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).     

Synthesis of 2′‐O‐[(Triisopropylsilyl)oxy]methyl (= tom)‐Protected Ribonucleoside Phosphoramidites Containing Various Nucleobase Analogues

The first results of a study aiming at an efficient preparation of a large variety of 2′‐O‐[(triisopropylsilyl)oxy]methyl(= tom)‐protected ribonucleoside phosphoramidite building blocks containing modified nucleobases are reported. All of the here presented nucleosides have already been incorporated into RNA sequences by several other groups, employing 2′‐O‐tbdms‐ or 2′‐O‐tom‐protected phosphoramidite building blocks (tbdms = (tert‐butyl)dimethylsilyl). We now optimized existing reactions, developed some new and shorter synthetic strategies, and sometimes introduced other nucleobase‐protecting groups. The 2′‐O‐tom, 5′‐O‐(dimethoxytrityl)‐protected ribonucleosides N²‐acetylisocytidine 5 , O²‐(diphenylcarbamoyl)‐N⁶‐isobutyrylisoguanosine 8 , N⁶‐isobutyryl‐N²‐(methoxyacetyl)purine‐2,6‐diamine ribonucleoside (= N⁸‐isobutyryl‐2‐[(methoxyacetyl)amino]adenosine) 11 , 5‐methyluridine 13 , and 5,6‐dihydrouridine 15 were prepared by first introducing the nucleobase protecting groups and the dimethoxytrityl group, respectively, followed by the 2′‐O‐tom group (Scheme 1). The other presented 2′‐O‐tom, 5′‐O‐(dimethoxytrityl)‐protected ribonucleosides inosine 17 , 1‐methylinosine 18 , N⁶‐isopent‐2‐enyladenosine 21 , N⁶‐methyladenosine 22 , N⁶,N⁶‐dimethyladenosine 23 , 1‐methylguanosine 25 , N²‐methylguanosine 27 , N²,N²‐dimethylguanosine 29 , N⁶‐(chloroacetyl)‐1‐methyladenosine 32 , N⁶‐{{{(1S,2R)‐2‐{[(tert‐butyl)dimethylsilyl]oxy}‐1‐{[2‐(4‐nitrophenyl)ethoxy]carbonyl}propyl}amino}carbonyl}}adenosine 34 (derived from L ‐threonine) and N⁴‐acetyl‐5‐methylcytidine 36 were prepared by nucleobase transformation reactions from standard, already 2′‐O‐tom‐protected ribonucleosides (Schemes 2–4). Finally, all these nucleosides were transformed into the corresponding phosphoramidites 37 – 52 (Scheme 5), which are fully compatible with the assembly and deprotection conditions for standard RNA synthesis based on 2′‐O‐tom‐protected monomeric building blocks.     

Nucleotides,Part LXVII,The 2‐Cyanoethyl and (2‐Cyanoethoxy)carbonyl Group for Base Protection in Nucleoside and Nucleotide Chemistry

The amino functions of the common 2′‐deoxyribo‐ and ribonucleosides were blocked by the (2‐cyanoethoxy)carbonyl group on treatment with 2‐cyanoethyl carbonochloridate ( 5 ) or 1‐[(2‐cyanoethoxy)carbonyl]‐3‐methyl‐1H‐imidazolium chloride ( 6 ) leading to 7 , 18 , 8 , 19 , 9 , and 20 . In 2′‐deoxyguanosine, the amide group was additionally blocked at the O⁶ position by the 2‐cyanoethyl (→ 27 ) and 2‐(4‐nitrophenyl)ethyl group (→ 31 , 32 ). Comparative kinetic studies regarding the cleavage of the ce/ceoc and npe/npeoc group by β‐elimination revealed valuable information about the ease and sequential deprotection of the various blocking groups at different sites of the nucleobases. Besides the 5′‐O‐(dimethoxytrityl)‐protected 3′‐(2‐cyanoethyl diisopropylphosphoramidites) 38 and 39 of N⁴‐[(2‐cyanoethoxy)carbonyl]‐2′‐deoxycytidine and N⁶‐[(2‐cyanoethoxy)carbonyl]‐2′‐deoxyadenosine, respectively, the N²‐[(2‐cyanoethoxy)carbonyl]‐2′‐deoxy‐O⁶‐[2‐(4‐nitrophenyl)ethyl]guanosine analog 40 is recommended as building block for oligo‐2′‐deoxyribonucleotide synthesis.     

