing adenine and thymine as nucleobases were synthesized as a part of a systematic study of the pairing properties of pentopyranosyl oligonucleotides. Contrary to earlier expectations based on qualitative conformational criteria, β‐D ‐xylopyranosyl‐(4′→2′)‐oligonucleotides show Watson‐Crick pairing comparable in strength to that shown by pyranosyl‐RNA.     

Design and Synthesis of Some New α‐Phenyl Cinnamoyl Derivatives for Selective Protection of Purine Nucleosides

Three new α‐phenylcinnamic acid derivatives [4‐methoxy‐α‐phenylcinnamic acid, α‐(4‐methoxyphenyl)‐cinnamic acid, and 4,4′‐bismethoxy‐α‐phenylcinnamic acid] were synthesized, characterized, and selectively used for protecting the exocyclic amino function of purine nucleosides (2′‐deoxyadenosine and 2′‐deoxyguanosine) via active ester generation. The acids were first activated using p‐nitrophenol, and these activated esters were used subsequently for the selective protection of amino groups. The N‐protected derivatives of 2′‐deoxyguanosine and 2′‐deoxyadenosine have been found to be sufficiently stable toward acids, thus minimizing depurination under oligodeoxyribonucleotide synthesis protocol. The ease of syntheses of N‐protected purine nucleosides, their stability under an acidic environment, and mild deprotection conditions are the key advantages of the new protecting groups.     

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.     

Cu‐Mediated Selective N‐Arylation of Aminotriazole Acyclonucleosides

Novel N‐aryltriazole nucleosides were synthesized via a Cu‐mediated C? N cross‐coupling reaction, using 3‐aminotriazole acyclonucleosides and various boronic acid reagents. Interestingly, N‐arylation proceeded much more rapidly on the amide group than on the amine group, leading to selective N‐arylation of the amide functionality on nucleosides containing both groups on the triazole nucleobase.     

Design,Synthesis, and Characterization of Photolabeling Probes for the Study of the Mechanisms of the Antiviral Effects of Ribavirin

Ribavirin, the only small molecule available so far for treating hepatitis‐C‐virus infection, was recently used in an emergency context to treat patients with severe acute respiratory syndrome (SARS) in the early stages of the disease. To study the mechanisms responsible for the antiviral effects of ribavirin by using a photolabeling approach, we designed, synthesized, and characterized the azidotriazole nucleosides 1 and 2 as photolabeling probes of ribavirin. These probes were synthesized either by performing nucleophilic substitution of the corresponding bromotriazole nucleoside with NaN₃ (Scheme 2) or by directly coupling the azidotriazole with the protected ribose sugar (Scheme 4). The azidotriazole nucleosides 1 and 2 showed a fast, clear‐cut photochemical reaction, which suggests that they are promising candidates for use in photolabeling studies.     

Nucleotides. Part LXXII

The synthesis of various N‐methylated nucleosides (m⁶A, m³C, m⁴C, m³U) is described. These minor nucleosides can be obtained by simple methylation with diazomethane of [2‐(4‐nitrophenyl)ethoxy]carbonyl(npeoc)‐protected nucleosides. These methylated compounds are easily further derivatized to fit into the scheme of the [2‐(dansyl)ethoxy]carbonyl (dnseoc) approach for RNA synthesis (dansyl=[5‐(dimethylamino)naphthalen‐1‐yl]sulfonyl). Various oligoribonucleotides containing N⁶‐methyladenosine were synthesized, underlining the usefulness of the dnseoc approach, especially for the synthesis of natural tRNA‐derived oligoribonucleotide sequences.     

Novel C‐Thionucleosides: Synthesis and Reactions of 1,5‐ and 1,3‐Dialkyl Derivatives of (1,5‐Dithio‐1‐thiomethyl‐α‐D,L‐arabinopentulo‐pyranos‐1‐yl)‐1H‐1,2,4‐triazole Nucleosides

Abstract

A series of novel C‐thionucleosides: 1,5‐ and 1,3‐dialkyl derivatives of (2,3,4,5‐tetra‐O‐acetyl‐1,5‐dithio‐1‐methylthio‐α‐D,L‐arabinopentulopyranos‐1‐yl)‐1H‐1,2,4‐triazole nucleosides 10a–d and 17a–c were synthesized, after spontaneous rearrangements, from concerted 1,3‐cycloaddition of the sugar nitrile 5 with the reactive 1‐(chloroalkyl)‐1‐aza‐2‐azoniaallenes 6 and 13 in the presence of a Lewis acid. Deblocking of the acylated nucleosides afforded the free nucleosides 11a–d and 18a–c. The structures of the synthesized compounds were confirmed by ¹H NMR and mass spectra.     

