N7-DNA: Synthesis and Base Pairing of Oligonucleotides containing 7-(2-Deoxy-β -D-erythro-pentofuranosyl)adenine (N7Ad)

The synthesis of oligonucleotides containing 7-(2-deoxy-β -D -erythro-pentofuranosyl)adenine (N⁷A_d; 1 ) is described. Compound 1 was obtained from the precursor 4-amino-1H -imidazole-5-carbonitrile 2-deoxyribonucleoside 6 and was found to be much more labile than A_d. The N⁶-benzoyl protecting group (see 8 ) destabilized the N-glycosylic bond further and was difficult to remove by NH₃-catalyzed hydrolysis. Therefore, a (dimethyl-amino)methylidene residue was introduced (→ 9 ). Amidine 9 was blocked at OH? C(5′) with the dimethoxytrityl residue ((MeO)₂Tr), and phosphonate 4 as well as phosphoramidite 5 were prepared under standard conditions. Phosphonate 4 was employed in solid-phase oligonucleotide synthesis. Homooligonucleotides as well as self-complementary oligonucleotides were prepared. The oligomer d[(N⁷A)₁₁-A] ( 11 ) formed a duplex with d(T₁₂) ( 13 ). Antiparallel chain polarity and reverse Watson-Crick base pairing was deduced from duplex formation of the self-complementary d[(N⁷A)₈-T₈] ( 14 ).     

Studies on the Base-Pairing Properties of N7-(2-Deoxy-β-D-erythro-pentofuranosyl)guanine (N7Gd)

The base-pairing properties of N⁷-(2-deoxy-β-D -erythro-pentofuranosyl)guanine (N⁷G_d; 1 ) are investigated. The nucleoside 1 was obtained by nucleobase-anion glycosylation. The glycosylation reaction of various 6-alkoxy-purin-2-amines 3a - i with 2-deoxy-3,5-di-O-(4-toluoyl)-α-D -erythro-pentofuranosyl chloride ( 8 ) was studied. The N⁹/N⁷-glycosylation ratio was found to be 1:1 when 6-isopropoxypurin-2-amine ( 3d ) was used, whereas 6-(2-methoxyethoxy)purin-2-arnine ( 3i ) gave mainly the N⁹-nucleoside (2:1). Oligonucleotides containing compound 1 were prepared by solid-phase synthesis and hybridized with complementary strands having the four conventional nucleosides located opposite to N⁷G_d. According to T_m values and enthalpy data of duplex formation, a base pair between N⁷G_d and dG is suggested. From the possible N⁷G_d dG base pair motives, Hoogsteen pairing can be excluded as 7-deaza-2′-deoxyguanosine forms the same stable base pair with N⁷G_d as dG.     

N 7-DNA: Base-Pairing Properties of N 7-(2′-Deoxy-β-D-erythro-pentofuranosyl)-Substituted Adenine,Hypoxanthine, and Guanine in Duplexes with Parallel Chain Orientation

Oligonucleotides containing N ⁷-(2′-deoxy-β-D -erythro-pentofuranosyl)adenine ( 1 ), -hypoxanthine ( 2 ), and -guanine ( 3 ) were synthesized on solid-phase using phosphonate and phosphoramidite chemistry. As part of the synthesis of compound 2 , the nucleobase-anion glycosylation of various 6-alkoxypurines with 2-deoxy-3,5-di-O-(4-toluoyl)-α-D -erythro-pentofuranosyl chloride ( 5 ) was investigated. The duplex stability of oligonucleotides containing N ⁷-glycosylated purines opposite to regular pyrimidines was determined, and thermodynamic data were calculated from melting profiles. Oligodeoxyribonucleotide duplexes containing N ⁷-glycosylated adenine⋅T_d or N ⁷-glycosylated guanine⋅C_d base pairs are more stable in the case of parallel strand orientation than in the case of antiparallel chains.     

3-Deazaguanine N7- and N9-(2′-Deoxy-β-D-ribofuranosides): Building Blocks for Solid-Phase Synthesis and Incorporation into Oligodeoxyribonucleotides

Oligonucleotides continuing 3-deaza-2′-deoxyguanosine ( I ) or its N⁷-regioisomer 2 were prepared by solid-phase synthesis using P¹¹¹ chemistry. Protection of ¹ or ² with N,N V-dimethylformamide diethyl acetal followed by 4,4′-dimethoxytritylation afforded imidazo[4,5-c]pyridines 10b and 11b , respectively. The latter were converted into the 3′-phosphonates 10c or lie, respectively; the cyanoethyl N,N-diisopropylphosphoramidite 10d was also prepared. The oligonucleotide building blocks were employed in automated solid-phase synthesis. 1 he self-complementary oligomers 13 , 15 , and 17 were prepared and characterized by enzymatic hydrolysis with snake-venom phosphodiesterase followed by alkaline phosphatase. There CD spectra exhibited the general structure of a B-DNA.     

