Investigation of the torsional angle at the glycosidic bond in 5′-amino-5′-deoxythymidine derivatives by carbon-13 n.m.r. spectroscopy

The conformational preference of the thymine base ring with respect to the sugar ring in β,β,β,-trichloroethyl 5′amino-5′-deoxythymidine-5′-phosphate has been studied by ¹³C n.m.r. spectroscopy. The magnitude of the three bond vicinal coupling constant, J(C-2, H-1′), for β,β,β-trichloroethyl 5′-amino-5′-deoxythymidine-5′-phosphate and the similarity between the chemical shifts for the furanose carbons C-1′, C-2′, and C-3′ in β,β,β-trichloroethyl 5-′-amino-5′-deoxythymidine-5′-phosphate and in β,β,β-trichloroethyl thymidine 5′-phosphate indicate that the amino analogue exists in aqueous solution predominantly in the anti conformation, as is the case with natural nucleotides.     

UV photoelectron and ab initio quantum mechanical characterization of nucleotides: The valence electronic structure of anionic 2′-deoxyadenosine-5′-phosphate

He(I) ultraviolet (UV) photoelectron spectroscopy and ab initio, self-consistent field (SCF) calculations with the 6-31G basis set have been employed to characterize the valence electronic structures of anionic 2′-deoxyadenosine-5′-phosphate (5′-dAMP⁻). Theoretical ionization potentials (IPs) of 5'-dAMP^-, of the neutral model compounds 9-methyladenine (9-MeA) and 3-hydroxytetrahydrofuran (3-OH-THF), and of the model anion CH₃HPO₄⁻ have been obtained by applying Koopmans' theorem to ab initio SCF results. The ionization potentials predicted from the SCF calculations have been compared to He(I) photoelectron spectra of 9-MeA and 3-OH-THF. The SCF calculations predict a value (8.45 eV), for the highest occupied π orbital in 9-MeA which agrees well with the experimental vertical IP (8.39 eV). However, IPs for the highest occupied lone-pair orbitals in 3-OH-THF are predicted to be more than 1.52 eV higher than the experimental IPs. Results from recently reported [H. S. Kim and P. R. LeBreton, Proc. Natl. Sci. USA 91, 3725–3729 (1994), and N. S. Kim and P. R. LeBreton, J. Am. Chem. Soc., 118, 3694 (1996)] second-order Møller-Plesset perturbation (MP2) calculations and configuration interaction calculations using the configuration interaction singles (CIS) method indicate that configuration interaction effects strongly influence the energies of the first five ionization events arising from removal of electrons from the closed-shell model anion CH₃HPO₄⁻. Results from the 6-31G SCF calculations of 5′-dAMP⁻, 9-MeA, 3-OH-THF, and CH₃HPO₄⁻ indicates that valence orbital electron distributions in the nucleotide and in the model compounds and anion are similar. The correspondence between the orbital structure of the nucleotide, and the model compounds and anion makes it possible, employing experimental photoelectron data and MP2/CIS computational results for the model compounds and anion, to individually correct IPs calculated for the nucleotide at the 6-31G SCF level. Here, this approach has provided values for the 13 lowest IPs of 5′-dAMP⁻ and indicates that the first IPs of the base, sugar, and phosphate groups are 6.1, 7.8, and 5.5 eV, respectively. © 1996 John Wiley & Sons, Inc.     

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.     

Interaction of dimethyltin(IV) dichloride with 5′‐IMP and 5′‐UMP

The formation constants of the species formed in the systems H⁺ + dimethyltin(IV) + 5′‐IMP and 5′‐UMP, H⁺ + 5′‐IMP and H⁺ + 5′‐UMP have been determined in aqueous solution in the pH range 1.5–9.5 at constant temperature (25 °C) and constant ionic strength (0.1 mol dm⁻³ NaClO₄), using spectrophotometric and potentiometric techniques. ¹H and ³¹P NMR investigations in aqueous solution confirmed the species formation. The precipitated complexes of IMP and UMP by Me₂Sn(IV)²⁺ at low pH values were characterized by elemental analysis and FTIR spectroscopy methods, the bonding sites of the ligands were determined and ruled out purine and pyrimidine moieties (N‐7 and N‐1 in IMP and N‐3 in UMP, respectively) while a bidentated coordination of the phosphate group is concluded in both cases. Finally, the experiments revealed the existence of complexes with trigonal bipyramidal structures that is in agreement with similar systems resulted previously. Copyright © 2008 John Wiley & Sons, Ltd.     

