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.     

Synthesis of 2-(o-chloropheny)- and 2-(2′,6′-dichlorophenyl)-4-formyl-1,2,3-triazoles

Mesoaldehyde 1,3-dioxime was treated with either o-chlorophenyl- or 2,6 dichloro-phenylhydrazine to give the corresponding 2-chlorophenylhydrazone. Hydrazones 1a and 1b were treated with acetic anhydride and cyclized to triazoles ( 3a and 6a ) with cesium carbonate. These were then hydrolized to the previously unknown chlorophenyltriazole aldehydes ( 4a and 4b ). They were also converted to a number of acid derivatives, alcohols, and amines.     

3-Deaza-2′-deoxyadenosine: Synthesis via 4-(methylthio)-1H-imidazo[4,5-c]pyridine 2′-deoxyribonucleosides and properties of oligonucleotides

The synthesis of 4-(methylthio)-1H-imidazo[4,5-c]pyridine 2′-deoxy-β-D -ribonucleosides 2 and 9 and the conversion of the N¹-isomer 2 into the 2′,3′-didehydro-2′,3′-dideoxyribonucleoside 3a or (via 7 ) 3-deaza-2′-deoxyadenosine ( 1 ) is described. Phosphonate building blocks of 1 were employed in solid-phase synthesis of self-complementary base-modified oligonucleotides. Their properties were studied with regard to duplex stability and hydrolysis by the restriction enzyme Eco RI.     

(6′RS,8′RS,2E)- und (6′RS,8′SR,2E)-3-Methyl-3-(2y,2′,6′-trimethyl-7′-oxabicyclo[4.3.0]non-9′-en-8′-yl)-2-propenal ([(5RS,8RS)- und (5RS,8SR)-5,8-Epoxy-5,8-dihydro-ionyloinden]acetaldehyd): Synthese und Röntgenstrukturanalyse

Synthesis and X-Ray Structure of (6′RS,8′RS,2E)- and (6′RS,8′SR,2E)-3-Methyl-3-(2′,2′,6′-trimethyl-7′-oxabicyclo[4.3.0]non-9′-en-8′-yl)-2-propenal ([(5RS,8RS)- and (5RS,8SR)-5,8-Epoxy-5,8-dihydro-ionylidene]acetaldehyde) To check our previous spectroscopic assignments of the structures of trans- and cis-substituted furanoid end groups of carotenoid-5,8-epoxides, we now have synthesized the title compounds. An X-ray structure determination of a single crystal of the trans-isomer (±)- -10A is in agreement with the ¹ H-NMR spectroscopic arguments: isomers with Δδ (H? C(7), H? C(8)) = 0.15–0.22 ppm and J > 1.4 for H? C(7) belong to the cis-series; Δδ in trans-compounds is < 0.07 ppm, and H? C(7) appears as a broad singulett.     

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.     

Synthesis and Characterization of Oligonucleotides Containing 2′‐Deoxyxanthosine Using Phosphoramidite Chemistry

Oligodeoxynucleotides containing 2′‐deoxyxanthosine (X_d) were synthesized in good yield from a O²,O⁶‐bis[2‐(4‐nitrophenyl)ethyl](NPE)‐protected phosphoramidite of X_d. Attempts to synthesize a O⁶‐monoNPE‐protected phosphoramidite resulted in formation of a major by‐product. The NPE protecting groups were removed by treatment with oximate ion after other protecting groups were removed with aqueous NH₄OH solution. The composition of the synthetic oligonucleotides was verified by enzymatic degradation and MALDI‐TOF mass spectrometry. The efficacy of this procedure allowed isolation of oligodeoxynucleotides containing multiple X_d residues.     

Mass spectral rearrangements of N,N-bis(4′-arylthio-2′-butynyl)anilines and N,N-bis(4′-arylsulfonyl-2′-butynyl)anilines

The title compounds display unusual modes of fragmentation under electron impact. One of the dominant modes is the concerted elimination of the two arylthio and arylsulfonyl moieties followed by further extrusion of the C₆H₄ unit as a cumulene. No elimination of SO₂ is observed from any of the sulfones nor an expulsion of the C₄H₄ fragment. Such behavior contrasts strikingly with that of 1,4-diarylsulfonyl-2-butynes and of the 1,6-diarylsulfonyl-2,4-hexadiynes.     