Synthesis and Biological Evaluation of 2-(2-Deoxy-β-D-ribofuranosyl)pyridine-4-carboxamide

A new protected 2-deoxy-D -ribose derivative, 5-O-[(tert-butyl)diphenylsilyl]-2-deoxy-3,4-O- isopropylidene-aldehydo-D -ribose ( 5 ), was synthesized starting from 2-deoxy-D -ribose. This compound was coupled with 2-lithio-4-(4,5-dihydro-4,4-dimethyloxazol-2-yl)pyridine giving a D /L -glycero-mixture 7 of 5-O-[(tert-butyl)diphenylsilyl]-2-deoxy-1-C-[4-(4,5 -dihydro-4,4-dimethyloxazol-2-yl)pyridin-2-yl]-3,4-O-isopropylidene- D -erythro-pentitol. The mixture 7 was 1-O-mesylated with methanesulfonyl chloride and subsequently treated with CF₃COOH/H₂O and ammonia to afford the α/β-D -anomers 10 of 2-(2-deoxy-D -ribofuranosyl)pyridine-4-carboxamide. Both anomers were purified and separated by HPLC and identified by NMR and DCI-MS. Anomer β-D - 10 was evaluated against a series of tumor-cell lines and a variety of viral strains. No antitumor or antiviral activity was observed.     

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.     

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).     

Synthesis and Pairing Properties of Oligodeoxynucleotides Containing N7‐(Purin‐2‐amine Deoxynucleosides)

A general synthesis of the four isomeric N⁷‐α‐D ‐, N⁷‐β‐D ‐, N⁹‐α‐D ‐, and N⁹‐β‐D ‐(purin‐2‐amine deoxynucleoside phosphoramidite) building blocks for DNA synthesis is described (Scheme). The syntheses start with methyl 3′,5′‐di‐O‐acetyl‐2′‐deoxy‐D ‐ribofuranoside ( 2 ) as the sugar component and the N²‐acetyl‐protected 6‐chloropurin‐2‐amine 1 as the base precursor. N⁷‐Selectivity was achieved by kinetic control, and N⁹‐selectivity by thermodynamic control of the nucleosidation reaction. The two N⁷‐(purin‐2‐amine deoxynucleosides) were introduced into the center of a decamer DNA duplex, and their pairing preferences were analyzed by UV‐melting curves. Both the N⁷‐α‐D ‐ and N⁷‐β‐D ‐(purin‐2‐amine nucleotide) units preferentially pair with a guanine base within the Watson‐Crick pairing regime, with ΔT_ms of −6.7 and −8.7 K, respectively, relative to a C⋅G base pair (Fig. 3 and Table 1). Molecular modeling suggests that, in the former base pair, the purinamine base is rotated into the syn‐arrangement and is able to form three H‐bonds with O(6), N(1), and NH₂ of guanine, whereas in the latter base pair, both bases are in the anti‐arrangement with two H‐bonds between the N(3) and NH₂ of guanine, and NH₂ and N(1) of the purin‐2‐amine base (Fig. 4).     

Die photochemische synthese von μ-(1-2-η:2-3-η-allen)-octacarbonyldimangan(0)

Novel dihydroiridium(III) complexes containing mono- and bi-dentate sulfur ligands have been isolated. The cationic complexes [Ir(COD)L₂]ClO₄ (COD = 1,5-cyclooctadiene, L = tetrahydrothiophene (tht) or trimethylene sulfide (tms); L₂ = (CH₃S)₂(CH₂)₃ (dth)), [Ir(COD)(L-L)]₂(ClO₄)₂ (L-L = 1,4-dithiacyclohexane (dt) or (t-BuS)₂(CH₂)₂ (tmdto)) and [Ir(CO)₂(tmdto)]₂-(ClO₄)₂ react with H₂ to give the corresponding iridium(III) dihydrides: [IrH₂COD)L₂]ClO₄ (Ia: L = tht, Ib: L = tms, Ic: L₂ = dth), [IrH₂(COD)-(L-L)]₂(ClO₄)₂ (IIa: L-L = tmdto, IIb: L-L = dt) and [IrH₂(CO)₂(tmdto)]₂-(ClO₄)₂ (III). The ¹H NMR chemical shifts and ν(IrH) data are discussed.     

