1-(2′-Deoxy-β-D-xylofuranosyl)thymine Building Blocks for Solid-Phase Synthesis and Properties of Oligo(2′-Deoxyxylonucleotides)

1-(2′-Deoxy-β-D -threo-pentofuranosyl)thymine (= 1-(2′-deoxy-β-D -xylofuranosyl)thymine; xT_d; 2 ) was converted into its phosphonate 3b as well as its 2-cyanoethyl phosphoramidite 3c . Both compounds were used for solid-phase synthesis of d[(xT)₁₂-T] ( 5 ), representing the first DNA fragment build up from 3′–5′-linked 2′-deoxy--β-D -xylonucleosides. Moreover, xT_d was introduced into the innermost part of the self-complementary dodecamer d(G-T-A-G-A-A-xT-xT-C-T-A-C)₂ (9). The CD spectrum of d[(xT)₁₂–T] ( 5 ) exhibits reversed Cotton effects compared to d(T₁₂) ( 6 ; see Fig. 1), implying a left-handed single strand. With d(A₁₂) ( 7 ) it could be hybridized to form a propably Left-handed double strand d(A₁₂) · d[(xT)₁₂–T] ( 7 · 5 ) which was confirmed by melting experiments in combination with temperature-dependent CD spectroscopy. While 5 was hydrolyzed by snake-venom phosphodiesterase, it was resistant towards calf-spleen phosphodiesterase. The modified, self-complementary duplex 9 was hydrolyzed completely by snake-venom phosphodiesterase, at a twelvefold slower rate compared to unmodified 8 ; calf-spleen phosphodiesterase hydrolyzed 9 only partially.     

Synthesis and Properties of 2′-Deoxy-1′,2′-seco-D-ribosyl (5′ → 3′)oligonucleotides (= 1′,2′-seco-DNA) containing adenine and thymine

Some 2′-deoxy-1′,2′-seco-D-ribosyl (5′→3′)oligonucleotides (= 1′,2′-seco-DNA), differing from natural DNA only by a bond scission between the centers C(1′) and C(2′), were synthesized and studied in order to compare their structure properties and pairing behavior with those of corresponding natural DNA and homo-DNA oligonucleotides (2′,3′-dideoxy-β-D-glucopyranosyl oligonucleotides). Starting from (?)-D-tartaric acid, 2′-deoxy-1′,2′-secoadenosine derivative 9a and 1′,2′-secothymidine ( 9b ) were obtained in pure crystalline form. Using the phosphoramidite variant of the phosphite-triester method, a dinucleotide monophosphate 1′,2′-seco-d(T₂) was synthesized in solution, while oligonucleotides 1′,2′-seco-d[(AT)₆], 1′,2′-seco-d(A₁₀) and 1′,2′-seco-d(T₁₀) were prepared on solid phase with either automated or manual techniques. Results of UV- and CD-spectroscopic as well as gel-electrophoretic studies indicated that neither adenine-thymine base pairing (as observed in natural DNA and homo-DNA), nor the adenine-adenine base pairing (as observed in homo-DNA) was effective in 1′,2′-seco-DNA, Furthermore, hybrid pairing was observed neither between 1′.2′-seco-DNA and natural DNA nor between 1′,2′-seco-DNA and homo-DNA.     

Nucleoside und Nucleotide. Teil 10. Synthese von Thymidylyl-(3′-5′) -thymidylyl-(3′-5′)-1-(2′-desoxy-β-D-ribofuranosyl)-2(1 H)-pyridon

Nucleosides and Nucleotides. Part 10. Synthesis of Thymidylyl-(3′-5′)-thymidylyl-(3′-5′)-1-(2′-deoxy-β-D - ribofuranosyl)-2(1 H)-pyridone The synthesis of 5′-O-monomethoxytritylthymidylyl-(3′-5′)-thymidylyl-(3′-5′)-1-(2′-deoxy-β-D -ribofuranosyl)-2(1H)-pyridone ((MeOTr)T_dpT_dp∏_d, 5 ) and of thymidylyl-(3′-5′)-thymidylyl-(3′-5′)-1-(2′-deoxy-β-D -ribofuranosyl)-2(1 H)-pyridone (T_dpT_dp∏_d, 11 ) by condensing (MeOTr) T_dpT_d ( 3 ) and p∏_d(Ac) ( 4 ) in the presence of DCC in abs. pyridine is described. Condensation of (MeOTr) T_dpT_dp ( 6 ) with Π_d(Ac) ( 7 ) did not yield the desired product 5 because compound 6 formed the 3′-pyrophosphate. The removal of the acetyl- and p-methoxytrityl protecting group was effected by treatment with conc. ammonia solution at room temperature, and acetic acid/pyridine 7 : 3 at 100°, respectively. Enzymatic degradation of the trinucleoside diphosphate 11 with phosphodiesterase I and II yielded T_d, pT_d and p∏_d, T_dp and Π_d, respectively, in correct ratios.     