Synthesis of 3′‐Thioamido‐Modified 3′‐Deoxythymidine 5′‐Triphosphates by Regioselective Thionation and Their Use as Chain Terminators in DNA Sequencing

The thioamide derivatives 3′‐deoxy‐5′‐O‐(4,4′‐dimethoxytrityl)‐3′‐[(2‐methyl‐1‐thioxopropyl)amino]thymidine ( 4a ) and 3′‐deoxy‐5′‐O‐(4,4′‐dimethoxytrityl)‐3′‐{{6‐{[(9H‐(fluoren‐9‐ylmethoxy)carbonyl]amino}‐1‐thioxohexyl}amino}thymidine ( 4b ) were synthesized by regioselective thionation of the corresponding amides 3a and 3b with 2,4‐bis(4‐methoxyphenyl)‐1,3,2,4‐dithiadiphosphetane 2,4‐disulfide (Lawesson's reagent). The addition of exact amounts of pyridine to the reaction mixture proved to be essential for an efficient transformation. The thioamides were converted into the corresponding 5′‐triphosphates 6a and 6b . Compound 6a was chosen for DNA sequencing experiments, and 6b was further labelled with fluorescein (→ 8 ).     

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.     

Novel Fluoride‐Labile Nucleobase‐Protecting Groups for the Synthesis of 3′(2′)‐O‐Aminoacylated RNA Sequences

With the aim to develop a general approach to a total synthesis of aminoacylated t‐RNAs and analogues, we describe the synthesis of stabilized, aminoacylated RNA fragments, which, upon ligation, could lead to aminoacylated t‐RNA structures. Novel RNA phosphoramidites with fluoride‐labile 2′‐O‐[(triisopropylsilyl)oxy]methyl (=tom) sugar‐protecting and N‐{{2‐[(triisopropylsilyl)oxy]benzyl}oxy}carbonyl (=tboc) base‐protecting groups were prepared (Schemes 4 and 5), as well as a solid support containing an immobilized N⁶‐tboc‐protected adenosine with an orthogonal (photolabile) 2′‐O‐[(S)‐1‐(2‐nitrophenyl)ethoxy]methyl (=(S)‐npeom) group (Scheme 6). From these building blocks, a hexameric oligoribonucleotide was prepared by automated synthesis under standard conditions (Scheme 7). After the detachment from the solid support, the resulting fully protected sequence 34 was aminoacylated with L ‐phenylalanine derivatives carrying photolabile N‐protecting groups (→ 42 and 43 ; Scheme 9). Upon removal of the fluoride‐labile sugar‐ and nucleobase‐protecting groups, the still stabilized, partially with the photolabile group protected precursors 44 and 45 , respectively, of an aminoacylated RNA sequence were obtained (Scheme 9 and Fig. 3). Photolysis of 45 under mild conditions resulted in the efficient formation of the 3′(2′)‐O‐aminoacylated RNA sequence 46 (Fig. 4). Additionally, we carried out model investigations concerning the stability of ester bonds of aminoacylated ribonucleotide derivatives under acidic conditions (Table) and established conditions for the purification and handling of 3′(2′)‐O‐aminoacylated RNA sequences and their stabilized precursors.     

