Conformational Transmission in 5′-PV and 5′-PV TBP Phosphorylated Nucleosides. Implications For DNA Structure and Dynamics

Abstract

Specific conformational changes in DNA and RNA can be induced via a transient pentacoordination of the phosphorus atoms in the helix backbone. The details of this conformational transmission mechanism are discussed briefly, using experimental data that were obtained with a set of 5′-pIV and 5′-pV phosphorylated tetrahydrofurfuryl systems. A conformational study on the more realistic model system, the dinucleotide 2 in which a stabilized pentacoordinated phosphorus forms the internucleoside linkage, is presented. Furthermore, it has been found that methylation of the phosphate groups in d(T_pT_pT_pT_pT_pT) results in the formation of a non-Watson & Crick type parallel duplex DNA structure, in which the two strands are joined via hydrogen bonding between the thymidine bases. Various physico-chemical techniques (e.g. NMR methods and UV hyperchromicity) were used to elucidate the structural details of the parallel duplex. Characteristic properties (parallellity, slimness, symmetry) are presented.     

Synthesis of 5′-benzoyl-2′-hydroxychalcones and related flavonoid compounds

Summary 5 -Benzoyl-2 -hydroxychalcones were synthesized by the condensation of 5 -benzoyl-2 -hydroxyacetophenone with aromatic aldehydes in presence of an ethanolic solution of potassium hydroxide. Derivatives of 6-benzoylflavonoids were prepared from chalcones.     

Synthesis and Crystal Structure Analysis of 5′-O-Tosyl-2,3′-anhydrothymidine

In this paper=5′-O-tosyl-2,3′-anhydrothymidine has been synthesized and its crystal structure was analyzed. The crystal belongs to the triclinic system=space group P1=with a=5.397(2)=b=6.1886(18)=c=3.507(5) =α =87.74(2)=β =89.84(4)=γ =73.79(2)°=C17H18N2O6S=Mr=378.39=Z=1=V=432.8(3)3=Dc=1.452 g/cm3=F(000)=198 and Flack =-0.11(14). No intermolecular hydrogen bonds exist in the crystal=and the angle between benzene ring and pyrimidine planes is 32.23°.     

Bonding Characteristics and Magnetic Coupling Interactions in One-dimensional α′-NaV_2O_5

The spin-polarized generalized gradient approximation(GGA)+U approach was employed to study the bonding characteristics and magnetic coupling interactions in room-temperature phase α′-NaV2O5. The calculated results indicate that the Vdxy orbital is split off from other 3d orbitals in the VO5 pyramidal ligand field. The Vdxy orbitals are hybridized strongly with the Opx/py orbitals, forming a V―O―V π bond in the ab plane. The ligand field effect together with the intra-atomic exchange splitting results in th...     

Acidity constants of adenosine-5′-mono- and diphosphate in various water-organic solvent mixtures

Summary The acidity constants of adenosine-5-mono- and diphosphate (AMP andADP) were determined at 25.00±0.1°C by potentiometric titration in pure water and different solvent mixtures (methanol, ethanol, N,N-dimethylformamide, dimethylsulfoxide, acetone, and dioxane). The ionization ofAMP andADP depends on both the proportion and the nature of the organic solvent used. ThepK _a1 values for bothAMP andADP are slightly influenced as the solvent is enriched in ethanol and methanol and remains practically constant in presence of different amounts ofDMF andDMSO. A pronounced change in thepK _a1 values is observed as the solvent is enriched in acetone or dioxane. It is concluded that the electrostatic effect has only a relatively small influence on the dissociation equilibrium, whereas other solvent effects such as solvent basicity, hydrogen bonding and protonsolvent interactions play an important role.

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Aciditätskonstanten von Adenosin-5-mono- und -diphosphat in verschiedenen organisch-wäßrigen Lösungsmittelgemischen

Zusammenfassung Die Aciditätskonstanten von Adenosin-5-mono- und -diphosphat wurden bei 25.0±0.1°C in reinem Wasser und in verschiedenen Lösungsmittelgemischen (Methanol, Ethanol, N,N-Dimethylformamid, Dimethylsulfoxid, Aceton und Dioxan) potentiometrisch bestimmt. Der Ionisierungsgrad vonAMP undADP hängt sowohl von der Menge als auch von der Art des organischen Lösungsmittels ab. DiepK _a1-Werte vonAMP undADP werden durch Zugabe von Methanol und Ethanol nur wenig, durch verschiedene Mengen vonDMF undDMSO gar nicht, durch Aceton und Dioxan jedoch deutlich beeinflußt. Offensichtlich haben elektrostatische Effekte nur geringe Auswirkungen auf das Dissoziationsgleichgewicht, wogegen andere Faktoren wie Basizität des Lösungsmittels, Wasserstoffbrückenbindungen und Lösungsmittel-Proton-Wechselwirkungen eine bedeutende Rolle spielen.