2′, 3′-Dideoxy-3′-fluorotubercidin and Related Dideoxyribonucleosides:. Synthesis via a 2′-deoxy-3′-oxoribofuranoside intermediate and conformation studies

An efficient synthesis of the unknown 2′-deoxy-D-threo-tubercidin ( 1b ) and 2′, 3′-dideoxy-3′-fluorotubercidin ( 2 ) as well as of the related nucleosides 9a, b and 10b is described. Reaction of 4-chloro-7-(2-deoxy-β-D-erythro-pentofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine ( 5 ) with (tert-butyl)diphenylsilyl chloride yielded 6 which gave the 3′-keto nucleoside 7 upon oxidation at C(3′). Stereoselective NaBH₄ reduction (→ 8 ) followed by deprotection with Bu₄NF(→ 9a )and nucleophilic displacement at C(6) afforded 1b as well as 7-deaza-2′-deoxy-D-threo-inosine ( 9b ). Mesylation of 4-chloro-7-{2-deoxy-5-O-[(tert-butyl)diphenylsilyl]-β-D-threo-pentofuranosyl}-7H-pyrrolo[2,3-d]-pyrimidine ( 8 ), treatment with Bu₄NF (→ 12a ) and 4-halogene displacement gave 2′, 3′-didehydro-2′, 3′-dideoxy-tubercidin ( 3 ) as well as 2′, 3′-didehydro-2′, 3′-dideoxy-7-deazainosne ( 12c ). On the other hand, 2′, 3′-dideoxy-3′-fluorotubercidin ( 2 ) resulted from 8 by treatment with diethylamino sulfurtrifluoride (→ 10a ), subsequent 5′-de-protection with Bu₄NF (→ 10b ), and Cl/NH₂ displacement. ¹H-NOE difference spectroscopy in combination with force-field calculations on the sugar-modified tubercidin derivatives 1b , 2 , and 3 revealed a transition of the sugar puckering from the ^3′T_2′ conformation for 1b via a planar furanose ring for 3 to the usual ^2′T_3′ conformation for 2.     

Synthesis,Base Pairing,and Structural Transitions of Oligodeoxyribonucleotides Containing 8-Aza-2′-deoxyguanosine

The synthesis of oligonucleotides containing 8-aza-2′-deoxyguanosine (z⁸G_d; 1 ) or its N⁸-regioisomer z⁸G_d^* ( 2 ) instead of 2′-deoxyguanosine (G_d) is described. For this purpose, the NH₂ group of 1 and 2 was protected with a (dimethylamino)methylidene residue (→ 5, 6 ), a 4,4′-dimethoxytrityl group was introduced at 5′-OH (→ 7, 8 ), and the phosphonates 3a and 4 as well as the phosphoramidite 3b were prepared. These building blocks were used in solid-phase oligonucleotide synthesis. The oligonucleotides were characterized by enzymatic hydrolysis and melting curves (T_m values). The thermodynamic data of the oligomers 12–15 indicate that duplexes were stabilized when 1 was replacing G_d. The aggregation of d(T-G-G-G-G-T) ( 18 ) was studied by RP 18 HPLC, gel electrophoresis and CD spectroscopy and compared with that of oligonucleotides containing an increasing number of z⁸G_d residues instead of G_d. Similarly to [d(C-G)]₃ ( 12a ), the hexamer d(C-z⁸G-C-z⁸G-C-G) ( 14 ) underwent salt-dependent B-Z transition.     

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).     