Zn2+ Complexes of 3,5‐Bis[(1,5,9‐triazacyclododecan‐3‐yloxy)methyl]phenyl Conjugates of Oligonucleotides as Artificial RNases: The Effect of Oligonucleotide Conjugation on Uridine Selectivity of the Cleaving Agent

2‐(3,5‐Bis{[1,5,9‐tris(trifluoroacetyl)‐1,5,9‐triazacyclododecan‐3‐yloxy]methyl}phenoxy)ethanol was synthesized and converted to a O‐(2‐cyanoethyl)‐N,N‐diisopropylphosphoramidite building block, 12 . 2′‐O‐Methyl oligoribonucleotides incorporating a 2‐[(2S,4S,5R)‐4‐hydroxy‐5‐(hydroxymethyl)tetrahydrofuran‐2‐yl)ethyl 4‐oxopentanoate or a 2‐{2‐[2‐({[(2R,4S,5R)‐4‐hydroxy‐5‐(hydroxymethyl)tetrahydrofuran‐2‐yl]acetyl}amino)ethoxy]ethoxy}ethyl 4‐oxopentanoate non‐nucleosidic unit close to the 3′‐terminus were assembled on a solid support, the 4‐oxopentanoyl protecting groups were removed by treatment with hydrazinium acetate on‐support, and 12 was coupled to the exposed OH function. The deprotected conjugates were purified by HPLC, and their ability to cleave a complementary RNA containing either uridine or some other nucleoside at the potential cleaving site was compared. Somewhat unexpectedly, conjugation to an oligonucleotide did not enhance the catalytic activity of the Zn²⁺? bis(azacrown) complex and virtually abolished its selectivity towards the uridine sites.     

Nucleotides. Part LXXIX

Two series of new ribonucleoside 3′‐phosphoramidites (see 36 – 42 ) carrying the photolabile [2‐(2‐nitrophenyl)propoxy]carbonyl group at the 5′‐O‐position were synthesized and characterized as monomeric building blocks for photolithographic syntheses of RNA chips. Base protection was achieved in the well‐known manner by the 2‐(4‐nitrophenyl)ethyl (npe) and the [2‐(4‐nitrophenyl)ethoxy]carbonyl (npeoc) group. The carbohydrate moiety carried in addition the 2′‐O‐(tetrahydro‐4‐methoxy‐2H‐pyran‐4‐yl) group for blocking the 2′‐OH function.     

Reliable Chemical Synthesis of Oligoribonucleotides (RNA) with 2′‐O‐[(Triisopropylsilyl)oxy]methyl(2′‐O‐tom)‐Protected Phosphoramidites

A method for the introduction of the 2′‐O‐[(triisopropylsilyl)oxy]methyl (=tom) group into N‐acetylated, 5′‐O‐dimethoxytritylated ribonucleosides is presented. The corresponding 2′‐O‐tom‐protected phosphoramidite building blocks were obtained in pure form and were successfully employed for the routine synthesis of oligoribonucleotides on DNA synthesizers. Under DNA coupling conditions (2.5 min coupling time for a 1.5‐μmol synthesis scale) and with 5‐(benzylthio)‐1H‐tetrazole (BTT) as activator, 2′‐O‐tom‐protected phosphoramidites exhibited average coupling yields >99.4%. The combination of N‐acetyl and 2′‐O‐tom protecting groups allowed a reliable and complete two‐step deprotection, first with MeNH₂ in EtOH/H₂O and then with Bu₄NF in THF, without concomitant destruction of the product RNA sequences.     

