Catalysis of accurate poly(C)-directed synthesis of 3'-5'-linked oligoguanylates by Zn2+

Zn²⁺ is an efficient catalyst for the oligomerization of guanosine 5′-phosphorimidazolide on a polycytidylic acid template. Up to 75% of the input ImpG² is converted to oligomers with a mean chain length up to 10. Material longer than (pG)₃₀ can be detected. The oligomeric products are predominantly 3′-5′-linked.If poly(C) is incubated with ImpG and an equimolar quantity of the 5′-phosphorimidazolides of adenosine, uridine or cytidine, in the presence of Zn²⁺, ImpG is incorporated at least 200 times more efficiently than “incorrect” nucleotides.     

DFT study of geometrical and vibrational features of a 3′,5′-deoxydisugar-monophosphate (dDSMP) DNA model in the presence of counterions and solvent

The B3LYP/6–31++G* theoretical level was used to study the influence of various hexahydrated monovalent (Li⁺, Na⁺, K⁺) and divalent (Mg²⁺) metal counterions in interaction with the charged PO₂^? group, on the geometrical and vibrational characteristics of the DNA fragments of 3′,5′-dDSMP, represented by four conformers (g⁺g⁺, g⁺t, g^?g^? and g^?t). All complexes were optimized through two solvation models [the explicit model (6H₂O) and the hybrid model (6H₂O/Continuum)]. The results obtained established that, in the hybrid model, counterions (Li⁺, Na⁺, K⁺, Mg²⁺) always remain in the bisector plane of the O1–P–O2 angle. When these counterions are explicitly hydrated, the smallest counterions (Li⁺, Na⁺) deviate from the bisector plane, while the largest counterions (K⁺ and Mg²⁺) always remain in the same plane. On the other hand, the present calculations reveal that the g⁺g⁺ conformer is the most stable in the presence of monovalent counterions, while conformers g⁺t and g^?t are the most stable in the presence of the divalent counterion Mg²⁺. Finally, the hybrid solvation model seems to be in better agreement with the available crystallographic and spectroscopic (Raman) experiments than the explicit model. Indeed, the six conformational torsions of the C4′-C3′-O3′-PO^?₂-O5′-C5′-C4′ segment of all complexes of the g^?g^? conformer in 6H₂O/Continuum remain similar to the available experimental data of A- and B-DNA forms. The calculated wavenumbers of the g⁺g⁺ conformer in the presence of the monovalent counterion and of g^?t conformer in presence of the divalent counterion in the hybrid model are in good agreement with the Raman experimental data of A- and B-DNA forms. In addition, the maximum deviation between the calculated wavenumbers in the 6H₂O/Continuum for the g⁺g⁺ conformer and experimental value measured in an aqueous solution of the DMP-Na⁺ complex, is <1.07% for the PO₂^? (asymmetric and symmetric) stretching modes and <2.03% for the O5′-C5′ and O3′-C3′ stretching modes.

Open image in new window

Graphical abstract dDSMP-(OO)^? Mg²⁺/6W/Continuum

     

MOLECULAR MODELLING OF 2′-OH MEDIATED HYDROGEN BONDING IN RIBONUCLEOS(T)IDES BY NMR CONSTRAINED AM1 AND MMX CALCULATIONS

The intra- and intermolecular hydrogen bonding (ΔGº_298K ≈ 2, kcal mol^?1) of 2′-OH in nucleos(t)ides has been reported by the temperature- and concentration-dependent NMR study in conjunction with dihedral dependence of the NMR derived both endo (³ J _H,H)- and exocyclic (³ JH,OH) coupling constants, nOe contacts and lineshape analyses of hydroxyl protons for EtpA (1), 3′-dA (2), rA (3), 2′-dA (4) [Fig. 1] in DMSO-d ₆ at 500 MHz.