Nucleotides. Part XXXV. Synthesis of 3′-deoxyadenylyl-(2′–5′)-3′-deoxyadenyIyl-(2′–ω)-9-(ω-hydroxyalkyl)adenines

Via the phosphotriester approach, new structural analogs of (2′–5′)oligoadenyiates, namely 3′-deoxyadenylyl-(2′–5′)-3′-dcoxyadenylyl-(2′–ω)-9-(ω-hydroxyalkyl)adenines 18 – 21 , have been synthesized (see Scheme) which should preserve biological activity and show higher stability towards phosphodiesterases. The newly synthesized oligonucleotides 18 – 21 have been characterized by ¹H-NMR spectra, TLC, and HPLC analysis.     

Synthesis of 2′-Deoxyisoguanosine 5′-Triphosphate and 2′-Deoxy-5-methylisocytidine 5′-Triphosphate

The syntheses of the 5′-triphosphates of 2′-deoxyisoguanosine (=p₃isoG_d) and 2′-deoxy-5-methylisocytidine (=p₃me⁵isoC_d), two new bases for the genetic alphabet, are described. The triphosphates were synthesized from the corresponding nucleosides using a transient-protection procedure. The introduction of a methyl group at the 5-position of 2′-deoxyisocytidine remarkably improved the stability of the triphosphate. Characterization of the triphosphates included enzymatic incorporation opposite the complementary base in a template oligonucleotide.     

19F and 1H NMR of aldimines of fluoroamino acids with pyridoxal-5′-phosphate

¹H and ¹⁹F NMR spectra were obtained for six Schiff bases (aldimines) formed by pyridoxal-5′-phosphate (PLP) with four fluorinated or their two parent non-fluorinated α-amino acids (phenylalanine and α-aminobutyric acid). pK_A Values were derived from ¹H and ¹⁹F titration curves. The imine nitrogen of the aldimines is very basic (～13) and sensitive to the electron withdrawing effect of fluorine. The pyridine nitrogen is less basic in the aldimines (～7) than in PLP (8.12) and is less sensitive to the electron withdrawing effect of the fluorine than is the imine nitrogen. The phosphate group has a pK in the same range (～6) and the chemical shifts of some nuclei are sensitive to both pK values. Protonation of the aldimine causes the ¹H signal to shift downfield at the methyl protons of the pyridine ring and at the aldehydic proton of the aldimine for the high pK value (except for the aldimines prepared from the β-fluorophenylalanine), but upfield at the aromatic proton and at the aldehydic proton of the aldimine for the low pK. Protonation of the aldimine causes the ¹⁹F signal of an aryl fluorine to shift downfield but gives an upfield shift at a β-fluorine. These data are related to the highly conjugated electronic structure of the Schiff bases.     

1H NMR study of the reaction of ornithine and lysine with pyridoxal-5′-phosphate

The composition of the mixture from the reaction of the basic amino acids ornithine or lysine with pyridoxal-5′-phosphate was investigated in D₂O by ¹H NMR and was found to be dependent on pH, α attack being favoured at acid pH and ω attack in basic solutions.     

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 ).     

A 13C NMR study of pyridoxal-5′-phosphate oxime

Pyridoxal-5′-phosphate amino-oxy acetate oxime was titrated in water, over the pH range 4–12, and the changes followed using ¹³C NMR. The results were compared to those of analogous Schiff's bases presented in the literature. The chemical shifts and titration curves of the oxime were appreciably different from those of the Schiff's bases, and the differences are explained as being due to the absence of ketoenamine-enolimine tautomerism in the oxime. The low chemical shift value and the large changes of the oxime azomethine carbon during titration, as compared to the Schiff's bases, are discussed. The high stability of the oximes in water makes them suitable as model compounds for some tautomeric forms of the Iess stable Schiff's bases.     

Nucleotides. Part XXXI. Modified Oligomeric 2′–5′ A Analogues: Synthesis of 2′–5′ oligonucleotides with 9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine and 9-(3′-amino-3′-deoxy-β-D-xylofuranosyl)adenine as modified nucleosides

A series of new 2′–5′ oligonucleotides carrying the 9-(3′-azido-3′deoxy-β-D-xylofuranosyl)adenine moiety as a building block has been synthesized via the phosphotriester method. The use of the 2-(4-nitrophenyl)ethyl (npe) and 2-(4-nitrophenyl)ethoxycarbonyl (npeoc) blocking groups for phosphate, amino, and hydroxy protection guaranteed straightforward syntheses in high yields and easy deblocking lo form the 2′–5′ trimers 21 , 22 , and 25 and the tetramer 23 . Catalytic reduction of the azido groups in [9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine]2′-yl-[2′-(O^p-ammonio)→ 5′]-[9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenin]-2′-yl-[2′-(O^p-ammonio)→ 5′]-9-(3′-azido-3′-deoxy-β-D-xylofuranosyl)adenine ( 21 ) led to the corresponding 9-(3′-amino-3′-deoxy-β-D-xylofuranosyl)-adenine 2′–5′ trimer 26 in which the two internucleotidic linkages are formally neutralized by intramolecular betaine formation.     