Crystalline Behavior and Structure of a Liquid Crystal Compound, 5‐{[4′‐(((Pentyl)oxy)‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne

Single crystals of two liquid crystal compounds, 5‐{[4′‐(((pentyl)oxy)‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne (A3EO5) and 5‐{[(4′‐nonyloxy‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne (A3EO9), have been prepared by solution growth technique. The morphologies and structures of A3EO5 and A3EO9 crystals were investigated by wide angle X‐ray diffraction (WXRD), atom force microscope (AFM) and transmission electron microscope (TEM). In contrast to the same series of compounds which have a longer alkyl tail, 5‐{[(4′‐heptoxy‐4‐biphenylyl)carbonyl]oxy}‐1‐pentyne (A3EO7), 5‐{[(4′‐heptoxy‐4‐biphenylyl)oxy]carbonyl}‐1‐pentyne (A3E′O7) and A3EO9, A3EO5 shows strikingly different crystalline behavior. The former three compounds have only one crystal form, whereas A3EO5 exhibits polymorphism. Specifically, A3EO5 crystals grown from toluene solution show two crystal forms. The first one is crystal I which adopts a monoclinic P112/m space group with unit cell parameters of a?5.79 Å, b?8.34 Å, c?43.92 Å, γ?96°, and the other one is crystal II which adopts a monoclinic P112 space group with unit cell parameters of a?5.55 Å, b?7.38 Å, c?31.75 Å, γ?94°. When using dioxane as the solvent to grow A3EO5 crystal, we can selectively obtain crystal I. A3EO5 melt‐grown crystals also have two crystal forms which derive from crystal I and crystal II, respectively. The different crystalline behavior of the compounds should correlate with their different electron dipole moment resulting from the different length of alkyl tail.     

Indium(III) Chloride‐Catalyzed Conversion of {[(Benzyloxy)carbonyl]amino}‐Substituted Sulfones with 2‐[(Trimethylsilyl)oxy]furan: A Facile Access to γ‐Butenolactone Derivatives Containing a Protected Amino Group

Treatment of {[(benzyloxy)carbonyl]amino}‐substituted sulfones 1 with 2‐[(trimethylsilyl)oxy]furan ( 2 ) in the presence of InCl₃ as a catalyst at room temperature produced the γ‐butenolactone derivatives 3 and 4 containing a protected amino group (Scheme 1). The products were formed in high yields (81–92%) within 3–10 h favoring the anti‐isomer 3 .     

Olefin Cross‐Metathesis: Studies towards the Total Synthesis of (+)‐Bitungolide F

A stereoselective synthesis of (5S,6S)‐6‐[(2S,5S,7R,8E,10E)‐5‐(benzyloxy)‐7‐{[(tert‐butyl)dimethylsilyl]oxy}‐11‐phenylundeca‐8,10‐dien‐2‐yl]‐5‐ethyl‐5,6‐dihydro‐2H‐pyran‐2‐one (=(+)‐9‐O‐benzyl‐11‐O‐[(tert‐butyl)dimethylsilyl]bitungolide F) is reported. The strategy involves Gilman reaction, olefin cross‐metathesis, and Horner? Wadsworth? Emmons olefination as key steps.     

Synthesis of the Anticodon Hairpin tRNAfMet Containing N‐{[9‐(β‐D‐Ribofuranosyl)‐9H‐purin‐6‐yl]carbamoyl}‐L‐threonine (=N6‐{{[(1S,2R)‐1‐Carboxy‐2‐hydroxypropyl]amino}carbonyl}adenosine,t6A)

As part of our studies on the structure of yeast ^tRNA_f^Met, we investigated the incorporation of N‐{[9‐(β‐D ‐ribofuranosyl)‐9H‐purin‐6‐yl]carbamoyl}‐L ‐threonine (t⁶A) in the loop of a RNA 17‐mer hairpin. The carboxylic function of the L ‐threonine moiety of t⁶A was protected with a 2‐(4‐nitrophenyl)ethyl group, and a (tert‐butyl)dimethylsilyl group was used for the protection of its secondary OH group. The 2′‐OH function of the standard ribonucleotide building blocks was protected with a [(triisopropylsilyl)oxy]methyl group. Removal of the base‐labile protecting groups of the final RNA with 1,8‐diazabicyclo[5.4.0]undec‐7‐ene (DBU) and then with MeNH₂ was done under carefully controlled conditions to prevent hydrolysis of the carbamate function, leading to loss of the L ‐threonine moiety.     