MOLECULAR MODELLING OF 2′-OH MEDIATED HYDROGEN BONDING IN RIBONUCLEOS(T)IDES BY NMR CONSTRAINED AM1 AND MMX CALCULATIONS

All authors

Parag Acharya, Irina Velikian, Sandipta Acharya & Jyoti Chattopadhyaya

https://doi.org/10.1081/NCN-100002521

Published online:

07 February 2007

Figure 1. The schematic representation of the bias of the dymanic two-state pseudorotational equilibrium between the North-type (N, C2′-exo -C3′-endo) and the South-type (S, C3′-exo-C2′-endo) [3a] Thibaudeau, C. and Chattopadhyaya, J. 1999. Stereoelectronic Effects in Nucleosides and Nucleotides and their Structural Implications Sweden: (ISBN 91-506-1351-0), Department of Bioorganic Chemistry, Uppsala University Press (fax: +4618554495). For review see: and references therein [Google Scholar] pseudorotamers of the sugar moeity for EtpA (1), 3′-dA (2), rA (3), 2′-dA (4) and torsion (Φ) around C2′/3′-O bond viz. Φ₁ = Φ_{H2′?C2′?O?H} and Φ₂ = Φ_{H3′?C3′?O?H} except in 1 where the torsion across C3′-O3′ bond is actually ?^? [C4′-C3′-O3′-P].     

4.

Partial purification and biochemical characterization of alkaline 5'-phosphodiesterase from barley malt sprouts   总被引：1，自引：0，他引：1  

Beluhan S  Karmelić I  Novak S  Marić V 《Biotechnology letters》2003,25(13):1099-1103

An alkaline 5-phosphodiesterase (5-PDE) from barley (Hordeum distichum) malt sprouts was partially purified by thermal treatment and acetone precipitation to diminish phosphomonoesterase (PME) activity. 5-PDE was purified 40-fold to a specific activity of 30 U mg^–1 protein with a final yield of about 32%. With synthetic substrate, the enzyme had an optimum pH of 8.9, maximum activity at 70 °C over 10 min, and a Km of 0.26 mM. The partially purified enzyme was activated by 10 mM Mg²⁺ up to 168% of the original activity, while Zn²⁺, Mn²⁺ and Cu²⁺ ions, chelating agent (EDTA) and NaN₃ (1–10 mM), and 5-ribonucleotides (1–5 mM) were inhibitory. Final enzyme preparation was stable over 8 d at 4 °C), at 70 °C for up to 120 min and without loss of activity over 90 d at –18 °C.     

5.

Stereochemistry of binding of thiophosphate analogs of ATP and ADP to carbamate kinase, glutamine synthetase, and carbamoyl-phosphate synthetase   总被引：1，自引：0，他引：1  

R P Pillai  F M Raushel  J J Villafranca 《Archives of biochemistry and biophysics》1980,199(1):7-15

Thiophosphate analogs of adenine nucleotides were used to establish the absolute stereochemistry of nucleotide substrates in the reactions of carbamate kinase (Streptococcus faecalis), unadenylylated glutamine synthetase (Escherichia coli), and carbamoyl-phosphate synthetase (E. coli). ³¹P NMR was used to determine that carbamate kinase uses the B isomer of Ado-5′-(2-thioPPP) in the presence of Mg²⁺. The stereospecificity of the reaction with carbamate kinase was not reversed by Cd²⁺ suggesting that the metal ion does not bind to the β-phosphoryl group or that both Mg²⁺ and Cd²⁺ bind to the sulfur atom. Carbamate kinase uses both A and B isomers of Ado-5′-(1-thioPP) with Mg²⁺ and Cd²⁺. We have previously reported that carbamoyl-phosphate synthetase uses the A isomer of Ado-5′-(2-thioPPP) at both ATP sites with Mg²⁺ (Raushel et al., 1978J. Biol. Chem.253, 6627). Current experiments show that the stereospecificity is reversed by Cd^2? and that both A and B isomers are used when Zn²⁺ is present. With Ado-5′-(1-thioPPP), the B isomer is used with Mg²⁺, the A isomer with Cd²⁺, and both isomers with Zn²⁺. Neither carbamate kinase nor carbamoyl-phosphate synthetase utilized Co(III)(NH₃)₄ATP as a substrate and thus we can only speculate that the Δ chelate ring configuration is the chelate structure utilized by carbamoyl-phosphate synthetase (based on the analogy between thiophosphate-ATP analogs and Co³⁺-ATP analogs utilized by hexokinase (E. K. Jaffe, and M. Cohn, 1978Biochemistry17, 652). If the sulfur of the β-phosphoryl of Ado-5′-(2-thioPPP) binds to the metal ion with carbamate kinase, then the Δ chelate ring is also used in this enzyme that catalyzes one of the steps in the overall reaction catalyzed by carbamoyl-phosphate synthetase. Glutamine synthetase reacts with the B isomer of both Ado-5′-(2-thioPPP) and Ado-5′-(1-thioPPP) in the presence of Mg²⁺. When Co²⁺ is used with this enzyme the A and B isomers of both thio-ATP compounds are substrates. Co(III)(NH₃)₄ATP is not a substrate for glutamine synthetase. Glutamine synthetase is therefore different from the two previously mentioned enzymes in that it used the opposite A ring configuration for the metal-ATP chelate.     

