Oligonucleosides with a Nucleobase‐Including Backbone,Part 7

The conformational analysis of 7 was carried out in (D₆)DMSO and in mixtures of (D₆)DMSO and CDCl₃ to evaluate the syn/anti conformations, relevant to the pairing propensity of this type of nucleotide analogue. The HO−C(5′) of unit I and of unit II of the dimer 7 form an intramolecular H‐bond to N(3). In (D₆)DMSO, the C(5′)−OH⋅⋅⋅N(3) H‐bond in unit I is partially broken, while that in unit II persists to a larger extent. The syn conformation prevails for unit I and particularly for unit II. The furanosyl moieties adopt predominantly a 2′‐endo conformation that is largely independent of the solvent.     

Oligonucleotide Analogues with a Nucleobase‐Including Backbone,Part 5, 2′‐Deoxy‐8‐(hydroxymethyl)adenosine‐ and 2′‐Deoxy‐6‐(hydroxymethyl)uridine‐Derived Phosphoramidites: Synthesis and Incorporation into 14‐Mer DNA Strands

The pairing propensity of new DNA analogues with a phosphinato group between O−C(3′) and a newly introduced OCH₂ group at C(8) and C(6) of 2′‐deoxyadenosine and 2′‐deoxyuridine, respectively, was evaluated by force‐field calculations and Maruzen model studies. These studies suggest that these analogues may form autonomous pairing systems, and that the incorporation of single modified units into DNA 14mers is compatible with duplex formation. To evaluate the incorporation, we prepared the required phosphoramidites 3 and 4 from 2′‐deoxyadenosine and 2′‐deoxyuridine, respectively. The phosphoramidite 5 was similarly prepared to estimate the influence of a CH₂OH group at C(8) on the duplex stability. The modified 14‐mers 6 – 9 were prepared by solid‐phase synthesis. Pairing studies show a decrease of the melting temperature by 2.5° for the duplex 13 ⋅ 9 , and of 6 – 8° for the duplexes 10 ⋅ 6 , 11 ⋅ 6 , 13 ⋅ 7 , and 14 ⋅ 8 , as compared to the unmodified duplexes.     

Oligonucleotide Analogues with a ‘Nucleobase‐Including Backbone’. Part 10

The dinucleoside analogues 24, 25, 28 – 30 , and 33 associate in CDCl₃ solution. Association constants, as determined from the concentration‐dependent chemical shift for H? N(3) of the uridine moiety and from thermodynamic parameters, range from 265 M ^?1 ( 33 ) to 3220 M ^?1 ( 30 ). The association of 31 in CDCl₃ is too strong to be determined (concentration independent δ(H? N(3)) of ca. 12.8 ppm) and the fully deprotected dimer 32 proved insufficiently soluble in CDCl₃. This observation strongly evidences that structural differentiation of oligonucleotides and their analogues into backbone and nucleobases is not required for pairing. The dinucleotide analogues were prepared by O‐alkylation of C(8)‐unsubstituted or of C(8)‐oxymethylated, partially protected adenosines by the C(6)‐mesyloxy‐ or C(6)‐halomethylated uridines 20 – 22 , followed by partial or total deprotection.     

Oligonucleotide Analogues with a Nucleobase‐Including Backbone:, Part 6, 2‐Deoxy‐D‐erythrose‐Derived Phosphoramidites: Synthesis and Incorporation into 14‐Mer DNA Strands

Two modified DNA 14‐mers have been prepared, containing either a 2‐deoxy‐D ‐erythrose‐derived adenosine analogue carrying a C(8)−CH₂O group (deA*), or a 2‐deoxy‐D ‐erythrose‐derived uridine analogue, possessing a C(6)−CH₂O group (deU*). These nucleosides are linked via a phosphinato group between O−C(3′) (deA* and deU*) and O−C(5′) of one neighbouring nucleotide, and between C(8)−CH₂O (deA*), or C(6)−CH₂O (deU*) and O−C(3′) of the second neighbour. N⁶‐Benzoyl‐9‐(β‐D ‐erythrofuranosyl)adenine ( 3 ) and 1‐(β‐D ‐erythrofuranosyl)uracil ( 4 ) were prepared from D ‐glucose, deoxygenated at C(2′), and converted into the required phosphoramidites 1 and 2 . The modified tetradecamers 31 and 32 were prepared by solid‐phase synthesis. Pairing studies show a decrease in the melting temperature of 7 to 8 degrees for the duplexes 31 ⋅ 30 and 32 ⋅ 29 , as compared to the unmodified DNA duplex 29 ⋅ 30 . A comparison with the pairing properties of tetradecamers similarly incorporating deoxyribose‐ instead of the deoxyerythrose‐derived nucleotides evidences that the CH₂OH substituent at C(4′) has no significant effect on the pairing.     