Stereoselective Synthesis of 8‐Oxabicyclo[3.2.1]octane‐2,3,4,6,7‐pentols and Total Asymmetric Synthesis of 2,6‐Anhydrohepturonic Acid Derivatives and of β‐C‐manno‐Pyranosides Suitable for the Construction of (1→3)‐C,C‐Linked Trisaccharides

Enantiomerically pure (+)‐(1S,4S,5S,6S)‐6‐endo‐(benzyloxy)‐5‐exo‐{[(tert‐butyl)dimethylsilyl]oxy}‐7‐oxabicyclo[2.2.1]heptan‐2‐one ((+)‐ 5 ) and its enantiomer (−)‐ 5 , obtained readily from the Diels‐Alder addition of furan to 1‐cyanovinyl acetate, can be converted with high stereoselectivity into 8‐oxabicyclo[3.2.1]octane‐2,3,4,6,7‐pentol derivatives (see 23 – 28 in Scheme 2). A precursor of them, (1R,2S,4R,5S,6S,7R,8R)‐7‐endo‐(benzyloxy)‐8‐exo‐hydroxy‐3,9‐dioxatricyclo[4.2.1.0^2,4]non‐5‐endo‐yl benzoate ((−)‐ 19 ), is transformed into (1R,2R,5S, 6S,7R,8S)‐6‐exo,8‐endo‐bis(acetyloxy)‐2‐endo‐(benzyloxy)‐4‐oxo‐3,9‐dioxabicyclo[3.3.1]non‐7‐endo‐yl benzoate ((−)‐ 43 ) (see Scheme 5). The latter is the precursor of several protected 2,6‐anhydrohepturonic acid derivatives such as the diethyl dithioacetal (−)‐ 57 of methyl 3,5‐di‐O‐acetyl‐2,6‐anhydro‐4‐O‐benzoyl‐D ‐glycero‐D ‐galacto‐hepturonate (see Schemes 7 and 8). Hydrolysis of (−)‐ 57 provides methyl 3,5‐di‐O‐acetyl‐2,6‐anhydro‐4‐O‐benzoyl‐D ‐glycero‐D ‐galacto‐hepturonate 48 that undergoes highly diastereoselective Nozaki‐Oshima condensation with the aluminium enolate resulting from the conjugate addition of Me₂AlSPh to (1S,5S,6S,7S)‐7‐endo‐(benzyloxy)‐6‐exo‐{[(tert‐butyl)dimethylsilyl]oxy}‐8‐oxabicyclo[3.2.1]oct‐3‐en‐2‐one ((−)‐ 13 ) derived from (+)‐ 5 (Scheme 12). This generates a β‐C‐mannopyranoside, i.e., methyl (7S)‐3,5‐di‐O‐acetyl‐2,6‐anhydro‐4‐O‐benzoyl‐7‐C‐[(1R,2S,3R,4S,5R,6S,7R)‐6‐endo‐(benzyloxy)‐7‐exo‐{[(tert‐butyl)dimethylsilyl]oxy}‐4‐endo‐hydroxy‐2‐exo‐(phenylthio)‐8‐oxabicyclo[3.2.1]oct‐3‐endo‐yl]‐L ‐glycero‐D ‐manno‐heptonate ((−)‐ 70 ; see Scheme 12), that is converted into the diethyl dithioacetal (−)‐ 75 of methyl 3‐O‐acetyl‐2,6‐anhydro‐4,5‐dideoxy‐4‐C‐{[methyl (7S)‐3,5,7‐tri‐O‐acetyl‐2,6‐anhydro‐4‐O‐benzoyl‐L ‐glycero‐D ‐manno‐heptonate]‐7‐C‐yl}‐5‐C‐(phenylsulfonyl)‐L ‐glycero‐D ‐galacto‐hepturonate ( 76 ; see Scheme 13). Repeating the Nozaki‐Oshima condensation to enone (−)‐ 13 and the aldehyde resulting from hydrolysis of (−)‐ 75 , a (1→3)‐C,C‐linked trisaccharide precursor (−)‐ 77 is obtained.     