     

Experimental measurement and modelling of solubility of inosine-5′-monophosphate disodium in pure and mixed solvents

The solubility of biological chemicals in solvents provide important fundamental data and is generally considered as an essential factor in the design of crystallization processes. The equilibrium solubility data of inosine-5′-monophosphate disodium (5′-IMPNa₂) in water, methanol, ethanol, acetone, as well as in the solvent mixtures (methanol + water, ethanol + water, acetone + water), were measured by an isothermal method at temperatures ranging from (293.15 to 313.15) K. The measured data in pure and mixed solvents were then modelled using the modified Apelblat equation, van’t Hoff equation, λh equation, ideal model and the Wilson model. The modified Apelblat equation showed the best modelling results, and it was therefore used to predict the mixing Gibbs free energies, enthalpies, and entropies of 5′-IMPNa₂in pure and binary solvents. The positive values of the calculated partial molar Gibbs free energies indicated the variations in the solubility trends of 5′-IMPNa₂. Water and ethanol (in the binary mixture with water) were found to be the most effective solvent and anti-solvent, respectively.     

Sequence-based analysis of 5′UTR and coding regions of CASP3 in terms of miRSNPs and SNPs in targetting miRNAs

Apoptosis is described as a mechanism of cell death occurring after adequate cellular harm. Deregulation of apoptosis occurs in many human conditions such as autoimmune disorders, ischemic damage, neurodegenerative diseases and different cancer types. Information relating miRNAs to cancer is increasing. miRNAs can affect development of cancer via many different pathways, including apoptosis. Polymorphisms in miRNA genes or miRNA target sites (miRSNPs) can change miRNA activity. Although polymorphisms in miRNA genes are very uncommon, SNPs in miRNA-binding sites of target genes are quite common. Many researches have revealed that SNPs in miRNA target sites improve or decrease the efficacy of the interaction between miRNAs and their target genes. Our aim was to specify miRSNPs on CASP3 gene (caspase-3) and SNPs in miRNA genes targeting 5′UTR and coding exons of CASP3, and evaluate the effect of these miRSNPs and SNPs of miRNA genes with respect to apoptosis. We detected 141 different miRNA binding sites (126 different miRNAs) and 7 different SNPs in binding sites of miRNA in 5′UTR and CDS of CASP3 gene. Intriguingly, miR-339-3p’s binding site on CASP3 has a SNP (rs35372903, G/A) on CASP3 5′UTR and its genomic sequence has a SNP (rs565188493, G/A) at the same nucleotide with rs35372903. Also, miR-339-3p has two other SNPs (rs373011663, C/T rs72631820, A/G) of which the first is positioned at the binding site. Here, miRSNP (rs35372903) at CASP3 5′UTR and SNP (rs565188493) at miR-339-3p genomic sequence cross-matches at the same site of binding region. Besides, miR-339-3p targets many apoptosis related genes (ZNF346, TAOK2, PIM2, HIP1, BBC3, TNFRSF25, CLCF1, IHPK2, NOL3) although it had no apoptosis related interaction proven before. This means that miR-339-3p may also have a critical effect on apoptosis via different pathways other than caspase-3. Hence, we can deduce that this is the first study demonstrating a powerful association between miR-339-3p and apoptosis upon computational analysis.     