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.     

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.     

Crystal and molecular structures of (η-xanthene)- (η-cyclopentadienyl)iron(II) hexafluorophosphate and (η-2-methylthianthrene)(η-cyclopentadienyl)iron(II) hexafluorophosphate

The neutral complexes (η⁵-C₅H₅NiXL (X = Cl, L = PPh₃ (I); L = PCy₃ (II); X = Br, L = PPh₃ (III); L = PCy₃ (IV); X = I, L = PPh₃ (V); L = PCy₃ (VI)) have been obtained by treating NiX₂L₂ with thallium cyclopentadienide. The same reaction in the presence of TlBF₄ gives cationic derivatives [(η⁵-C₅H₅)NiL₂]BF₄ (L = 2PPh₂Me (VII); L = dppe (VIII)), whereas mononuclear complexes containing two different ligands (L₂ = PPh₃ + PCy₃ (IX)) or dinuclear [(η⁵-C₅H₅)Ni(PPh₃)]₂dppe(BF₄)₂ (X) are obtained from the reaction of III with TlBF₄ in the presence of a different ligand. Reduction of cationic complexes with Na/Hg gives very unstable nickel(I) derivatives (η⁵-C₅H₅)NiL₂, which could not be isolated purely. Similar reduction of neutral complexes under CO gives a mixture of decomposition products containing [(η⁵-C₅H₅)Ni(CO)]₂ and nickel(o) carbonyls, whereas in the presence of acetylenes, dinuclear [(η⁵-C₅H₅)Ni]₂(RCCR′) (R = R′ = Ph; R = Ph, R′ = H) are obtained.     

Synthesis and Crystal Structures of the Molybdenum(II) Complexes with the N,N‐dimethylthiocarbamoyl Containing Ligand: Crystal Structures of β [Mo(CO)2{η2‐S2P(OEt)2}(η2‐SCNMe2)(PPh3)] and [Mo(CO)2(η3‐Tp)(η2‐SCNMe2)(PPh3)]

Reactions of the thiocarbamoyl‐molybdenum complex [Mo(CO)₂(η²‐SCNMe₂)(PPh₃)₂Cl] 1 , and ammonium diethyldithiophosphate, NH₄S₂P(OEt)₂, and potassium tris(pyrazoyl‐1‐yl)borate, KTp, in dichloromethane at room temperature yielded the seven coordinated diethyldithiophosphate thiocarbamoyl‐molybdenum complexe [Mo(CO)₂{η²‐S₂P(OEt)₂}(η²‐SCNMe₂)(PPh₃)] β‐3 , and tris(pyrazoyl‐1‐yl)borate thiocabamoyl‐molybdenum complex [Mo(CO)₂(η³‐Tp)(η²‐SCNMe₂)(PPh₃)] 4 , respectively. The geometry around the metal atom of compounds β‐3 and 4 are capped octahedrons. The α‐ and β‐isomers are defined to the dithio‐ligand and one of the carbonyl ligands in the trans position in former and two carbonyl ligands in the trans position in later. The thiocabamoyl and diethyldithiophosphate or tris(pyrazoyl‐1‐yl)borate ligands coordinate to the molybdenum metal center through the carbon and sulfur and two sulfur atoms, or three nitrogen atoms, respectively. Complexes β‐3 and 4 are characterized by X‐ray diffraction analyses.     

Organometallic chemistry of fullerenes: η2- and η5-(π)complexes

The reactivity of the fullerenes is primarily a function of their strain, as measured by the pyramidalization angle or curvature of the conjugated carbon atoms. A consideration of the orientation of the π-orbitals shows that η²-complexation reactions lead to reaction products with the fullerenes that are very similar to those obtained from unstrained alkenes. Furthermore, a large amount of strain energy is released in this reaction, so it is clear just why this reaction is important in fullerene chemistry. On the other hand, it is shown that the π-orbitals of C₆₀ are poorly oriented for overlap with an exohedral metal atom centered over the five- or six-membered rings, but well disposed for overlap with an endohedral metal atom centered under the five- or six-membered rings. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 139–143, 1998