Synthesis of Photolabile 5′‐O‐Phosphoramidites for the Photolithographic Production of Microarrays of Inversely Oriented Oligonucleotides

The photolabile 3′‐O‐{[2‐(2‐nitrophenyl)propoxy]carbonyl}‐protected 5′‐phosphoramidites ( 16 – 18 ) were synthesized (see Scheme) for an alternative mode of light‐directed production of oligonucleotide arrays. Because of the characteristics of these monomeric building blocks, photolithographic in situ DNA synthesis occurred in 5′→3′ direction, in agreement with the orientation of enzymatic synthesis. Synthesis yields were as good as those of conventional reactions. The resulting oligonucleotides are attached to the surface via their 5′‐termini, while the 3′‐hydroxy groups are available as substrates for enzymatic reactions such as primer extension upon hybridization of a DNA template (see Fig. 2). The production of such oligonucleotide chips adds new procedural avenues to the growing number of applications of DNA microarrays.     

Amphiphilic block glycopolymers via atom transfer radical polymerization: Synthesis,self‐assembly and biomolecular recognition

In this work the synthesis of poly(butyl acrylate)‐b‐poly(2‐{[(D ‐glucosamin‐2‐N‐yl)carbonyl]oxy}ethyl methacrylate) (PBA‐b‐PHEMAGl) diblock glycopolymer and poly(2‐{[(D ‐glucosamin‐2‐N‐yl)carbonyl]oxy}ethyl methacrylate)‐b‐poly(butyl acrylate)‐b‐poly(2‐{[(D ‐glucosamin‐2‐N‐yl)carbonyl]oxy}ethyl methacrylate) (PHEMAGl‐b‐PBA‐b‐PHEMAGl) was performed via atom transfer radical polymerization. Monofunctional and difunctional poly(butyl acrylate) macroinitiators were used to synthesize the well‐defined diblock and triblock glycopolymers by chain extension reaction with the glycomonomer HEMAGl. The self‐assembly of these glycopolymers in aqueous solution was studied by dynamic light scattering and transmission electron microcopy, showing the coexistence of spherical micelles and polymeric vesicles. In addition, the biomolecular recognition capacity of these micelles and vesicles, containing glucose moieties in their coronas, was investigated using the lectin Concanavalin A, Canavalia Ensiformis, which specifically interacts with glucose groups. The binding capacity of Concanavalin A with glycopolymer is influenced by the copolymer composition, increasing with the length of HEMAGl glycopolymer segment in the block copolymer. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

First Total Synthesis of N‐(3‐Guanidinopropyl)‐2‐(4‐hydroxyphenyl)‐2‐oxoacetamide

The first total synthesis of the α‐oxo amide‐based natural product, N‐(3‐guanidinopropyl)‐2‐(4‐hydroxyphenyl)‐2‐oxoacetamide ( 3 ), isolated from aqueous extracts of hydroid Campanularia sp., has been achieved. The α‐oxo amide 12 , prepared via the oxidative amidation of 1‐[4‐(benzyloxy)phenyl]‐2,2‐dibromoethanone ( 9a ) with 4‐{[(tert‐butyl)(dimethyl)silyl]oxy}butan‐1‐amine ( 10a ), has been used as the key intermediate in the total synthesis of 3 as HBr salt. On the way, an expeditious total synthesis of polyandrocarpamide C ( 2c ), isolated from marine ascidian Polyandrocarpa sp., was carried out in four steps.     