1-(2′-Deoxy-β-D-xylofuranosyl)cytosine: Base pairing of oligonucleotides with a configurationally altered sugar-phosphate backbone

Solid-phase synthesis of the oligo(2′-deoxynucleotides) 19 and 20 containing 2′-deoxy-β-D -xylocytidine ( 4 ) is described. For this purpose, 1-(2-deoxy-β-D -threo-pentofuranosyl)cytosine ( = 1-(2-deoxy-β-D -xylofuranosyl)-cytosine; 4 ) was protected at its 4-NH₂ group with a benzoyl (→ 5 ) or an isobutyryl (→ 8 ) residue, and a dimethoxytrityl group was introduced at 5′-OH (→ 7, 10 ; Scheme 2). Compounds 7 and 10 were converted into the 3′-phosphonates 11a,b . While 19 could be hybridized with 21 and 22 under formation of duplexes with a two-nucleotide overhang on both termini ( 19 · 21 : T_m 29°; 19 · 22 : T_m 22°), the decamer 20 bearing four xC_d residues could no longer be hybridized with one of the opposite strands. Moreover, the oligonucleotides d[(xC)₈? C] ( 13 ), d[(xC)₄? C] ( 14 ), d[C? (xC)₄? C] ( 15 ), and d[C? (xC)₃? C] ( 16 ) were synthesized. While 13 exhibits an almost inverted CD spectrum compared to d(C₉) ( 17 ), the other oligonucleotides show CD spectra typical for regular right-handed single helices. At pH 5, d[(xC)₈? C] forms a stable hemi-protonated duplex which exhibits a T_m of 60° (d[(CH⁺)₉] · d(C₉): T_m 36°). The thermodynamic parameters of duplex formation of ( 13H ⁺ · 13 ) and ( 17H ⁺ · 17 ) were calculated from their melting profiles and were found to be identical in ΔH but differ in ΔS ( 13H ⁺ · 13 : ΔS = ?287 cal/K mol; 17H ⁺ · 17 : ΔS = ?172 cal/K mol).     

Regioselective synthesis of pentacyclic polyheterocycles: Sequential [3,3] sigmatropic rearrangement of 4‐(4′‐aryloxybut‐2′‐ynyloxy)‐1‐phenyl‐1,8‐naphthyridin‐2(1H)‐ones

A number of 4‐aryloxymethyl‐6‐phenyl‐2H‐pyrano[3,2‐c][1,8]naphthyridin‐5(6H)‐ones ( 4a‐f ) are regioselectively synthesized in 72‐78% yield by the Claisen rearrangement of 4‐(4′‐aryloxybut‐2′‐ynyloxy)‐1‐phenyl‐1,8‐naphthyridin‐2(1H)‐ones ( 3a‐f ) in refluxing chlorobenzene for 4‐6 h. These products are then subjected to a second Claisen rearrangement catalyzed by anhydrous AlCl₃ at room temperature for 2 h to give hitherto unreported pentacyclic heterocycles ( 5a‐f ) in 78‐85% yield.     

N6-(Carbamoylmethyl)-2′-deoxyadenosine,a rare DNA Constituent: Phosphoramidite Synthesis and Properties of Palindromic Dodecanucleotides

N⁶-(Carbamoylmethyl)-2′-deoxyadenosine ( 1 ), a modified nucleoside occurring in bacteriophage Mu, was synthesized by two different routes. Glycinamide was introdued by nucleophilic displacement of(2,4,6,-triisopro-pylphenyl)sulfonyloxy or ethylsulfinyl groups at C(6) of the purine moiety. Compound 1 was converted into the protected phosphoramidite 6b and employed in solid-phase synthesis of the self-complementary oligonucleotides 7–14 . Replacement of 2′-deoxyadenosine by 1 led to a strong decrease of the T_m values of the oligomers d(A-T)₆ ( 7 ) and d(A-T-G-A-A-G-C-T-T-C-A-T)( 10 ), respectively. As the oligemer 10 contains the recognition site d(A-A-G-C-T-T) of the endodeoxyribonuclease Hind III, it was subjected to sequence-specific hydrolysis experiments. Replacement of the first or second A_d by 1 prevented enzymatic phosphodiester hydrolysis (results with 11 and 12 ). In contrast, slow hydrolysis was observed if the less bulky N⁶-methyl-2′-deoxyadenosine replaced the second A _d residue (results with 14 ).     

Synthesis of (2′S)‐2′‐Deoxy‐2′‐C‐methylpurine Nucleosides and Their Phosphoramidites

We describe the stereoselective synthesis of (2′S)‐2′‐deoxy‐2′‐C‐methyladenosine ( 12 ) and (2′S)‐2′‐deoxy‐2′‐C‐methylinosine ( 14 ) as well as their corresponding cyanoethyl phosphoramidites 16 and 19 from 6‐O‐(2,6‐dichlorophenyl)inosine as starting material. The methyl group at the 2′‐position was introduced via a Wittig reaction (→ 3 , Scheme 1) followed by a stereoselective oxidation with OsO₄ (→ 4 , Scheme 2). The primary‐alcohol moiety of 4 was tosylated (→ 5 ) and regioselectively reduced with NaBH₄ (→ 6 ). Subsequent reduction of the 2′‐alcohol moiety with Bu₃SnH yielded stereoselectively the corresponding (2′S)‐2′‐deoxy‐2′‐C‐methylnucleoside (→ 8a ).     