Rosenmund-Braun Reaction Products 4′,5′-Dicyanobenzo-15-crown-5 and 4′,5′-Dicyanobenzo-15-crown-5,4′-cyano-5′-cyano(bromo)benzo-15-crown-5 Hydrates: Spectroscopic Properties and Crystal Structure

The products of 4′,5′-dibromobenzo-15-crown-5 (I) cyanation by the Rosenmund-Braun reaction are studied by the ¹H NMR and IR spectroscopy methods. X-ray diffraction analysis of two isolated products, i.e., di(4′,5′-dicyanobenzo-15-crown-5) 1.6 hydrate {(CN)₂B15C5}₂ · 1.6H₂O (IIa) and 4′,5′-dicyanobenzo-15-crown-5,4′-cyano-5′-cyano(bromo)benzo-15-crown-5 dihydrate (CN)_3.85Br_0.15(B15C5)₂ · 2H₂O (III) is performed. Crystals IIa are monoclinic, a = 15.882(2) Å, b = 11.412(2) Å, c = 18.484(3) Å, β = 100.717(3)°, V = 3291.7(9) ų, Z = 4, space group P2₁/c, R = 0.0746 for 4775 reflections with I > 2σ(I). Crystals III are monoclinic, a = 15.956(3) Å, b = 11.425(2) Å, c = 18.865(4) Å, β = 99.32(3)°, V = 3394(1) ų, Z = 4, space group _P2₁/_{c, R} = 0.0692 for 2070 reflections with I > 2σ(I). Compounds IIa and III have similar structures with two crystallographically independent molecules in each (A and B in IIa; C and D in III). Four of the five O atoms of a macrocycle in molecules A and C form hydrogen bonds with the water molecules. The latter molecules lie above and below the cycle plane at a distance of ～2 Å from this plane. The A and C molecules have identical conformations (TTG TTG TTG TTG TTC) that differ from those of molecules B (TTG TGG STT SSG TTC) and D (TTC TSG STT SSG TTC).     

Cotton-mouton constants and spatial structure of 2,2′- and 4,4′-dipyridyls and their salts in solutions

Magnetic birefringence has been used in studying the spatial structure of a series of dipyridyl derivatives in hydrochloric acid solutions, and also some of their quaternary salts in water. It has been shown that when the change is made from the molecular forms of the 2,2- and 4,4-dipyridyls to their protonated mono and bis derivatives, the angles of rotation of the aromatic rings are very little changed; in the methylated cation, the degree of acoplanarity increases.Deceased.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 12, pp. 2771–2775, December, 1991.     

High-Performance Liquid Chromatography of 2′-5′Oligoadenylates and Related Oligonucleotides

Abstract

HPLC has been used for the analysis and separation of the components of p_x (A2′p)_n A (x = 1 to 3, n = 1 to ≥4). Weak anion exchange columns give excellent resolution, but their instability in phosphate buffers makes them impractical for routine use. Reverse phase chromatography using C18 columns provides a satisfactory alternative method. For preliminary analysis of crude material, ammonium phosphate pH7.0 with a linear 1:1 methanol/H₂O gradient gives a good basic separation of the individual oligomers. Resolution of the 5′ mono-, di-and triphosphorylated oligomers or of the nonphosphorylated components can be obtained using ammonium phosphate pH6.0 and potassium phosphate pH6.5 buffers respectively. The C18 columns are very stable and any one column will give retention times reproducible within 0.2%.     

A general approach to nucleoside 3′- and 5′- monophosphates

Diallyloxyphosphorylation of nucleoside hydroxyls followed by palladium(0)-catalyzed deallylation provides a new, general method for the preparation of the 3′- and 5′-monophosphates.     

Thermal analysis of 5′-deoxy-5′-iodo-2′,3′-O-isopropylidene-5-fluorouridine

The melting temperature, melting enthalpy, and specific heat capacities (C _p) of 5′-deoxy-5′-iodo-2′,3′-O-isopropylidene-5-fluorouridine (DIOIPF) were measured using DSC-60 Differential Scanning Calorimetry. The melting temperature and melting enthalpy were obtained to be 453.80 K and 33.22 J g^?1, respectively. The relationship between the specific heat capacity and temperature was obtained to be C _p/J g^?1 K^?1 = 2.0261 – 0.0096T + 2 × 10^?5 T ² at the temperature range from 320.15 to 430.15 K. The thermal decomposition process was studied by the TG–DTA analyzer. The results showed that the thermal decomposition temperature of DIOIPF was above 487.84 K, and the decomposition process can be divided into three stages: the first stage is the decomposition of impurities, the mass loss in the second stage may be the sublimation of iodine and thermal decomposition process of the side-group C₄H₂O₂N₂F, and the third stage may be the thermal decomposition process of both the groups –CH₃ and –CH₂OCH₂–. The obtained thermodynamic basic data are helpful for exploiting new synthetic method, engineering design, and commercial process of DIOIPF.     