Oligonucleosides with a Nucleobase‐Including Backbone. Part 12

In contradistinction to the corresponding Grignard reagent, bis[(trimethylsilyl)ethynyl]zinc reacted with the 5′‐oxoadenosine 3 diastereoselectively to the β‐D ‐allo‐hept‐6‐ynofuranosyladenine 5 . Lithiation/iodination of the monomeric propargyl alcohol 5 and of the dimeric propargyl alcohol 22 provided the 8‐iodoadenosines 7 and 18 , respectively, considerably shortening the synthesis of the dimeric O‐silylated 8‐iodoadenosine 25 . The mixed uridine‐ and adenosine‐derived tetramers 21 and 32 were synthesised. The tetramer 21 was prepared by a linear sequence. Sonogashira coupling of 9 and 13 yielded the trimer 16 that was C‐desilylated to 17 . A second Sonogashira coupling of 17 and 19 yielded the tetramer 21 . Tetramer 32 was prepared in higher yields by a convergent route, coupling the acetylene 29 and the iodide 30 . The uridine‐derived iodides proved more reactive than the adenosine‐derived analogues, and the N⁶‐unprotected adenosine‐derived alkynes were more reactive than their N⁶‐benzoylated analogues.     

Oligonucleosides with a Nucleobase‐Including Backbone,Part 2, Synthesis and Structure Determination of Adenosine‐Derived Monomers

The synthesis and structure determination of adenosine‐derived monomeric building blocks for new oligonucleosides are described. Addition of Me₃Si‐acetylide to the aldehyde derived from the known partially protected adenosine 1 led to the epimeric propargylic alcohols 2 and 3 , which were oxidised to the same ketone 4 , while silylation and deprotection led to 7 and 9 (Scheme 1). Introduction of an I substituent at C(8) of the propargylic silyl ethers 10 and 11 was not satisfactory. The protected adenosine 12 was, therefore, transformed in high yield into the 8‐chloro derivative 13 by deprotonation and treatment with PhSO₂Cl; the iodide 15 was obtained in a similar way (Scheme 2). The 8‐Cl and the 8‐I derivatives 13 and 15 were transformed into the propargylic alcohols 17 , 18 , 25 , and 26 , respectively (Scheme 3). The propargylic derivatives 2 , 10 , 17 , 19 , 23 , 25 , and 27 were correlated, and their (5′R) configuration was determined on the basis of NOEs of the anhydro nucleoside 19 ; similarly, correlation of 3 , 11 , 18 , 20 , 24 , 26 , and 28 , and NOE's of 20 evidenced their (5′S)‐configuration.     

Oligonucleosides with a Nucleobase‐Including Backbone,Part 3, Synthesis of Acetyleno‐Linked Adenosine Dimers