Synthesis of a New C(1→2)‐Linked Iminodisaccharide Starting from Levoglucosenone

Methyl 2‐deoxy‐2‐[(1S)‐2,5‐dideoxy‐2,5‐imino‐L ‐ribitol‐1‐C‐yl)‐α‐D ‐glucopyranoside ((+)‐ 6 ) was obtained from the product of Nozaki‐Kishi coupling of 2,5‐{[(tert‐butoxy)carbonyl]imino}‐2,5‐dideoxy‐3,4‐O‐isopropylidene‐L ‐ribose ((−)‐ 9 ) and 4‐O‐benzyl‐6‐O‐[(benzyloxy)methyl]‐3‐deoxy‐2‐O‐[(trifluoromethyl)sulfonyl]‐α‐D ‐erythro‐hex‐2‐enopyranoside ((+)‐ 12 ). The alkenyl triflate (+)‐ 12 was derived from levoglucosenone ( 1 ).     

Oligonucleotides Containing 7‐Deaza‐2′‐deoxyxanthosine: Synthesis,Base Protection,and Base‐Pair Stability

Oligonucleotides incorporating 7‐deaza‐2′‐deoxyxanthosine ( 3 ) and 2′‐deoxyxanthosine ( 1 ) were prepared by solid‐phase synthesis using the phosphoramidites 6 – 9 and 16 which were protected with allyl, diphenylcarbamoyl, or 2‐(4‐nitrophenyl)ethyl groups. Among the various groups, only the 2‐(4‐nitrophenyl)ethyl group was applicable to 7‐deazaxanthine protection being removed with 1,8‐diazabicyclo[5.4.0]undec‐7‐ene (DBU) by β‐elimination, while the deprotection of the allyl residue with Pd⁰ catalyst or the diphenylcarbamoyl group with ammonia failed. Contrarily, the allyl group was found to be an excellent protecting group for 2′‐deoxyxanthosine ( 1 ). The base pairing of nucleoside 3 with the four canonical DNA constituents as well as with 3‐bromo‐1‐(2‐deoxy‐β‐D ‐erythro‐pentofuranosyl)‐1H‐pyrazolo[3,4‐d]pyrimidine‐4,6‐diamine ( 4 ) within the 12‐mer duplexes was studied, showing that 7‐deaza‐2′‐deoxyxanthosine ( 3 ) has the same universal base‐pairing properties as 2′‐deoxyxanthosine ( 1 ). Contrary to the latter, it is extremely stable at the N‐glycosylic bond, while compound 1 is easily hydrolyzed under slightly acidic conditions. Due to the pK_a values 5.7 ( 1 ) and 6.7 ( 3 ), both compounds form monoanions under neutral conditions (95% for 1 ; 65% for 3 ). Although both compounds form monoanions at pH 7.0, pH‐dependent T_m measurements showed that the base‐pair stability of 7‐deaza‐2′‐deoxyxanthosine ( 3 ) with dT is pH‐independent. This indicates that the 2‐oxo group is not involved in base‐pair formation.     

Nucleotides. Part LXXIII

The (2‐cyano‐1‐phenylethoxy)carbonyl (2c1peoc) group was developed as a new base‐labile protecting group for the 5′‐OH function in solid‐phase synthesis of oligoribonucleotides via the phosphoramidite approach. The half‐lives of its β‐elimination process by 0.1M DBU (1,8‐diazabicyclo[5.4.0]undec‐7‐ene) were determined to be 7–14 s by HPLC investigations. The 2′‐OH function was protected with the acid‐labile tetrahydro‐4‐methoxy‐2H‐pyran‐4‐yl (thmp) group, while the 2‐(4‐nitrophenyl)ethyl (npe) and 2‐(4‐nitrophenyl)ethoxycarbonyl (npeoc) groups were used for the protection of the base and phosphate moieties. The syntheses of the monomeric building blocks, both phosphoramidites and nucleoside‐functionalized supports, as well as the build‐up of oligoribonucleotides by means of this approach are described.