NMR and FT-IR conformational studies of 8-substituted guanine nucleosides and nucleotides and their metal adducts and cancer

NMR and FT-IR Studies of the conformational changes of guanosine and guanosine-5′-monophosphate upon substitution of the H8 of guanine by a heavy, large atom, such as bromine, are presented. The conformational forms, syn, anti, C2′-endo and C3′-endo and gg, gt and tg rotamers of the above molecules are compared to those of their metal (Mg²⁺ and P^t2+) adducts, where the metal is fixed to the N7 nitrogen atom of guanine. The antitumor activity of cisplatin is discussed with relation to the conformational form and the effect of cisplatin is compared to the effects of the Mg²⁺ ion and carcinogens.     

Enzymic analysis of cyclic 3', 5'-AMP in mammalian tissues and urine

The details are presented for the analysis of 3′,5′ cyclic adenosine monophosphate (3′5′CAMP) in milligram amounts of mammalian tissues (muscles, liver, brain, and kidney) and in microliter samples of urine. An examination of the sources of difficulty and how they are effectively handled is also included. In the determination of tissue 3′5′CAMP the cyclic nucleotide is first separated from 5′-nucleoside mono-, di-, and triphosphates by cellulose thin-layer chromatography following Ba(OH)₂-ZnSO₄ precipitation of extracts. After quantitative recovery 3′,5′CAMP is converted to 5′ AMP and subsequently to ATP by the actions of phosphodiesterase, myokinase, and pyruvate kinase. Enzymic cycling with the hexokinase-pyruvate kinase system is then used to produce a proportional concentration of G-6-P equivalent to several thousand fold the ATP concentration and the G-6-P measured fluorometrically. Cyclic adenylate in urine samples is determined directly without prior separation from any urinary components. Examples are presented of the analytical procedures applied to the measurement of 3′5′CAMP levels in tissues and urine after various experimental treatments. These include the effects of epinephrine in skeletal muscle in vitro and in vivo, of adrenalectomy and hydrocortisone in liver, of ischemia in brain, and of hypertonic infusion on urinary excretion of 3′5′CAMP.     

FT-IR spectroscopic evidence of sugar ring conformational changes in GpC and CpG on platination and intercalation

An FT-IR spectroscopic study concerning changes in the conformation of sugar in the dinucleotides; GpC and CpG, on platination and intercalation is presented. The results are compared with the FT-IR spectral data of 5′-CMP, 5′-GMP, 3′-GMP and their metal adducts. The spectra of free GpC, free CpG, proflavine-GpC, proflavine-CpG, and cis-[Pt(NH₃)₂(GpC)₂]²⁺ exhibit the diagnostic band at 800 cm⁻¹ which was assigned to a sugar phosphate vibrational mode and diagnostic of C3′-endo sugar pucker. In the case of 9-aminoacridine-GpC and cis-[Pt(NH₃)₂(CpG]⁺ the diagnostic bands of the C2′-endo and C3′-endo conformations are observed at 810–820 cm⁻¹ and near 800 cm⁻¹ respectively. The results are in good agreement with X-ray data. The infrared diagnostic bands are important for distinguishing the sugar pucker conformational changes.     

Some observations on the minor products of the reaction of 2,2′-dilithiobiphenyl with mercuric chloride

Reaction of 2,2′-dilithiobiphenyl (formed from 2,2′-diiodobiphenyl and lithium in diethyl ether) with mercuric chloride gives the ortho-biphenylenemercury trimer (I) with 2,2′-bis(iodomercury)biphenyl (II) as an isolatable intermediate. The mass spectrum of impure 2,2′-bis(iodomercury)biphenyl at high sensitivity shows ion clusters which are interpreted as the ions of a polyphenyl iodomercury complex [Hg₃(C₆H₄)₄I₂] (III) which is identified as a further intermediate in the production of ortho-biphenylenemercury trimer and several iodomercury cations of general formula [Hg_xI_y]⁺, where x, y = 1, 2, 3. A fragmentation scheme is presented to account for these unusual iodomercury cations. Reaction mechanisms are presented to account for the production of II and III.     

A simple method of the preparation of 2′-O-Methyladenosine Methylation of adenosine with methyl iodide in anhydrous alkaline medium

A simple and effective method of the methylation on the 2′-O position of adenosine is described. Adenosine is treated with CH₃I in an anhydrous alkaline medium at 0°C for 4 h. The major products of this reaction are monomethylated adenosine at either the 2′-O or 3′-O position (total of 64%) and the side products are dimethylated adenosine (2′,3′-O-dimethyladenosi, 21%, and N⁶-2′-O-dimethyladenosine, 11%). The ratio of 2′-O- and 3′-O-methyladenosine has been found to be 8 to 1. Therefore, this reaction preferentially favors the synthesis of 2′-O-methyladenosine. The monomethylated adenosine is isolated from reaction mixture by a silica gel column chromatography. Then the pure 2′-O-methyladenosine can be separated by crystallization in ethanol from the mixture of 2′-O and 3′-O-methylated isomers. The overall yield of 2′-O-methyladenosine is 42%.     