The adenosine‐derived dimers 14a – d and 15b – d have been prepared by coupling the protected 8‐iodoadenosines 3 and 13 with the C(5′)‐ethynylated adenosine derivatives 5 , 6 , 11 , and 12 (Scheme 4). Similarly, the 5′‐epimeric dimer 16 was prepared by coupling 3 with the alkyne 8 (Scheme 5). The propargylic alcohol 4 was transformed into the N‐benzoylated alkyne 5 and into the amine 6 , while the epimeric alcohol 7 was converted to the epimeric amine 8 and the 5′‐deoxy analogues 11 and 12 (Scheme 3). Cross‐coupling of the iodoadenosine 13 with the alkyne 5 to 14a was optimised; it is influenced by the N‐benzoyl and the Et₃SiO group of the alkyne, but hardly by the N‐benzoyl group of the 8‐iodoadenosine. The alkyne is most reactive when it is O‐silylated, but not N‐benzoylated. Cross‐coupling of the 5′‐deoxyalkynes proceeded more slowly. The dimers 14a – d , 15b – d , and 16 were obtained in good yields (Table 2). Deprotection of 14d and 16 led to 18 and 20 , respectively (Scheme 5). The diols 17 and 19 and the hexols 18 and 20 prefer the syn‐conformation in (D₆)DMSO, completely for unit II and ≥80% for unit I; they exhibit partially persistent intramolecular O(5′)−H⋅⋅⋅N(3) H‐bonds. The persistence increases from 18% (unit I of 19 ), 32% (unit II of 17 and 19 ), 45% (unit I of 17 ), 52% (unit II of 18 and 20 ), and 55% (unit I of 20 ) to 82% (unit I of 18 ).     

Oligonucleosides with a Nucleobase‐Including Backbone,Part 4, A Convergent Synthesis of Ethynediyl‐Linked Adenosine Tetramers

Deprotection of the tetramer 24 , obtained by coupling the iodinated dimer 18 with the alkyne 23 gave the 8′,5‐ethynediyl‐linked adenosine‐derived tetramer 27 (Scheme 3). As direct iodination of C(5′)‐ethynylated adenosine derivatives failed, we prepared 18 via the 8‐amino derivative 17 that was available by coupling the imine 15 with the iodide 7 ; 15 , in its turn, was obtained from the 8‐chloro derivative 12 via the 4‐methoxybenzylamine 14 (Scheme 2). This method for the introduction of the 8‐iodo substituent was worked out with the N‐benzoyladenosine 1 that was transformed into the azide 2 by lithiation and treatment with tosyl azide (Scheme 1). Reduction of 2 led to the amine 3 that was transformed into 7 . 1,3‐Dipolar cycloaddition of 3 and (trimethylsilyl)acetylene gave 6 . The 8‐substituted derivatives 4a – d were prepared similarly to 2 , but could not be transformed into 7 . The known chloride 8 was transformed into the iodide 11 via the amines 9 and 10 . The amines 3 , 10 , and 16 form more or less completely persistent intramolecular C(8)N−H⋅⋅⋅O(5′) H‐bonds, while the dimeric amine 17 forms a ca. 50% persistent H‐bond. There is no UV evidence for a base‐base interaction in the protected and deprotected dimers and tetramers.     

7‐Halogenated 7‐Deazapurine 2′‐Deoxyribonucleosides Related to 2′‐Deoxyadenosine, 2′‐Deoxyxanthosine,and 2′‐Deoxyisoguanosine: Syntheses and Properties

A series of 7‐fluorinated 7‐deazapurine 2′‐deoxyribonucleosides related to 2′‐deoxyadenosine, 2′‐deoxyxanthosine, and 2′‐deoxyisoguanosine as well as intermediates 4b – 7b, 8, 9b, 10b , and 17b were synthesized. The 7‐fluoro substituent was introduced in 2,6‐dichloro‐7‐deaza‐9H‐purine ( 11a ) with Selectfluor (Scheme 1). Apart from 2,6‐dichloro‐7‐fluoro‐7‐deaza‐9H‐purine ( 11b ), the 7‐chloro compound 11c was formed as by‐product. The mixture 11b / 11c was used for the glycosylation reaction; the separation of the 7‐fluoro from the 7‐chloro compound was performed on the level of the unprotected nucleosides. Other halogen substituents were introduced with N‐halogenosuccinimides ( 11a → 11c – 11e ). Nucleobase‐anion glycosylation afforded the nucleoside intermediates 13a – 13e (Scheme 2). The 7‐fluoro‐ and the 7‐chloro‐7‐deaza‐2′‐deoxyxanthosines, 5b and 5c , respectively, were obtained from the corresponding MeO compounds 17b and 17c , or 18 (Scheme 6). The 2′‐deoxyisoguanosine derivative 4b was prepared from 2‐chloro‐7‐fluoro‐7‐deaza‐2′‐deoxyadenosine 6b via a photochemically induced nucleophilic displacement reaction (Scheme 5). The pK_a values of the halogenated nucleosides were determined (Table 3). ¹³C‐NMR Chemical‐shift dependencies of C(7), C(5), and C(8) were related to the electronegativity of the 7‐halogen substituents (Fig. 3). In aqueous solution, 7‐halogenated 2′‐deoxyribonucleosides show an approximately 70% S population (Fig. 2 and Table 1).     