6.

Oligomerization reactions of ribonucleotides: The reaction of the 5′-phosphorimidazolide of nucleosides on montmorillonite and other minerals     

James P. Ferris  Gözen Ertem 《Origins of life and evolution of the biosphere》1992,22(6):369-381

The reaction of ImpA in the presence of Na⁺-montmorillonite 22A or Na⁺-Volclay in aqueous, pH 8 solution gives a 50–60% yield of dimers and trimers (pA)₂ and (pA)₃. The ratio of 3,5-phosphodiester bond formation is twice as great as 2,5-bond formation. The reaction requires the presence of Mg²⁺ and is inhibited by 0.4 M imidazole. N-methylimidazole enhances the rate of the reaction but does not cause major changes in yield or product composition. Higher yields were obtained when Li⁺- or Ca²⁺-montmorillonites were used in place of Na⁺-montmorillonite. Little or no phosphodiester bond formation was observed with Mg²⁺- or Al³⁺-montmorillonite. Montmorillonites other than 22A and Volclay exhibited little or no catalysis. In addition, little or no catalysis was exhibited in ferrugenous smectite, nontronite, allophane, imogolite or sepiolite. Oligomers were also formed by the reaction of ImpG, 2-methylImpG, ImpC and ImpU in the presence of Na⁺-montmorillonite. The pyrimidine nucleotides gave significantly lower yields of oligomers.     

7.

Conformation and Antiherpes Activity of 3′- and 5′-Azido and Amino Analogs of 5-Methoxymethyl-2′-Deoxyuridine     

Guy Tourigny  Allan L. Stuart  Irena Ekiel  Philip J. Aduma  Sagar V. Gupta 《Nucleosides, nucleotides & nucleic acids》2013,32(7):1189-1200

Abstract

The molecular conformations of 3′- and 5′-azido and amino derivatives of 5-methoxymethyl-2′-deoxyuridine, 1, were investigated by nmr. The glycosidic conformation of 5-methoxymethyl-5′-amino-2′,5′-dideoxy-uridine, 5 had a considerable population of the syn form. The 5′-derivatives show a preference for the S conformation of the furanose ring as in 1. In contrast, the 3′-derivatives show preference for the N conformation. For 5-methoxymethyl-3′-amino-2′,3′-dideoxyuridine, 3, the shift towards the N state is pH dependent. The preferred conformation for the exocyclic (C4′,C5′) side chain is g⁺ for all compounds except 5 which has a strong preference for the t rotamer (79%). Compounds 1, 3 and 5 inhibited growth of HSV-1 by 50% at 2, 18 and 70 μg/ml respectively, whereas 2 and 4 were not active up to 256 μg/ml (highest concentration tested). The compounds were not cytotoxic up to 3,000 μM.     

8.

Synthesis and in vitro Biological Evaluation of Novel Thymidine Analogs Containing 1H-1,2,3-Triazolyl, 1H-Tetrazolyl,and 2H-Tetrazolyl Fragments     

Elena A. Popova  Gayane K. Ovsepyan  Aleksandra V. Protas  Elena B. Erkhitueva  Marina K. Kukhanova  Yana L. Yesaulkova 《Nucleosides, nucleotides & nucleic acids》2013,32(10):713-731