Reversible Photoswitching of RNA Hybridization at Room Temperature with an Azobenzene C‐Nucleoside

Photoregulation of RNA remains a challenging task as the introduction of a photoswitch entails changes in the shape and the stability of the duplex that strongly depend on the chosen linker strategy. Herein, the influence of a novel nucleosidic linker moiety on the photoregulation efficiency of azobenzene is investigated. To this purpose, two azobenzene C‐nucleosides were stereoselectively synthesized, characterized, and incorporated into RNA oligonucleotides. Spectroscopic characterization revealed a reversible and fast switching process, even at 20 °C, and a high thermal stability of the respective cis isomers. The photoregulation efficiency of RNA duplexes upon trans‐to‐cis isomerization was investigated by using melting point studies and compared with the known D ‐threoninol‐based azobenzene system, revealing a photoswitching amplitude of the new residues exceeding 90 % even at room temperature. Structural changes in the duplexes upon photoisomerization were investigated by using MM/MD calculations. The excellent photoswitching performance at room temperature and the high thermal stability make these new azobenzene residues promising candidates for in‐vivo and nanoarchitecture photoregulation applications of RNA.     

Metal‐Ion‐Binding Analogs of Ribonucleosides: Preparation and Formation of Ternary Pd2+ and Hg2+ Complexes with Natural Pyrimidine Nucleosides

Four metal‐ion‐binding nucleosides, viz. 2,6‐bis(1‐methylhydrazinyl)‐9‐(β‐D ‐ribofuranosyl)‐9H‐purine ( 2a ) and its N‐acetylated derivative, 2b , 2,4‐bis(3,5‐dimethyl‐1H‐pyrazol‐1‐yl)‐5‐(β‐D ‐ribofuranosyl)pyrimidine ( 3 ), and 2,4‐bis(1‐methylhydrazinyl)‐5‐(β‐D ‐ribofuranosyl)pyrimidine ( 4 ) have been synthesized. The ability of these nucleosides and the previously prepared 2,6‐bis(3,5‐dimethyl‐1H‐pyrazol‐1‐yl)‐9‐(β‐D ‐ribofuranosyl)‐9H‐purine to form Pd²⁺‐ and Hg²⁺‐mediated complexes with uridine has been studied by ¹H‐NMR spectroscopy. To obtain additional support for the interpretation of the NMR data, comparative measurements on the ternary‐complex formation between pyridine‐2,6‐dicarboxamide ( 5 ), pyrimidine nucleosides, and K₂PdCl₄ were carried out.     

A Direct Synthesis for a New Series of 2‐Oxo(thioxo)nicotinonitrile Nucleosides as Antimicrobial Agents

A facile synthesis of a new series of cyclic and acyclic nucleosides of polyfunctionalized 2‐oxo(thioxo)nicotinonitrile derivatives 1 and 2 was performed. Glycosylation of 2‐pyridone 1 and 2‐thiopyridone 2 with glycosyl/galactosyl bromides in the existence of KOH afforded the N‐nucleoside and S‐nucleoside analogues 3 , 5 , 7 , and 9 , respectively. Deacetylation of nucleosides 3 , 5 , 7 , and 9 gave the deacetylated nucleosides 4 , 6 , 8 , and 10 , respectively. Alkylation of 2‐pyridone 1 with glycone analogues [namely, 4‐bromobutyl acetate, (2‐acetoxyethoxy)methyl bromide, 3‐chloropropane‐1,2‐diol, and allyl and / propargyl bromides] in the existence of K₂CO₃ afforded the corresponding O‐acyclic nucleoside analogues 11 , 13 , and 15–17 , respectively. Finally, treating of compounds 11 and 13 with a small amount of Et₃N tolerated the 6‐hydroxy deacetylated derivatives 12 and 14 , respectively. The synthesized nucleosides and alkylated products were tested against Gram (+ve) (Staphylococcus aureus and Bacillus cereus) and (Pseudomonas aeruginosa and Escherichia coli) as Gram (?ve) and Fungi (Aspergillus flavus and Aspergillus niger) and showed moderate antibacterial and antifungal activity.     