Effective gene silencing activity of prodrug-type 2′-O-methyldithiomethyl siRNA compared with non-prodrug-type 2′-O-methyl siRNA

Small interfering RNAs (siRNAs) are an active agent to induce gene silencing and they have been studied for becoming a biological and therapeutic tool. Various 2′-O-modified RNAs have been extensively studied to improve the nuclease resistance. However, the 2′-O-modified siRNA activities were often decreased by modification, since the bulky 2′-O-modifications inhibit to form a RNA-induced silencing complex (RISC). We developed novel prodrug-type 2′-O-methyldithiomethyl (MDTM) siRNA, which is converted into natural siRNA in an intracellular reducing environment. Prodrug-type 2′-O-MDTM siRNAs modified at the 5′-end side including 5′-end nucleotide and the seed region of the antisense strand exhibited much stronger gene silencing effect than non-prodrug-type 2′-O-methyl (2′-O-Me) siRNAs. Furthermore, the resistances for nuclease digestion of siRNAs were actually enhanced by 2′-O-MDTM modifications. Our results indicate that 2′-O-MDTM modifications improve the stability of siRNA in serum and they are able to be introduced at any positions of siRNA.     

CD correlation of C-2′substituted monocyclic carotenoids

The scope and limitation of circular dichroism (CD) correlations of several C-2′ substituted monocyclic monochiral, homodichiral and heterodichiral carotenoids have been investigated, aiming at the assignment of absolute configuration at C-2′ by using the diester and 2′-β-d-tetraacetylglucosyl derivative of (2′R)-plectaniaxanthin and a synthetic chiral C₄₅-carotene as key references. The correlations are based on the additivity hypothesis, the conformational rule and a comparison of CD spectra, preferably conservative ones. Quantitative aspects of the conformational rule are considered. Substituent effects at C-2′ and C-1′ have been studied. Absolute configurations are suggested for (2′)-phleixanthophyll (3S,2′S)-2′-hydroxyflexixanthin, (3R,2′S)-myxoxanthophyll, (3S,2′S-4-ketomyxoxanthophyll (3R,2′S)-myxol-2′-O-methyl methylpentoside and (2R,2′S)-Cp. 473 from relevant CD correlations. The chiralities of (2′S)-4-ketophleixanthophyll and (2R,6R,2′S)-A.g. 471 are suggested from biogenetic considerations. A chemosystematic consideration of chirality and source is included.     

Flavonoid variation in the liverwort Conocephalum conicum: Evidence for geographic races

The flavonoids of 2 samples of Conocephalum conicum gametophyte tissue have been studied, one from U.S.A. and the other from Germany. Common to both samples were vicenin-2, lucenin-2, the 7-O-glucuronides of apigenin, chrysoeriol and luteolin and the previously unknown 7-O-glucuronide 4′-O-rhamnosides of apigenin, chrysoeriol and luteolin. Additionally the German sample contained the 7,4′-di-O-glucuronides of apigenin and luteolin and a new compound, apigenin 7-O-diglucuronide 4′-O-glucuronide. The North American sample contained, additionally, luteolin 7,3′-di-O-glucuronide, luteolin 7-O-glucuronide 3′,4′-di-O-rhamnoside (a new triglycoside) and 2 further derivatives of luteolin 7-O-glucuronide. Evidence is presented for the existence of geographic faces of C. conicum and for the qualitative invariability of the flavonoid patterns with changing season or environment.     

2′-Deoxy-1-methylpseudocytidine,a stable analog of 2′-deoxy-5-methylisocytidine

2′-Deoxy-5-methylisocytidine is widely used in assays to personalize the care of patients infected with HIV, hepatitis C, and other infectious agents. However, oligonucleotides that incorporate 2′-deoxy-5-methylisocytidine are expensive, because of its intrinsic chemical instability. We report here a C-glycoside analog that is more stable and, in oligonucleotides, pairs with 2′-deoxyisoguanosine, contributing to duplex stability about as much as a standard 2′-deoxycytidine and 2′-deoxyguanosine pair.     