Abstract

3′-Azidothymidine (AZT) reacts with 1-propargyl-5-R-1H- and 2-propargyl-5-R-2H-tetrazoles (R?=?H, Me, CH₂COOEt, CH₂CON(CH₃)₂, Ph, 2-CH₃-C₆H₄, or 4-NO₂-C₆H₄) via the Cu(I)-catalyzed asymmetric [3?+?2] cycloaddition to give 3′-modified thymidine analogs incorporating 1H-1,2,3-triazolyl, 1H-, and 2H-tetrazolyl fragments in 41–76% yield. The structures of the obtained compounds have been elucidated by means of HRESI⁺-MS, ¹H and ¹³ Ostrovskii, V. A.; Popova, E. A.; Trifonov, R. E. Developments in Tetrazole Chemistry (2009–16). Advances in heterocyclic chemistry. 2017, 123, 2–62.[Web of Science ®] , [Google Scholar]C{¹H} NMR, and single crystal X-ray diffraction {for 3′-[4-(1H-5-N,N-dimethylaminocarbonylmethyltetrazol-1-yl)-1H-1,2,3-triazol-1-yl]thymidine 10d}. In vitro biological evaluation of the prepared compounds has been performed; they have exhibited low activity against phenotypic HIV-1_899A. Moderate anti-influenza activity against influenza virus A/Puerto Rico/8/34 (H1N1) strain has been observed in the cases of 3′-(4-(1H-tetrazol-1-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 10a (IC₅₀ 39.6?μg/mL), 3′-(4-(2H-5-ethoxycarbonyltetrazol-2-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 11c (IC₅₀ 31.6?μg/mL), and 3′-(4-(2H-5-(4-nitrophenyl)-tetrazol-2-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 11g (IC₅₀ 46.4?μg/mL). The tested compounds possess very low cytotoxicity towards MDCK and MT4 cells as well as tumor human cervical carcinoma HeLa and promyelocytic leukemia HL-60 cells.     

9.

Template-directed synthesis of oligoguanylates in the presence of metal ions   总被引：2，自引：0，他引：2  

J H van Roode  L E Orgel 《Journal of molecular biology》1980,144(4):579-585

We have studied the condensation reaction of ImpG² on a poly(C) template, in the presence of various metal ions. With Mg²⁺ as co-catalyst we confirmed that Pb²⁺ and Zn²⁺ are effective catalysts. A catalytic effect was also observed for Bi³⁺, Sb³⁺ and Mn²⁺. Bi³⁺ and Sn²⁺, like Pb²⁺, favored the formation of 2′-5′ linkages. With Mn²⁺ a rather complex mixture of oligomers is formed, some of which contain pyrophosphate linkages. None of the metal ions investigated behaved like Zn²⁺ in favoring the formation of the naturally occurring 3′-5′ linkages.     

10.

Heteropolynucleotides as templates for non-enzymatic polymerizations   总被引：1，自引：0，他引：1  

J. Ninio  L. E. Orgel 《Journal of molecular evolution》1978,12(2):91-99

Summary We have studied a number of condensation reactions involving ImpU, ImpT, ImpC, ImpA, ImpG, ImpUpG and ImpCpA as activated nucleotide donors and a variety of homo- and hetero-polynucleotides as templates. We did not obtain any evidence of a template effect with ImpU and ImpT, but observed some condensation of ImpC with GpG on appropriate templates. ImpA and ImpG take part in a number of more or less efficient template-directed reactions, as do ImpUpG and ImpCpA.Our results suggest that, on the primitive Earth, pyrimidine nucleotides could most easily have been incorporated into polymers as constituents of short oligomers, which contained one or more purine nucleotide. The linkage of the product depends strongly on the nature of the substrates; the percentage of the natural 3-5-linkage was, in some cases, less than 10% and, in others, as high as 70%. Wobble-pairing was often very effective in promoting condensations, suggesting that transition mutations would have been very frequent in prebiotic polynucleotide replication.Abbreviations and Conventions U uridine - T thymidine - C cytidine - A adenosine - G guanosine - pN nucleoside-5-phosphate - Np a mixture of 2- and 3-phosphates of a nucleoside - pNp a mixture of the 2-5-diphosphate and 3-5-diphosphate of a nucleoside - N₁ ² pN₂ a 2-5-linked dinucleoside monophosphate - N₁ ³ pN₂ a 3-5-linked dinucleoside monophosphate - N⁵ ppN a pyrophosphate derived from a nucleoside-5-phosphate. ImpN and ImpN₁pN₂ are 5-phosphorimidazolides of nucleosides and 3-5-linked dinucleoside monophosphates, respectively - poly(N) a homopolynucleotide - poly (U₁ C₂ A₄ G₃) a random copolymer derived from a substrate mixture containing U, C, A, G in ratio 1:2:4:3 - ODU optical density units measured at 260 nm     

11.

Isolation and properties of 5′-mononucleotidase from a membrane fraction of bovine cerebral cortex     

Ryo Tanaka  Hiroyuki Morita  Akira Teruya 《生物化学与生物物理学报:生物膜》1973,298(4):842-849

     

12.