Isomerisierung bei der Komplexbildung von 3-Acetyl-tetramsäure: Struktur und magnetische Eigenschaften des CuII- und NiII-Komplexes von 2,7-Bis(1′, 5′, 5′-trimethylpyrrolidin-2′, 4′-dion-3′ -yl)-3, 6-diazaocta-2, 6-dien

Isomerization at the Complexation of 3-Acetyltetramic Acid: Structure and Magnetic Properties of the Cu^II- and Ni^II-Complex of 2,7-Bis (1′, 5′, 5′ -trimethylpyrrolidin-2′,4′ -dion-3′ -yl)-3,6-diazaocta-2,6-dien 2,7-Bis(1′, 5′, 5′ -trimethylpyrrolidin-2′, 4′ -dion-3′ -yl)-3,6-diazaoctadien formes Cu^II and Ni^II complexes with different constitutions (because of the Z/E isomerization). Results of X-ray analysis of N,N′ -ethylenbis(1′, 5′, 5′ -trimethylpyrrolidin-2′, 4′ -dion-3′ -acetiminato)nickel(II) 1 respectively -copper(II) 2 shows, that the complexing agent in 1 occurs in the E-form, whereas the ligand of the Cu^II complex forms the Z-form. Magnetic susceptibility and shift effects of the ¹³C-NMR signals point to a weak paramagnetism of the Ni^II complex. ESR-spectra are obtained from 2 only. Furthermore, the Cu^II complex reduces the relaxation times T₁ and T₂ of ¹H and ¹⁷O nuclei spins from water. From the temperature dependence of the shortening of the relaxation times an activation energy is calculated which describes the reorientation of the copper complex in the “water matrix”.     

Die Reduktion von Azulen mit Natrium zum Kontaktionen-Tripel [Dinatrium-(1,1′,6,6′-Tetrahydro-6,6′-bi(azulen)-1,1′-diid)–bis (diglyme)]∞

The Sodium Reduction of Azulene to the Contact-Ion Triple [Disodium-(1,1′,6,6′-Tetrahydro-6,6′-bi(azulene)-1,1′-diide)–bis(diglyme)]_∞ Colorless air-sensitive single crystals can be grown from a diglyme solution after the reduction of azulene by a Na-metal mirror. Structure determination at 150 K reveals a dimer dianion, in which the seven-membered rings are connected in 6,6′-positions and doubly diglyme-solvated Na⁺ counter cations η⁵-coordinate to the five-membered rings. Based on preceding cyclovoltammetric measurements in aprotic azulene solutions as well as on extensive MNDO enthalpy of formation calculations, a proposal is forwarded how possibly the contact ion triple is formed along a microscopic pathway.     

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.     

Nucleotides part XXX Chemical synthesis of adenylyl-(2′ → 5′)-adenylyl-(2′ → 5′)-8-azidoadenosine,and activation and photoaffinity labelling of RNase L by [32P]p5′A2′p5′A2′p5′N38A

The chemical synthesis of adenylyl-(2′–5′)-adenylyl-(2′–5′)-8-azidoadenosine ( 15 ) was performed by the phosphotriester approach. Enzymatic phosphorylation of 15 by [γ-³²P]ATP led to the corresponding labelled 5′-monophosphate 16 . Photoinsertion of 16 took place on UV irradiation by covalent cross linking to a protein of M_r 80 K known to be RNase L. Radiobinding and core-cellulose assays as well as photoaffinity labelling experiments with 16 are described.     

Determination of the rate of formation of the schiff bases of pyridoxal 5′-phosphate with polyallylamine

The formation constants of the Schiff bases of pyridoxal 5′-phosphate with polyallylamine were determined over the p^H range of the acetic-acetate buffer (3.9–5.5) at an ionic strength of 0.1 M and a temperature of 25°C. The results were consistent with the rapid formation of an ionized carbinolamine, T⁺, followed by deprotonation, in the rate-determining step, to a neutral carbinolamine, T°. Subsequent dehydration of T° in a rapid step yields the final Schiff base. The formation of T⁺ is a concerted process subject to specific acid catalysis. © 1995 John Wiley & Sons, Inc.     

Metallophilic interactions in iodido(2,2′:6′,2′′‐terpyridine)platinum(II) diiodidoaurate(I)

In the title compound, [PtI(C₁₅H₁₁N₃)][AuI₂], the [PtI(terpy)]⁺ cations (terpy is 2,2′:6′,2′′‐terpyridine) stack in pairs about inversion centers through Pt...Pt interactions of 3.5279 (5) Å. The [AuI₂]⁻ anions also exhibit pairwise stacking, with Au...I distances of 3.7713 (5) Å. The [PtI(terpy)]⁺ cations and [AuI₂]⁻ anions aggregate forming infinite arrays of stacked ...({[PtI(terpy)]⁺...[PtI(terpy)]⁺}...{[AuI₂]⁻...[AuI₂]⁻})... units.     