Enzymatic epimerization of d-erythro-dihydroneopterin triphosphate to l-threo-dihydroneopterin triphosphate

An enzyme has been discovered in Escherichia coli that catalyzes the conversion of the triphosphate ester of 2-amino-4-hydroxy-6-(d-erythro-1′,2′,3′-trihydroxypropyl)-7,8-dihydropteridine, (i.e. d-erythro-dihydroneopterin triphosphate) to an epimer of this compound, l-threo-dihydroneopterin triphophate. The enzyme, which is here named “d-erythro-dihydroneopterin triphosphate 2′-epimerase,” needs a divalent cation (Mg²⁺ or Mn²⁺ is most effective) for maximal activity. Its molecular weight is estimated at 87 000–89 000. Little or no activity can be detected if either the monophosphate or the phosphate-free form of the substrate is incubated with the enzyme. Evidence is presented to establish that all three phosphate residues of the substrate are retained in the product and that the product is of the l-threo configuration.     

The determination of 2'-O-methylnucleosides in RNA

A rapid and sensitive procedure is described for determining the 2′-O-methylnucleoside methylnucleoside composition of an RNA sample. The RNA is enzymatically hydrolyzed to nucleosides and the 2′-O-methylnucleoside fraction is isolated by DEAE-cellulose (borate) column chromatography. Boric acid is removed as its methyl ester and the 2′-O-methylnucleosides are resolved by liquid chromatography in the presence of ethylene glycol. The sensitivity of this method is sufficient to distinguish RNA samples which differ only 2–3% in 2′-O-methylnucleoside composition.     

Chemical and physicochemical studies of lysylphosphatidylglycerol derivatives. Occurrence of a2' yields 3' lysyl migration

Syntheses of 1,2-didodecanoyl-sn-glycero-3-phosphoryl-1′-(3′-O-L-lysyl)-sn-glycerol (IV) and 1,2-didodecanoyl-sn-glycero-3-phosphoryl-1′-(2′-O-L-lysyl)-sn-glycerol (VIII) as well as 1,2-didodecanoyl-sn-glycerol-3-phosphoryl-1′-sn-glycerol (XII) are described. 2′- and 3′-lysylphosphatidylglycerol are obtained as pure isomers and can be distinguished spectroscopically (infrared, 100 and 300 MHZ NMR). By these criteria a migration of the lysyl group from the 2′ to the 3′ position of the glycerol occurs in the presence of a strong acid catalyst such as HCl. On the other hand, a weak acid such as acetic acid appears ineffective in inducing lysyl migration, even at very high concentrations.Spectroscopic analysis furthermore demonstrated that lysylphosphatidylglycerol extracted from the Staphylococcus aureus membrane, is a 3′-isomer.     

Synthesis and characterization of modified nucleotides in the 970 hairpin loop of Escherichia coli 16S ribosomal RNA

The synthesis of the 6-O-DPC-2-N-methylguanosine (m²G) nucleoside and the corresponding 5′-O-DMT-2′-O-TOM-protected 6-O-DPC-2-N-methylguanosine phosphoramidite is reported [DPC, diphenyl carbamoyl; DMT, 4,4′-dimethoxytrityl; TOM, [(triisopropylsilyl)oxy]methyl]. The availability of the phosphoramidite allows for syntheses of hairpin RNAs with site-selective incorporation of 2-N-methylguanosine modification. Four 18-nt hairpin RNA analogues representing the 970-loop region (helix 31 or h31; U960–A975) of Escherichia coli 16S rRNA were synthesized with and without modifications in the loop region. Subsequently, stabilities and conformations of the singly and doubly modified RNAs were examined and compared with the corresponding unmodified RNA. Thermodynamic parameters and circular dichroism spectra are presented for the four helix 31 RNA analogues. Surprisingly, methylations in the loop region of helix 31 slightly destabilize the hairpin, which may have subtle effects on ribosome function. The hairpin construct is suitable for future ligand-binding experiments.     

Synthesis and properties of 4′-C-aminoalkyl-2′-fluoro-modified RNA oligomers

Synthesis and properties of double-stranded RNAs (dsRNAs) and small interfering RNAs (siRNAs) containing 4′-C-aminoethyl-2′-deoxy-2′-fluorouridine are described. Thermal denaturation studies showed that incorporation of 4′-C-aminoethyl-2′-fluoro analog improved the thermal stabilities of dsRNAs and siRNAs compared to the corresponding 4′-C-aminoethyl-2′-O-methyl analog. siRNA incorporating eight 4′-aminoethyl-2′-fluoro analogs in the passenger strand showed sufficient RNAi activity at 1?nM concentration, which was similar to that of the unmodified siRNA. Furthermore, the siRNA containing the 4′-C-aminoethyl-2′-fluoro analog exhibited high stability in a buffer containing 20% bovine serum. Forty-eight percent of the siRNA remained intact after 48?h of incubation. Thus, modification of siRNAs by the 4′-C-aminoethyl-2′-fluoro analog would be useful for the development of therapeutic siRNA molecules.     