Oligonucleotide formation catalyzed by divalent metal ions. The uniqueness of the ribosyl system     

Hiroaki Sawai 《Journal of molecular evolution》1988,27(3):181-186

Summary Polymerization of various nucleoside-5-phosphorimidazolides has been conducted in neutral aqueous solution using divalent metal ions as catalysts. Oligonucleotide formation took place from each of the ribonucleoside-5-phosphorimidazolides, ImpC, ImpU, ImpA, ImpG, and ImpI. The yields and distributions of the resulting oligonucleotides varied depending on the difference of the nucleic acid base and the metal ions used. The catalytic effect of divalent metal ions on the formation of oligocytidylates occurred in the following order: Pb²⁺>Zn²⁺>Co²⁺, Mn²⁺>Cd²⁺>Cu²⁺>Ni²⁺>Ca²⁺, Mg²⁺, none >Hg²⁺. The order changes slightly for other types of oligoribonucleotide formation. Oligoribonucleotides up to hexamers were obtained in 35–55% overall yield, when Pb²⁺ ion was used as a catalyst. Zn²⁺ ions yielded oligoribonucleotides up to tetramers in 10–20% overall yield. The resulting oligonucleotides contained mainly 2–5 internucleotide linkages.Little or no oligonucleotide was obtained from nucleoside-5-phosphorimidazolides modified in the sugars, Imp(3-dA), Imp(2-dA), Imp(Ara), Imp(Aris), and Imp(Nep). The results indicate that a ribosyl system is required for the metal ion-catalyzed synthesis of oligonucleotides. Abbreviations. EDTA, ethylenediaminetetraacetic acid; Versenol,N-hydroxyethylethylenediaminetriacetic acid; Tris, tris-(hydroxymethyl)aminomethane; pN (N is A, C, G, U, I, 3-dA, 2-dA, AraA, Aris, or Nep), nucleoside-5-phosphate; Np, nucleoside-2(3)-phosphate; I, inosine; 3-dA, 3-deoxyadenosine; 2-dA, 2-deoxyadenosine; AraA, arabinosyladenine; Aris, aristeromycin; Nep, neplanocin A; ImpN, nucleoside-5-phosphorimidazolide; NppN, P₁,P₂-dinucleoside-5,5-pyrophosphate; (pN)_n (n=2, 3, ...), oligomers of pN, numbers given between a nucleoside and a phosphate indicate the type of internucleotide linkage, e.g., pC₂ p₅C is 5-phosphorylcytidyl-(2–5)-cytidine; , cyclic dimers of pN; BAP, bacterial alkaline phosphatase; N.Pl, nuclease Pl; VPDase, venom phosphodiesterase; HPLC, high pressure liquid chromatography     

13.

THE NMR CONFORMATION STUDY OF THE COMPLEXES OF DEOXYCYTIDINE KINASE (dCK) AND 2′-DEOXYCYTIDINE/2′-DEOXYADENOSINE     

《Nucleosides, nucleotides & nucleic acids》2013,32(4-7):1225-1228

The structures of the bound ¹³C/²H double-labelled 2′(R/S), 5′(R/S)-²H₂-1′,2′,3′,4′,5′-¹³C₅-2′-deoxyadenosine and the corresponding 2′-deoxycytidine moieties in the complexes with human deoxycytidine kinase (dCK) have been characterized for the first time by the solution NMR spectroscopy, using Transferred Dipole-Dipole Cross-correlated Relaxation and Transferred nOe experiments. It has been shown that the ligand adopts a South-type sugar conformation when bound to dCK.     

14.

DNA binding,photocleavage, antimicrobial and cytotoxic properties of Ru(II) polypyridyl complexes containing BOPIP ligand, (BOPIP = {2-(4-(benzyloxy) phenyl)-1H-imidazo [4,5-f] [1,2]phenanthroline})     

Srinivas Gopu  Vuradi Ravi kumar  Kotha Laxma Reddy  Putta Venkat Reddy 《Nucleosides, nucleotides & nucleic acids》2019,38(5):349-373