Oligonucleosides with a Nucleobase‐Including Backbone,Part 1, Concept,Force‐Field Calculations,and Synthesis of Uridine‐Derived Monomers and Dimers

A new type of oligonucleosides has been devised to investigate the potential of oligonucleosides with a nucleobase‐including backbone to form homo‐ and/or heteroduplexes (cf. Fig. 2). It is characterised by ethynyl‐linkages between C(5′) and C(6) of uridine, and between C(5′) and C(8) of adenosine. Force‐field calculations and Maruzen model studies suggest that such oligonucleosides form autonomous pairing systems and hybridize with RNA. We describe the syntheses of uridine‐derived monomers, suitable for the construction of oligomers, and of a dimer. Treatment of uridine‐5′‐carbaldehyde ( 2 ) with triethylsilyl acetylide gave the diastereoisomeric propargylic alcohols 6 and 7 (1 : 2, 80%; Scheme 1). Their configuration at C(5′) was determined on the basis of NOE experiments and X‐ray crystal‐structure analysis. Iodination at C(6) of the (R)‐configured alcohol 7 by treatment with lithium diisopropylamide (LDA) and N‐iodosuccinimide (NIS) gave the iodide 17 (62%), which was silylated at O−C(5′) to yield 18 (89%; Scheme 2). C‐Desilylation of 7 with NaOH in MeOH/H₂O led to the alkyne 10 (98%); O‐silylation of 10 at O−C(5′) gave 16 (84%). Cross‐coupling of 18 and 16 yielded 63% of the dimer 19 , which was C‐desilylated to 20 in 63% yield. Cross‐coupling of 10 and the 6‐iodouridine 13 (70%), followed by treatment of the resulting dimer 14 with HF and HCl in MeCN/H₂O, gave the deprotected dimer 15 (73%).     

(2′‐O‐Methyl‐RNA)‐3′‐PNA Chimeras: A New Class of Mixed Backbone Oligonucleotide Analogues with High Binding Affinity to RNA

The automated on‐line synthesis of DNA‐3′‐PNA chimeras 1 – 4 and (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras 5 – 8 is described, in which the 3′‐terminal part of the oligonucleotide is linked to the N‐terminal part of the PNA via N‐(ω‐hydroxyalkyl)‐N‐[(thymin‐1‐yl)acetyl]glycine units (alkyl=Et, Ph, Bu, and pentyl). By means of UV thermal denaturation, the binding affinities of all chimeras were directly compared by determining their T_m values in the duplex with complementary DNA and RNA. All investigated DNA‐3′‐PNA chimeras and (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras form more‐stable duplexes with complementary DNA and RNA than the corresponding unmodified DNA. Interestingly, a N‐(3‐hydroxypropyl)glycine linker resulted in the highest binding affinity for DNA‐3′‐PNA chimeras, whereas the (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras showed optimal binding with the homologous N‐(4‐hydroxybutyl)glycine linker. The duplexes of (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras and RNA were significantly more stable than those containing the corresponding DNA‐3′‐PNA chimeras. Surprisingly, we found that the charged (2′‐O‐methyl‐RNA)‐3′‐PNA chimera with a N‐(4‐hydroxybutyl)glycine‐based unit at the junction to the PNA part shows the same binding affinity to RNA as uncharged PNA. Potential applications of (2′‐O‐methyl‐RNA)‐3′‐PNA chimeras include their use as antisense agents acting by a RNase‐independent mechanism of action, a prerequisite for antisense‐oligonucleotide‐mediated correction of aberrant splicing of pre‐mRNA.     