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.     

Oligonucleotides Containing 7‐Deaza‐2′‐deoxyinosine as Universal Nucleoside: Synthesis of 7‐Halogenated and 7‐Alkynylated Derivatives,Ambiguous Base Pairing,and Dye Functionalization by the Alkyne–Azide ‘Click’ Reaction

Oligonucleotides containing 7‐deaza‐2′‐deoxyinosine derivatives bearing 7‐halogen substituents or 7‐alkynyl groups were prepared. For this, the phosphoramidites 2b – 2g containing 7‐substituted 7‐deaza‐2′‐deoxyinosine analogues 1b – 1g were synthesized (Scheme 2). Hybridization experiments with modified oligonucleotides demonstrate that all 2′‐deoxyinosine derivatives show ambiguous base pairing, as 2′‐deoxyinosine does. The duplex stability decreases in the order C_d>A_d>T_d>G_d when 2b – 2g pair with these canonical nucleosides (Table 6). The self‐complementary duplexes 5′‐d(F⁷c⁷I‐C)₆, d(Br⁷c⁷I‐C)₆, and d(I⁷c⁷I‐C)₆ are more stable than the parent duplex d(c⁷I‐C)₆ (Table 7). An oligonucleotide containing the octa‐1,7‐diyn‐1‐yl derivative 1g , i.e., 27 , was functionalized with the nonfluorescent 3‐azido‐7‐hydroxycoumarin ( 28 ) by the Huisgen–Sharpless–Meldal cycloaddition ‘click’ reaction to afford the highly fluorescent oligonucleotide conjugate 29 (Scheme 3). Consequently, oligonucleotides incorporating the derivative 1g bearing a terminal C?C bond show a number of favorable properties: i) it is possible to activate them by labeling with reporter molecules employing the ‘click’ chemistry. ii) Space demanding residues introduced in the 7‐position of the 7‐deazapurine base does not interfere with duplex structure and stability (Table 8). iii) The ambiguous pairing character of the nucleobase makes them universal probes for numerous applications in oligonucleotide chemistry, molecular biology, and nanobiotechnology.     

Stereoselective Synthesis of [5‐[4,4,4,4′,4′,4′‐Hexafluoro‐N‐(2‐hydroxyethoxy)‐D‐valine]]‐ and [5‐[4,4,4,4′,4′,4′‐Hexafluoro‐N‐(2‐hydroxyethoxy)‐L‐valine]cyclosporin A

Addition of various amines to the 3,3‐bis(trifluoromethyl)acrylamides 10a and 10b gave the tripeptides 11a – 11f , mostly as mixtures of epimers (Scheme 3). The crystalline tripeptide 11f ₂ was found to be the N‐terminal (2‐hydroxyethoxy)‐substituted (R,S,S)‐ester HOCH₂CH₂O‐D ‐Val(F₆)‐MeLeu‐Ala‐O^tBu by X‐ray crystallography. The C‐terminal‐protected tripeptide 11f ₂ was condensed with the N‐terminus octapeptide 2b to the depsipeptide 12a which was thermally rearranged to the undecapeptide 13a (Scheme 4). The condensation of the epimeric tripeptide 11f ₁ with the octapeptide 2b gave the undecapeptide 13b directly. The undecapeptides 13a and 13b were fully deprotected and cyclized to the [5‐[4,4,4,4′,4′,4′‐hexafluoro‐N‐(2‐hydroxyethoxy)‐D ‐valine]]‐ and [5‐[4,4,4,4′,4′,4′‐hexafluoro‐N‐(2‐hydroxyethoxy)‐L ‐valine]]cyclosporins 14a and 14b , respectively (Scheme 5). Rate differences observed for the thermal rearrangements of 12a to 13a and of 12b to 13b are discussed.     