A novel ligand BOPIP (BOPIP?=?{2-(4-(benzyloxy)phenyl)-1H-imidazo[4,5-f][1,10]phenanthroline}) and its mononuclear Ru(II) polypyridyl complexes [Ru(phen)₂ BOPIP]²⁺(1) (phen?=?1,10-Phenanthrolene), [Ru(bpy)₂ BOPIP]²⁺(2) (bpy?=?2,2′ bipyridyl), [Ru(dmb)₂ BOPIP]²⁺(3) (dmb?=?4, 4′ -dimethyl 2, 2′ -bipyridine), [Ru(Hdpa)₂ BOPIP]²⁺(4) (Hdpa?=?2,2′dipyridylamine) have been synthesized successfully and characterized by elemental analysis, UV-vis, IR, ¹H, ¹³ Gill, M. R.; Garcia-Lara, J.; Foster, S. J.; Smythe, C.; Battaglia, G.; Thomas, J. A. A Ruthenium(II) polypyridyl Complex for Direct Imaging of DNA Structure in Living Cells. Nat. Chem. 2009, 1, 662–667.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]C-NMR, and ESI-MS Spectroscopy. The interaction of these complexes with CT-DNA was studied using absorption, emission techniques, viscosity measurements and molecular docking studies. The docking study also supports the binding ability of complexes obtained through the absorption and emission techniques. These studies reveal that the Four Ru(II) polypyridyl complexes bind to DNA predominantly by intercalation. The Antimicrobial activity and cytotoxicity of these complexes are also reported.     

15.

Association of polymorphic markers of chemokine genes,their receptors,and <Emphasis Type="Italic">CD14</Emphasis> gene with coronary atherosclerosis     

T. R. Nasibullin  L. F. Yagafarova  I. R. Yagafarov  Ya. R. Timasheva  V. V. Erdman  I. A. Tuktarova  O. E. Mustafina 《Russian Journal of Genetics》2016,52(8):860-867

Atherosclerosis represents an inflammatory response to the disturbance of the endothelial layer in the arterial bloodstream. In the present study, an analysis of associations of polymorphic markers for the genes controlling synthesis of proteins involved in atherosclerosis pathogenesis in coronary atherosclerosis (CA) patients (217 subjects) and in a control group (250 subjects) was conducted. The following genes were examined: rs991804 (CCL2 gene), rs1126579 (CXCR2 gene), rs4074 (CXCL1 gene), rs4073 (CXCL8 gene), rs333 (CCR5 gene), rs2471859 (CXCR4 gene), rs1801157 (CXCL12 gene), and rs2569190 (CD14 gene). Using the Monte Carlo and Markov chain (APSampler) method, allele/genotype combinations associated with both low and high CA risk were revealed. The most important findings included the following: CXCR4*T/T + CCL2*C + CCR5*I/I (P_perm = 1 × 10^–6, OR = 0.44, 95% CI 0.3–0.63), CXCR2*C + CD14*C + CXCL12*G + CCL2*C + CCR5*D (P_perm = 4 × 10^–6, OR = 5.78, 95% CI 2.34–14.28), CD14*C + CCL2*C/C + CCR5*D (P_perm = 6.3 × 10^–6, OR = 5.81, 95% CI 2.17–15.56), CXCL8*A + CXCR2*C + CD14*T + CXCR4*C (P_perm = 0.01, OR = 3.21, 95% CI 1.63–6.31).     

16.

Temperature-dependent modification of divalent cation flux in the rat parotid gland basolateral membrane     