Angiotensin-II Analogues. I: Synthesis and incorporation of the halogenated amino acids 3-(4′-iodophenyl)alanine, 3-(3′,5′-dibromo-4′-chlorophenyl)alanine, 3-(3′,4′,5′-tribromophenyl)alanine,and 3-(2′,3′,4′,5′,6′-pentabromophenyl)alanine

The synthesis of the polyhalogenated phenylalanines Phe(3′,4′,5′-Br₃) ( 3 ), Phe(3′,5′-Br₂-4′-Cl) ( 4 ) and DL -Phe (2′,3′,4′,5′,6′-Br₅) ( 9 ) is described. The trihalogenated phenylalanines 3 and 4 are obtained stereospecifically from Phe(4′-NH₂) by electrophilic bromination followed by Sandmeyer reaction. The most hydrophobic amino acid 9 is synthesized from pentabromobenzyl bromide and a glycine analogue by phase-transfer catalysis. With the amino acids 4, 9 , Phe(4′-I) and D -Phe, analogues of [1-sarcosin]angiotensin II ([Sar¹]AT) are produced for structure-activity studies and tritium incorporation. The diastereomeric pentabromo peptides L - and D - 13 are separated by HPLC. and identified by catalytic dehalogenation and comparison to [Sar¹]AT ( 10 ) and [Sar¹, D -Phe⁸]AT ( 14 ).     

(1H‐Pyrazole‐κN2)(2,2′:6′,2′′‐terpyridine‐κ3N,N′,N′′)platinum(II) bis(perchlorate) nitromethane monosolvate

The reaction between [PtCl(terpy)]·2H₂O (terpy is 2,2′:6′,2′′‐terpyridine) and pyrazole in the presence of two equivalents of AgClO₄ in nitromethane yields the title compound, [Pt(C₃H₄N₂)(C₁₅H₁₁N₃)](ClO₄)₂·CH₃NO₂, as a yellow crystalline solid. Single‐crystal X‐ray diffraction shows that the dicationic platinum(II) chelate is square planar with the terpyridine ligand occupying three sites and the pyrazole ligand occupying the fourth. The torsion angle subtended by the pyrazole ring relative to the terpyridine chelate is 62.4 (6)°. Density functional theory calculations at the LANL2DZ/PBE1PBE level of theory show that in vacuo the lowest‐energy conformation has the pyrazole ligand in an orientation perpendicular to the terpyridine ligand (i.e. 90°). Seemingly, the stability gained by the formation of hydrogen bonds between the pyrazole NH group and the perchlorate anion in the solid‐state structure is sufficient for the chelate to adopt a higher‐energy conformation.     

Mass spectra of some 2-(4′-butyl-3,′5′-dimethylpyrazol-1′-yl)-6-substituted benzothiazoles

The fragmentation of the title compounds on electron impact has been studied and the major processes interpreted. The base peak invariably appears at [M ? 43]⁺ whose origin from the butyl chain has been traced with the help of metastable ion studies and accurate mass measurements. Loss of methyl cyanide, involving the decomposition of the pyrazole moiety, is observed only from the fragment ions.     

Separation of (3R, 3′ R)-, (3R, 3′ S; meso)-, (3S, 3′ S)- Zeaxanthin, (3R, 3′ R, 6′ R)-, (3R, 3′ S, 6′ S)- and (3S, 3′ S, 6′ S)-Lutein via the dicarbamates of (S)-(+)-α-(1-naphthyl) ethyl isocyanate

A method is described for the qualitative and quantitative determination of configurational isomers of zeaxanthin (=3,3′ -dihydroxy-β, β -carotene) and lutein (=3,3′ -dihydroxy-α -cartotene). It is based on the reaction of these zeaxathin and lutein isomers with (S)-(+)-α-(1-naphthyl) ethyl isocyanate to afford diastereomeric dicarbamates, which are analyzed by HPLC.     

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.     

(Nitro‐κN)[2‐(phenyldiazenyl‐κN2)pyridine‐κN](2,2′:6′,2′′‐terpyridine‐κ3N)ruthenium(II) tetrafluoroborate

The Ru—N bond distances in the title complex, [Ru(NO₂)(C₁₁H₉N₃)(C₁₅H₁₁N₃)]BF₄ or [Ru(NO₂)(tpy)(azpy)]BF₄, [tpy is 2,2′:6′,2′′‐ter­pyridine and azpy is 2‐(phenyl­azo)­pyridine], are Ru—N_py 2.063 (4), Ru—N_azo 2.036 (4), Ru—N_nitro 2.066 (3) Å, and Ru—N_tpy 2.082 (4), 1.982 (3) and 2.074 (4) Å. The azo N atom is trans to the nitro group. The azo N=N bond length is 1.265 (5) Å, which is the shortest found in such complexes to date. This indicates a multiple bond between Ru and the N atom of the nitro group, and π‐­backbonding [dπ(Ru) π*(azo)] is decreased.     