Ternary complexes in solution. Comparison of the coordination tendency of some biologically important zwitterionic buffers toward the binary complexes of Cu(II) and adenosine 5′-mono-, 5′-di-, and 5′-triphosphate

Summary Potentiometric equilibrium measurements have been made at 25.0±0.1 °C and ionic strengthI=0.1 mol dm^–3 KNO₃ for the interaction of adenosine 5-mono-, 5-di-, and 5-triphosphate (AMP,ADP andATP) and Cu(II) with biologically important secondary ligand zwitterionic buffers (N,N-bis-(2-hydroxyethyl)-2-aminoethanesulphonic acid (BES), N-tris-(hydroxymethyl)-methyl-2-aminoethanesulphonic acid (TES), N,N-bis-(2-hydroxyethyl)-glycine (Bicine) andtris-(hydroxymethyl)-methylaminopropane sulphonic acid (TAPS)) in a 1:1:1 ratio and the formation of various 1:1:1 mixed ligand complex species inferred from the potentiometricpH titration curves. Initial estimates of the formation constants of the resulting species and the acid dissociation constants ofAMP,ADP,ATP, and secondary ligands have been refined with the SUPERQUAD computer program. Negative and positive logK values were obtained for the ternary systems studied. In some Cu(II) ternary systems studied the interligand interactions or some cooperativity between the coordinate ligands, possibly H bond formation, has been found to be most effective in deciding the stability of the ternary complexes formed in solution. Stabilities of mixed ligand complexes increase in the orderAMP<ADP<ATP. The trend in stability constants of the mixed-ligand complexes of the title zwitterionic buffer ligands is found to beTAPS>Bicine>TES>BES.

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Ternäre Komplexe in Lösung. Vergleich der Koordinationstendenz einiger biologisch wichtiger zwitterionischer Puffer an binäre Komplexe von Cu(II) und Adenosin-5-mono-, -5-di- und-5-triphosphat

Zusammenfassung Die Wechselwirkungen zwischen Adenosin-5-mono, -5-di- und-5-triphosphat (AMP,ADP undATP), Cu(II) und biologisch wichtigen zwitterionischen Puffern mit Sekundärligandeigenschaften (N,N-bis-(2-Hydroxyethyl)-2-aminoethansulfonsäure (BES), N-tris-(Hydroxymethyl)-methyl-2-aminoethansulfonsäure (TES), N,N-bis-(2-Hydroxyethyl)-glycin (Bicin) undtris-(Hydroxymethyl)-methylaminopropansulfonsäure (TAPS) im Verhältnis 1:1:1 wurden mittels potentiometrischer Gleichgewichtsmessungen bei 25.0±0.1 °C undI=0.1 mol·dm^–3 KNO₃ untersucht. Die Titrationskurven lassen auf verschiedene Komplexe mit gemischten Liganden im Verhältnis von 1:1:1 schließen. Erste Abschätzungen der Bildungskonstanten der entstehenden Produkte und der Dissoziationskonstanten vonAMP,ADP,ATP und der Sekundärliganden wurden mit HIlfe des Programms SUPERQUAD verfeinert. Für die untersuchten ternären Systeme wurden negative und positive Werte für logK erhalten. In einigen der Cu(II)-Komplexe wird die Stabilität des ternären Systems in Lösung hauptsächlich durch Wechselwirkungen zwischen den Liganden, möglicherweise durch die Ausbildung von Wasserstoffbrückenbindungen, bestimmt. Die Stabilität der Komplexe steigt in der ReihenfolgeAMP<ADP<ATP. Der entsprechende Trend der Stabilitätskonstanten bei den gemischten Komplexen mit den im Titel genannten zwitterionischen Puffern lautetTAPS>Bicin>TES>BES.