(–)‐(1′S,4aS,7R,8aR)‐4a‐Ethyl‐7‐hydroxy‐1‐(1′‐phenylethyl)perhydroquinolinium bromide

In the structure of the title compound, C₁₉H₃₀NO⁺·Br^?, the rings of the perhydro­quinolinium moiety are cis fused. The successful reduction of the ketone functionality of the quinolinone used as starting material is confirmed by the hydroxy C—O bond length of 1.428 (3) Å.     

Synthesis of Boron‐Containing ADP and GDP Analogues: Nucleoside 5′‐(Pα‐Boranodiphosphates)

New 5′‐(P^α‐boronated) analogues of the naturally occurring nucleoside diphosphates ADP and GDP were synthesized in good yields, i.e., adenosine 5′‐(P^α‐boranodiphosphate) (ADPαB; 5a ) and guanosine 5′‐(P^α‐boranodiphosphate) (GDPαB; 5b ). Their diastereoisomers were successfully separated by reversed‐phase HPLC, and chemical structures were established via spectroscopic methods. The isoelectronic substitution of borane (BH₃) for one of the non‐bridging O‐atoms in phosphate diesters should impart an increase in lipophilicity and change in polarity in ADPαB and GDPαB. The boronated nucleoside diphosphates could be employed for investigations of the stereochemical course and metal requirements of enzymatic reactions involving ADP and GDP, and as carriers of ¹⁰B in boron neutron‐capture therapy (BNCT) for the treatment of cancer.     

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.     

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).     

Silver Ions in Non‐canonical DNA Base Pairs: Metal‐Mediated Mismatch Stabilization of 2′‐Deoxyadenosine and 7‐Deazapurine Derivatives with 2′‐Deoxycytidine and 2′‐Deoxyguanosine

Novel silver‐mediated dA?dC, dA*?dC, and dA*?dG base pairs were formed in a natural DNA double helix environment (dA* denotes 7‐deaza‐dA, 7‐deaza‐7‐iodo‐dA, and 7‐cyclopropyl‐7‐deaza‐dA). 7‐Deazapurine nucleosides enforce silver ion binding and direct metal‐mediated base pair formation to their Watson–Crick face. New phosphoramidites were prepared from 7‐deaza‐dA, 7‐deaza‐7‐iodo‐dA, and 7‐cyclopropyl‐7‐deaza‐dA, which contain labile isobutyryl protecting groups. Solid‐phase synthesis furnished oligonucleotides that contain mismatches in near central positions. Increased thermal stabilities (higher T_m values) were observed for oligonucleotide duplexes with non‐canonical dA*?dC and dA?dC pairs in the presence of silver ions. The stability of the silver‐mediated base pairs was pH dependent. Silver ion binding was not observed for the dA?dG mismatch but took place when mismatches were formed between 7‐deazaadenine and guanine. The specific binding of silver ions was confirmed by stoichiometric UV titration experiments, which proved that one silver ion is captured by one mismatch. The stability increase of canonical DNA mismatches might have an impact on cellular DNA repair.     

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.     

Pentopyranosyl Oligonucleotide Systems,Communication No. 10 , The α‐L‐Lyxopyranosyl‐(4′→2′)‐oligonucleotide System

To determine whether the remarkable chemical properties of the pyranosyl isomer of RNA as an informational Watson‐Crick base‐pairing system are unique to the pentopyranosyl‐(4′→2′)‐oligonucleotide isomer derived from the RNA‐building block D ‐ribose, studies on the entire family of diastereoisomeric pyranosyl‐(4′→2′)‐oligonucleotide systems deriving from D ‐ribose, L ‐lyxose, D ‐xylose, and L ‐arabinose were carried out. The result of these extended studies is unambiguous: not only pyranosyl‐RNA, but all members of the pentopyranosyl‐(4′→2′)‐oligonucleotide family are highly efficient Watson‐Crick base‐pairing systems. Their synthesis and pairing properties will be described in a series of publications in this journal. The present paper describes the α‐L ‐lyxopyranosyl‐(4′→2′)‐system.