Saturated heterocycles. 242. Synthesis of 2-substituted-6-(6′,7′-dimethoxy-3′,4′-dihydro-1′-isoquinolyl)-5,6,7,8-tetrahydro- quinazolin-4(3H)-one Derivatives

In the reactions of the recently synthesized β-ketoesters 1-[(3′-methoxycarbonyl- and 1-[(3′-ethoxycarbonyl-4′-oxo)-1′-cyclohexyl]-3,4-dihydroisoquinoline 4, 5 with amidines or cyclic guanidines, a number of 2-substituted-6-(6′,7′-dimethoxy-3′,4′-dihydro-1′-isoquinolyl)-5,6,7,8-tetrahydroquinazolin-4(3H)-one derivatives 6–8 were prepared. The new compounds possess various pharmacological actions.     

Nucleotides. Part XLV. Synthesis of new (2′–5′)adenylate trimers,containing 5′-amino-5′-deoxyadenosine residues at the 5′-end of the oligoadenylate chain,and of its analogues,carrying a 9-[(2-hydroxyethoxy)methyl]adenine residue at the 2′-terminus

The 5′-amino-5′-deoxy-2′,3′-O-isopropylideneadenosine ( 4 ) was obtained in pure form from 2′,3′-O-isopropylideneadenosine ( 1 ), without isolation of intermediates 2 and 3 . The 2-(4-nitrophenyl)ethoxycarbonyl group was used for protection of the NH₂ functions of 4 (→7) . The selective introduction of the palmitoyl (= hexadecanoyl) group into the 5′-N-position of 4 was achieved by its treatment with palmitoyl chloride in MeCN in the presence of Et₃N (→ 5 ). The 3′-O-silyl derivatives 11 and 14 were isolated by column chromatography after treatment of the 2′,3′-O-deprotected compounds 8 and 9 , respectively, with (tert-butyl)dimethylsilyl chloride and 1H-imidazole in pyridine. The corresponding phosphoramidites 16 and 17 were synthesized from nucleosides 11 and 14 , respectively, and (cyanoethoxy)bis(diisopropylamino)phosphane in CH₂Cl₂. The trimeric (2′–5′)-linked adenylates 25 and 26 having the 5′-amino-5′-deoxyadenosine and 5′-deoxy-5′-(palmitoylamino)adenosine residue, respectively, at the 5′-end were prepared by the phosphoramidite method. Similarly, the corresponding 5′-amino derivatives 27 and 28 carrying the 9-[(2-hydroxyethoxy)methyl]adenine residue at the 2′-terminus, were obtained. The newly synthesized compounds were characterized by physical means. The synthesized trimers 25–28 were 3-, 15-, 25-, and 34-fold, respectively, more stable towards phosphodiesterase from Crotalus durissus than the trimer (2′–5′)ApApA.     

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.     

3′-(1,2,3-Triazol-1-yl)-2′,3′-dideoxythymidine and 3′-(1,2,3-triazol-1-yl)-2′,3′-dideoxyuridine

Cycloaddition of different acetylenic compounds on the azido function of 3′-azido-2′,3′-dideoxythymidine and 3′-azido-2′,3′-dideoxyuridine afforded products with a 1,2,3-triazol-1-yl substituent in the 3′-position. In contrast with the parent compounds, these triazolyl derivatives had no appreciable activity against human immunodeficiency virus (HIV-1).     

{μ‐N,N′‐Bis[2‐(dimethylamino)ethyl]oxamidato(2–)‐κ6N,N′,O′:N′′,N′′′,O}bis[(2,2′‐bipyridine‐κ2N,N′)copper(II)] bis(perchlorate)

In the crystal structure of the title complex, [Cu₂(C₁₀H₂₀N₄O₂)(C₁₀H₈N₂)₂](ClO₄)₂, the deprotonated dmaeoxd²⁻ ligand {H₂dmaeoxd is N,N′‐bis[2‐(dimethylamino)ethyl]oxamide} occupies an inversion centre at the mid‐point of the central C—C bond and is thus in a trans conformation. The two Cu^II atoms are located in slightly distorted square‐based pyramidal environments. The binuclear units interact with each other viaπ–π interactions to form a one‐dimensional chain extending in the c direction.