Hoogsteen-Duplex DNA: Synthesis and base pairing of oligonucleotides containing 1-deaza-2′-deoxyadenosine

Oligodeoxyribonucleotides containing 1-deaza-2′-deoxyadenosine ( = 7-amino-3-(2-deoxy-β-D -erythro-pentofuranosyl)-3H-imidazo[4, 5-b]pyridine; 1b ) form Hoogsteen duplexes. Watson-Crick base pairs cannot be built up due to the absence of N(1). For these studies, oligonucleotide building blocks – the phosphonate 3a and the phosphoramidite 3b – were prepared from 1b via 4a and 5 , as well as the Fractosil-linked 6b , and used in solid-phase synthesis. The applicability of various N-protecting groups (see 4a – c ) was also studied. The Hoogsteen duplex d[(c¹A)₂₀] · d(T₂₀) ( 11 · 13 ; T_m 15°) is less stable than d(A₂₀) · d(T₂₀) ( 12 · 13 ; T_m 60°). The block oligomers d([c¹A)₁₀–;T₁₀] ( 14 ) and d[T₁₀–(c¹A)₁₀] ( 15 ) containing purine and pyrimidine bases in the same strand are also able to form duplexes with each other. The chain polarity was found to be parallel.     

Single‐Stranded DNA: Replacement of Canonical by Base‐Modified Nucleosides in the Minihairpin 5′‐d(GCGAAGC)‐3′ and Constructs with the Aptamer 5′‐d(GGTTGGTGTGGTTGG)‐3′

The minihairpin 5′‐d(GCGAAGC)‐3′ ( 1 ) was modified either in the loop region, in the base‐paired stem, or at the 5′‐terminus by incorporation of base‐modified nucleosides. The thermal melting was correlated to the structural changes induced by the various donor‐acceptor properties of the nucleosides. Overhanging nonpaired nucleosides at the 5′‐terminus stabilized the hairpin, while a reverse of the dG³?dA⁵ sheared base pair to dA³?dG⁵ severely affected the stability. The combination of the minihairpin 5′‐d(GCGAAGC)‐3′ ( 1 ) and the thrombin‐binding aptamer 5′‐d(GGTTGGTGTGGTTGG)‐3′ ( 2 (= 46 )) resulted in the new construct 5′‐d(GGTTGGGCGAAGC GGTTGG)‐3′ ( 43 ) arising by replacement of the 5′‐d(TGT)‐3′ loop of 2 by the minihairpin. The fused oligonucleotide 43 exhibits a two‐phase thermal transition indicating the presence of the two unaltered moieties. According to slight changes of the T_m values of the construct 43 as compared to the separate units 1 and 2 , cooperative distorsions are discussed.     

Facile Synthesis of 2′-Deoxyisoguanosine and Related 2′,3′-Dideoxyribonucleosides

The 2′-deoxyisoguanosine ( 1 ) was synthesized by a two-step procedure from 2′-deoxyguanosine ( 5 ). Amination of silylated 2′-deoxyguanosine yielded 2-amino-2′-deoxyadenosine ( 6 ) which was subjected to selective deamination of the 2-NH₂ group resulting in compound 1 . Also 2′,3′-dideoxyisoguanosine ( 2 ) was prepared employing the photo-substitution of the 2-substituent of 2-chloro-2′,3′-dideoxyadenosine ( 4 ). The latter was synthesized by Barton deoxygenation from 2-chloro-2′-deoxyadenosine ( 3 ) or via glycosylation of 2,6-dichloropurine ( 12 ) with the lactol 13 . Compound 1 was less stable at the N-glycosylic bond than 2′-deoxyguanosine ( 5 ). The dideoxynucleoside 2 was deaminated by adenosine deaminase affording 2′,3′-dideoxyxanthosine ( 17 ).     

Synthesis of 2‐(sulfamoylphenyl)‐4′‐(iminoaryl/hetroaryl)‐4‐(4′′‐hydroxyphenyl)‐thiazoles and their O‐glucosides

In continuation of our work, we synthesized 2‐(sulfamoylphenyl)‐4′‐amino‐4‐(4″‐hydroxyphenyl)‐thiazole ( 3a ), which were reacted with various (aryl/hetroaryl) aldehyde to form 2‐(sulfamoylphenyl)‐4′‐(iminoaryl/hetroaryl)‐4‐(4″‐hydroxyphenyl)‐thiazoles ( 4a , 4b , 4c , 4d , 4e , 4f ). Glucosylation of compounds ( 4a , 4b , 4c , 4d , 4e , 4f ) have been done by using acetobromoglucose as a glucosyl donor to afford 2‐(sulfamoylphenyl)‐4′‐(iminoaryl/hetroaryl)‐4‐(2,3,4,6‐tetra‐O‐acetyl‐4″‐O‐β‐D ‐glucosidoxyphenyl)‐thiazoles ( 5a , 5b , 5c , 5d , 5e , 5f ), further on deacetylation to produce 2‐(sulfamoylphenyl)‐4′‐(iminoaryl/hetroaryl)‐4‐(4″‐O‐β‐D ‐glucosidoxyphenyl)‐thiazoles ( 6a , 6b , 6c , 6d , 6e , 6f ). The compounds are confirmed by FTIR, ¹H‐NMR, ¹³C‐NMR, and ES‐Mass spectral analysis. J. Heterocyclic Chem., (2011).     