NMR study of dideoxynucleotides with anti-human immunodeficiency virus (HIV) activity

The molecular structures of 3′-azido-2′,3′-dideoxyribosylthymine 5′-triphosphate (AZTTP), 2′,3′-dideoxyribosylinosine 5′-triphosphate (ddITP), 3′-azido-2′,3′-dideoxyribosylthymine 5′-monophosphate (AZTMP) and 2′,3′-dideoxyribosyladenine 5′-monophosphate (ddAMP) have been studied by NMR to understand their anti-HIV activity. For ddAMP and ddITP, conformations are almost identical with their nucleoside analogues with sugar ring pucker equilibriating between C3′-endo (∼75%) and C2′-endo (∼25%). AZTMP and AZTTP on the other hand show significant variations in the conformational behaviour compared with 3′-azido-2′,3′-dideoxyribo-sylthymine (AZT). The sugar rings for these nucleotides have a much larger population of C2′-endo (∼75%) conformers, like those observed for natural 2′-deoxynucleosides and nucleotides. The major conformers around C5′-O5′, C4′-C5′ and the glycosidic bonds are the β^t, γ⁺ and anti, respectively.     

Apotrisporin-E: A new sesquiterpenoid isolated fromPhycomyces blakesleeanus andBlakeslea trispora

A new sesquiterpenoid has been identified in two species of Mucorales. It is apotrisporin-E: 2,4,4-trimethyl-3-[5′-hydroxyl-3′-methylpenta-(1′E,3′E)-dienyl]-(5S)-hydroxylcyclohex-2-enone. Nuclear Overhauser enhancement studies indicated that thecis-trans isomeric assignments at carbon atom 3′ based upon the NMR signals for the hydrogens on carbon atoms 1′ and 2′ were valid. The existence of apotrisporin-E implies that trisporin-D and trisporin-E, two putative pheromones, are made by the Mucorales.     

New flavans isolated from the leaves and stems of Cratylia mollis (Leguminosae)

Cratylia mollis Mart ex. Benth is a species belonging to the Leguminosae family that exists throughout South America, and it is one of the most abundant plants in northeastern Brazil, especially in the semiarid region. This plant is popularly known as “camaratu” and “camaratuba”, and the leaves and stems of this species are used as a substitute for cattle's alimentation during the dry season. The chemical investigation of the methanolic extract from leaves and stems of C. mollis led to the isolation of new flavans named 4,2′,3′-trihydroxy-4′-methoxy-6,7-(methylenedioxy) isoflavan, 7,2′-dihydroxy-6-methoxyflavan, 7,3′-dihydroxy-6,2′-dimethoxyflavan, 7-hydroxy-6-methoxyflavan, 2′-hydroxy-6,7-(methylenedioxy) flavan, 2R*,3S*-7,2′-dihydroxy-6-methoxy-flavan-3-ol, and 2R*,3S*-7,3-dihydroxy-6,2′-dimethoxyflavan-3-ol and an unusual flavan (11H-benzofuro[3,2-b][1] benzopyran-2-methoxy,3-hydroxy,5a,10a-dihydro) named (3R*,2R*)-3-O-2′-7-hydroxy-6-methoxyflavan. The structures of the new compounds were determined using spectroscopic methods.     

Control by bacteriophage T4 of two sequential phosphorylations of the alpha subunit of Escherichia coli RNA polymerase

The effect of 2′-O-methylation upon the base-stacking properties of dinucleoside monophosphates has been studied by circular dichroism measurements over the temperature range from ?20 °C to +80 °C at high and at low salt concentration of 13 2′-O-methyl derivatives in neutral aqueous solution. It is found that 2′-O methylation generally enhances the stacking propensity of dinucleoside monophosphates except for the dimers with adenine in the 3′-linked nucleoside, where the converse trend is observed. The influence of 2′-O-methylation upon the base-stacking property of a dimer correlates in part with the effect of a reduction in salt concentration, suggesting that the 2′-O-methyl group effects the stacking by displacing ions from the immediate environment of the dimer as well as by intramolecular steric effects. The dimers which exhibit an enhanced stacking due to the 2′-O-methylation are found in a larger than statistical abundance in yeast transfer RNA, whereas those showing a reduced stacking occur in minor abundance. These observations are discussed in relation to some current views on the role of modified nucleosides in the conformation of ribonucleic acids.