Design,Regiospecific Green Synthesis,Chemical Computational Analysis,and Antimicrobial Evaluation of Novel Phthalazine Heterocycles

Phthalazines have received considerable attention for their wide antimicrobial activity. Regiospecific nucleophilic attack of 4‐benzylphthalazin‐1‐ol by the 1‐oxo rather than the aza group on different alkyl halides gave novel phthalazine heterocyclic derivatives. Moreover, a variety of nucleosides bonded to electron‐withdrawing groups were synthesized using 4‐benzylphthalazine‐1‐ol. The density functional theory has been used to investigate the electronic structure of the synthesized compounds. All of the synthesized derivatives showed remarkable activity when tested against Gram‐positive and Gram‐negative bacteria, Aspergillus niger, and Candida albicans. The reactivity of these nucleosides was expected to arise from their bonding with the lone pair of N‐atom of the macromolecules of bacteria. These bonding were expected to inhibit the enzyme by forming highly stable complex with lower highest occupied molecular orbital energy. The structures of these synthesized derivatives were established by Fourier transform infrared, ¹H‐NMR, and ¹³C‐NMR spectroscopic evidence.     

Nucleotides,Part LXV,Synthesis of 2′‐Deoxyribonucleoside 5′‐Phosphoramidites: New Building Blocks for the Inverse (5′‐3′)‐Oligonucleotide Approach

The syntheses of the 3′‐O‐(4,4′‐dimethoxytrityl)‐protected 5′‐phosphoramidites 25 – 28 and 5′‐(hydrogen succinates) 29 – 32 , which can be used as monomeric building blocks for the inverse (5′‐3′)‐oligodeoxyribonucleotide synthesis are described (Scheme). These activated nucleosides and nucleotides were obtained by two slightly different four‐step syntheses starting with the base‐protected nucleosides 13 – 20 . For the protection of the aglycon residues, the well‐established 2‐(4‐nitrophenyl)ethyl (npe) and [2‐(4‐nitrophenyl)ethoxy]carbonyl (npeoc) groups were used. The assembly of the oligonucleotides required a slightly increased coupling time of 3 min in application of the common protocol (see Table 1). The use of pyridinium hydrochloride as an activator (instead of 1H‐tetrazole) resulted in an extremely shorter activation time of 30 seconds. We established the efficiency of this inverse strategy by the synthesis of the oligonucleotide 3′‐conjugates 33 and 34 which carry lipophilic caps derived from cholesterol and vitamin E, respectively, as well as by the formation of (3′‐3′)‐ and (5′‐5′)‐internucleotide linkages (see Table 2).     

Nucleosides and Oligonucleotides with Diynyl Side Chains: Base Pairing and Functionalization of 2′‐Deoxyuridine Derivatives by the Copper(I)‐Catalyzed Alkyne?Azide ‘Click’ Cycloaddition

Oligonucleotides containing the 5‐substituted 2′‐deoxyuridines 1b or 1d bearing side chains with terminal C?C bonds are described, and their duplex stability is compared with oligonucleotides containing the 5‐alkynyl compounds 1a or 1c with only one nonterminal C?C bond in the side chain. For this, 5‐iodo‐2′‐deoxyuridine ( 3 ) and diynes or alkynes were employed as starting materials in the Sonogashira cross‐coupling reaction (Scheme 1). Phosphoramidites 2b – d were prepared (Scheme 3) and used as building blocks in solid‐phase synthesis. T_m Measurements demonstrated that DNA duplexes containing the octa‐1,7‐diynyl side chain or a diprop‐2‐ynyl ether residue, i.e., containing 1b or 1d , are more stable than those containing only one triple bond, i.e., 1a or 1c (Table 3). The diyne‐modified nucleosides were employed in further functionalization reactions by using the protocol of the Cu^I‐catalyzed Huisgen–Meldal–Sharpless [2+3] cycloaddition (‘click chemistry’) (Scheme 2). An aliphatic azide, i. e., 3′‐azido‐3′‐deoxythymidine (AZT; 4 ), as well as the aromatic azido compound 5 were linked to the terminal alkyne group resulting in 1H‐1,2,3‐triazole‐modified derivatives 6 and 7 , respectively (Scheme 2), of which 6 forms a stable duplex DNA (Table 3). The Husigen–Meldal–Sharpless cycloaddition was also performed with oligonucleotides (Schemes 4 and 5).