Synthèse et détermination de la structure de la 3H-(indazolyl-3′)-5 oxadiazol-1,3,4-one-2 par RMN 13C et spectrometrie de masse

The 3H-5-(3′-indazolyl)-1,3,4-oxadiazol-2-one was obtained by cyclising the hydrazide of the 3-indazolecarboxylic acid with carbonyl chloride. The structure was assigned by ¹³C nmr and mass spectrometry comparing the 2H, 3H-triazino-1,2,3[4,5-b]indazoledione-1,4. Rearrangement into 3H-5-(3′-indazolyl)-1,3,4-oxadiazol-2-one precedes the fragmentation of 2H,3H-triazino-1,2,4-[4,5-b]indazoledione-1,4 upon electron-impact.     

Type I Photosensitization of 2′‐deoxyadenosine 5′‐monophosphate (5′‐dAMP) by Biopterin and its Photoproduct Formylpterin

Biopterin (Bip) and its photoproducts 6‐formylpterin (Fop) and 6‐carboxypterin (Cap) accumulate in the skin of patients suffering from vitiligo, a chronic depigmentation disorder where the protection against UV radiation fails because of the lack of melanin. These compounds absorb in the UV‐A inducing a potential photosensitizing action that can cause damage to DNA and other biomolecules. In this work, we have investigated the capability of these pterin derivatives (Pt) to act as photosensitizers under UV‐A irradiation for the degradation of 2′‐deoxyadenosine 5′‐monophosphate (5′‐dAMP) in aqueous solutions, as model DNA target. Steady‐state and time‐resolved experiments were performed and the effect of pH was evaluated. The results showed that photosensitized degradation of 5′‐dAMP was only observed under acidic conditions, and a mechanistic analysis revealed the participation of the triplet excited state of the pterin derivatives (³Pt*) by electron transfer yielding the corresponding pair of radical ions (Pt^?? and 5′‐dAMP^?+), with successive photosensitizer recovery by electron transfer from Pt^?? to O₂. Finally, 5′‐dAMP^?+ participates in subsequent reactions to yield degradation products.     

Factors Affecting DNA–DNA Interstrand Cross‐Links in the Antiparallel 3′–3′ Sense: A Comparison with the 5′–5′ Directional Isomer

Reported herein is a study of the unusual 3′–3′ 1,4‐GG interstrand cross‐link (IXL) formation in duplex DNA by a series of polynuclear platinum anticancer complexes. To examine the effect of possible preassociation through charge and hydrogen‐bonding effects the closely related compounds [{trans‐PtCl(NH₃)₂}₂(μ‐trans‐Pt(NH₃)₂{NH₂(CH₂)₆NH₂}₂)]⁴⁺ (BBR3464, 1 ), [{trans‐PtCl(NH₃)₂}₂(μ‐NH₂(CH₂)₆NH₂)]²⁺ (BBR3005, 2 ), [{trans‐PtCl(NH₃)₂}₂(μ‐H₂N(CH₂)₃NH₂(CH₂)₄)]³⁺ (BBR3571, 3 ) and [{trans‐PtCl(NH₃)₂}₂{μ‐H₂N(CH₂)₃‐N(COCF₃)(CH₂)₄}]²⁺ (BBR3571‐COCF₃, 4 ) were studied. Two different molecular biology approaches were used to investigate the effect of DNA template upon IXL formation in synthetic 20‐base‐pair duplexes. In the “hybridisation directed” method the monofunctionally adducted top strands were hybridised with their complementary 5′‐end labelled strands; after 24 h the efficiency of interstrand cross‐linking in the 5′–5′ direction was slightly higher than in the 3′–3′ direction. The second method involved “postsynthetic modification” of the intact duplex; significantly less cross‐linking was observed, but again a slight preference for the 5′–5′ duplex was present. 2D [¹H, ¹⁵N] HSQC NMR spectroscopy studies of the reaction of [¹⁵N]‐ 1 with the sequence 5′‐d{TATACATGTATA}₂ allowed direct comparison of the stepwise formation of the 3′–3′ IXL with the previously studied 5′–5′ IXL on the analogous sequence 5′‐d(ATATGTACATAT)₂. Whereas the preassociation and aquation steps were similar, differences were evident at the monofunctional binding step. The reaction did not yield a single distinct 3′–3′ 1,4‐GG IXL, but numerous cross‐linked adducts formed. Similar results were found for the reaction with the dinuclear [¹⁵N]‐ 2 . Molecular dynamics simulations for the 3′–3′ IXLs formed by both 1 and 2 showed a highly distorted structure with evident fraying of the end base pairs and considerable widening of the minor groove.