     

Induction of senescence in cancer cells by 5′-Aza-2′-deoxycytidine: Bioinformatics and experimental insights to its targets

5′-Aza-2′-deoxycytidine (5-Aza-dC) is a demethylating drug that causes genome-wide hypomethylation resulting in the expression of several tumor suppressor genes causing growth arrest of cancer cells. Cancer is well established as a multifactorial disease and requires multi-module therapeutics. Search for new drugs and their approval by FDA takes a long time. Keeping this in view, research on new functions of FDA-approved anticancer drugs is desired to expand the list of multi-module functioning drugs for cancer therapy. In this study, we conducted an analysis for new functions of 5-Aza-dC by applying bio-chemo-informatics approach. The potential of 5-Aza-dC bioactivity was analyzed by PASS online and Molinspiration. Target proteins were predicted by SuperPred. The protein networks and biological processes were analyzed by Biological Networks using Gene Ontology tool, BINGO, based on BIOGRID database. Interactions between 5-Aza-dC and targeted proteins were examined by Autodoc Vina integrated into pyrx software. Induction of p53 by 5-Aza-dC was tested in vitro using cancer cells. Bioinformatics analyses predicted that 5-Aza-dC functions as a p53 inducer, radiosensitizer, and inhibitor of some enzymes. It was predicted to target proteins including MDM2, POLA1, POLB, and CXCR4 that are involved in the induction of DNA damage response and p53-HDM2-p21 signaling. In this study, we provide experimental evidence showing HDM2 is one of the targets of 5-AZA-dC leading to activation of p53 pathway and growth arrest of cells. Furthermore, we found that the combinatorial treatment of 5-AZA-dC with three other drugs caused drug resistance. We discuss that 5-Aza-dC-induced senescence is a multi-module drug that controls cell proliferation phenotype not only by proteins but also by noncoding miRNAs. Further studies are warranted to dissect these mechanisms and establish 5-Aza-dC as an effective multi-module anticancer reagent.     

Synthesis of 5′-deoxy-5′-[18F]fluoro-adenosine by Radiofluorination of 5′-deoxy-5′-haloadenosine Derivatives

5-Deoxy-5-[¹⁸F]fluoro-adenosine was synthesised by nucleophilic radiofluorination reactions of 5-deoxy-5-haloadenosines. The homogeneous isotope exchange in 5-deoxy-5-fluoro-adenosine was also investigated. The conversion of these reactions was found to be rather low and depends on the strength of the halogen-carbon bond: 0.248% for chloride-, 0.488% for bromide- and 1.070% for iodide-derivative; there was no reaction observed in the case of fluoro-compound.     

Concise Synthesis and Cellular Evaluation of 3′-Formyl-4′,6′-dihydroxy-2′-methoxy-5′-methylchalcone (FMC) and Its Analogues

3′-Formyl-4′,6′-dihydroxy-2′-methoxy-5′-methylchalcone (FMC) was a natural product isolated from Cleistocalyx operculatus. A four-step synthetic strategy toward FMC and its four analogues (1b–1e) was first developed. All compounds were synthesized from commercially available 2,4,6-trihydroxyacetophenone; formylation at 3′ position under Vilsmeier–Haack conditions was followed by the introduction of a methyl group at 5′ position. The key step of selective methylation at 2′ position was achieved by trimethylsilyldiazomethane (TMSCHN₂). Then substituted aromatic aldehydes were condensed through Claisen–Schmidt reaction in the presence of potassium hydroxide. All structures were confirmed by ¹H NMR, ¹³C NMR, and high-resolution mass spectra. FMC and analogues were screened for their antiproliferative activity.     

Synthesis of 2′-5′,3′-5′ linked triadenylates

2′-5′,3′-5′ Linked triadenylates have been synthesized by direct bisadenylylation of adenosine 2′ and 3′ hydroxyls with an adenosine 5′-phosphorochloridite followed by oxidation.     

A Repressor in 5′-UTR of hKv4.3 Gene

Introduction Therearemanyionchannelssuchassodiumchan nels,calciumchannels,chlorinechannels,potassium channelsandsoon,inexcitingtissues.Theseion channelsdeterminetheelectrophysiologicalcharacterof cellsortissues.Whentheexcitabilityoftissuesisal tered,theac…     

Chemical 5′-phosphorylation of oligonucleotidesvaluable in automated DNA synthesis

A new method has been developed for the chemical 5′-phosphorylation ofoligonucleotides starting from easily available phosphorous-III compounds using phosphate protecting groups which can be cleaved off via β-elimination. The hydrophobic 2-(p-nitrophenyl)-ethyl group, at the phosphodiester level can serve as a purification handle in reversed phase HPLC. Moreover, the procedure has been adapted to automated DNA synthesis.