Different nucleobase orientations in two cyclic 2′,3′‐phosphates of purine ribonucleosides: Et3NH(2′,3′‐cAMP) and Et3NH(2′,3′‐cGMP)·H2O

The crystal structures of triethyl­ammonium adenosine cyclic 2′,3′‐phosphate {systematic name: triethyl­ammonium 4‐(6‐amino­purin‐9‐yl)‐6‐hydroxy­methyl‐2‐oxido‐2‐oxoperhydro­furano[3,4‐c][1,3,2]dioxaphosphole}, Et₃NH(2′,3′‐cAMP) or C₆H₁₆N⁺·C₁₀H₁₁N₅O₆P⁻, (I), and guanosine cyclic 2′,3′‐phosphate monohydrate {systematic name: triethyl­ammonium 6‐hydroxy­methyl‐2‐oxido‐2‐oxo‐4‐(6‐oxo‐1,6‐dihydro­purin‐9‐yl)perhydro­furano[3,4‐c][1,3,2]dioxaphosphole monohydrate}, [Et₃NH(2′,3′‐cGMP)]·H₂O or C₆H₁₆N⁺·C₁₀H₁₁N₅O₇P⁻·H₂O, (II), reveal different nucleobase orientations, viz. anti in (I) and syn in (II). These are stabilized by different inter‐ and intra­molecular hydrogen bonds. The structures also exhibit different ribose ring puckering [₄E in (I) and ³T₂ in (II)] and slightly different 1,3,2‐dioxaphospho­lane ring conformations, viz. envelope in (I) and puckered in (II). Infinite ribbons of 2′,3′‐cAMP⁻ and helical chains of 2′,3′‐cGMP⁻ ions, both formed by O—H⋯O, N—H⋯X and C—H⋯X (X = O or N) hydrogen‐bond contacts, characterize (I) and (II), respectively.     

Aza-Claisen Rearrangement: Synthesis of 5′-branched 5′-aminothymidines

The syntheses of both diastereoisomers of 5′-ethyl-substituted thymidine dimers, the (5′R)- and (5′S)-configurated 33a and 33b respectively, in which the natural phosphodiester linkage is replaced by an amide group (C(3′)-CH₂CONH-CH(5′)(Et)), arc described. Their fully protected derivatives 35a and 35b , respectively, are suitable for incorporation into antisense oligonucleotides. Unexpectedly, an attempted Pd^II-catalysed aza-Claisen rearrangement of trichloroacetimidate 7 provided the diastereoisomerically pure cyclopropane derivative 17 , whose structure was confirmed by X-ray analysis.     

1,7-Dideaza-2′-deoxyadenosine: Building blocks for solid-phase synthesis and secondary structure of base-modified oligodeoxyribonucleotides

The 1,7-dideaza-2′-deoxyadenosine (c¹c⁷A_d; 1 ) was converted into building blocks 3a , b for solid-phase oligodeoxyribonucleotide synthesis. Testing various N-protecting groups – benzoyl, phenoxyacetyl, [(fluoren-9-yl)methoxy]carbonyl, and (dimethylamino)methylidene – only the latter two were found to be suitable ( 1 → 4b, d ). Ensuing 4,4′-dimethoxytritylation of 4d and phosphitylation afforded the 3′-phosphonate 3a or the 3′-[(2-cyanoethyl)diisopropylphosphoramidite] 3b . Self-complementary oligonucleotides with alternating dA or c¹c⁷A_d and dT residues ( 7 and 8 ) as well as palindromic oligomers such as d(C-G-C-G-c¹c⁷ A-c¹c⁷ A-T-T-C-G-C-G) ( 10 ) and d(G-T-A-G-c¹c⁷ A-c¹c⁷ A-T-T-C-T-A-C) ( 12 ) were synthesized. Duplex stability was decreased because 1 cannot form Watson-Crick or Hoogsteen base pairs if incorporated into oligonucleotides. On the other hand, the structural modifications in 10 and 12 forced these palindromic oligomers to form hairpin structures.