T. P. Lockwich  I. H. Kim  I. S. Ambudkar 《The Journal of membrane biology》1994,141(3):289-296

Divalent cation (Mn²⁺, Ca²⁺) entry into rat parotid acinar cells is stimulated by the release of Ca²⁺ from the internal agonist-sensitive Ca²⁺ pool via a mechanism which is not yet defined. This study examines the effect of temperature on Mn²⁺ influx into internal Ca²⁺ pool-depleted acini (depl-acini, as a result of carbachol stimulation of acini in a Ca²⁺-free medium for 10 min) and passive ⁴⁵Ca²⁺ influx in basolateral membrane vesicles (BLMV). Mn²⁺ entry into deplacini was decreased when the incubation temperature was lowered from 37 to 4°C. At 4°C, Mn²⁺ entry appeared to be inactivated since it was not increased by raising extracellular [Mn²⁺] from 50 m up to 1 mm. The Arrhenius plot of depletion-activated Mn²⁺ entry between 37 and 8°C was nonlinear, with a change in the slope at about 21°C. The activation energy (Ea) increased from 10 kcal/mol (Q₁₀=1.7) at 21–37°C to 25 kcal/mol (Q₁₀=3.0) at 21-8°C. Under the same conditions, Mn²⁺ entry into basal (unstimulated) cells and ionomycin (5 m) permeabilized depl-acini exhibit a linear decrease, with E _a of 7.8 kcal/mol (Q₁₀=1.5) and 6.2 kcal/mol (Q₁₀ < 1.5), respectively. These data suggest that depletion-activated Mn²⁺ entry into parotid acini is regulated by a mechanism which is strongly temperature dependent and distinct from Mn²⁺ entry into unstimulated acini.As in intact acini, Ca²⁺ influx into BLMV was decreased (by 40%) when the temperature of the reaction medium was lowered from 37 to 4°C. Kinetic analysis of the initial rates of Ca²⁺ influx in BLMV at 37°C demonstrated the presence of two Ca²⁺ influx components: a saturable component, with K _Ca =279 ± 43 m, V_max = 3.38 ± 0.4 nmol Ca²⁺/mg protein/min, and an apparently unsaturable component. At 4°C, there was no significant change in the affinity of the saturable component, but V_max decreased by 61% to 1.3 ± 0.4 nmol Ca²⁺/mg protein/min. There was no detectable change in the unsaturable component. When BLMV were treated with DCCD (5 mm) or trypsin (1100, enzyme to membrane) for 30 min at 37°C there was a 40% decrease in Ca²⁺ influx. When BLMV were treated with DCCD or trypsin at 4°C and subsequently assayed for Ca²⁺ uptake at 37°C there was no significant loss of Ca²⁺ influx. These data suggest that the temperature sensitive high affinity Ca²⁺ flux component in BLMV is mediated by a protein which undergoes a modification at low temperatures, resulting in decreased Ca²⁺ transport.We thank Dr. Bruce Baum, Dr. Yukiharu Hiramatsu, Dr. Ofer Eidelman, and our other colleagues for their support during this work.     

17.

Limiting concentrations of activated mononucleotides necessary for poly(C)-directed elongation of oligoguanylates     

Anastassia Kanavarioti  Sherwood Chang  Diann J. Alberas 《Journal of molecular evolution》1990,31(6):462-469

Summary Selected imidazolide-activated nucleotides have been subjected to hydrolysis under conditions similar to those that favor their template-directed oligomerization. Rate constants of hydrolysis of the P–N bond in guanosine 5-monophosphate 2-methylimidazolide (2-MeImpG) and in guanosine 5-monophosphate imidazolide (ImpG), k_h, have been determined in the presence/absence of magnesium ion as a function of temperature and polycytidylate [poly(C)] concentration. Using the rate constant of hydrolysis of 2-MeImpG and the rate constant of elongation, i.e., the reaction of an oligoguanylate with 2-MeImpG in the presence of poly(C) acting as template, the limiting concentration of 2-MeImpG necessary for oligonucleotide elongation to compete with hydrolysis can be calculated. The limiting concentration is defined as the initial concentration of monomer that results in its equal consumption by hydrolysis and by elongation. These limiting concentrations of 2-MeImpG are found to be 1.7 mM at 37°C and 0.36 mM at 1°C. Boundary conditions in the form of limiting concentration of activated nucleotide may be used to evaluate a prebiotic model for chemical synthesis of biopolymers. For instance, the limiting concentration of monomer can be used as a basis of comparison among catalytic, but nonenzymatic, RNA-type systems.We also determined the rate constant of dimerization of 2-MeImpG, k₂=0.45±0.06 M^–1 h^–1 in the absence of poly(C), and 0.45±0.06k₂0.97±0.13 M^–1 h^–1 in its presence at 37°C and pH 7.95. This dimerization, as well as the trimerization of 2-MeImpG, which represent the first steps in the oligomerization reaction, are markedly slower than the elongation of longer oligoguanylates, (pG) _n n>6. This means that in the presence of low concentrations of 2-MeImpG (1.7 mM) the system directs the elongation of longer oligomers more efficiently than the formation of short oligomers such as dimers and trimers. These results will be discussed as a possible example of chemical selection in template-directed reactions of nucleotides.     

18.

Improved Synthesis of 2′-Fluoro-2′-Deoxyadenosine and Synthesis and Carbon-13 NMR Spectrum of Its 3′,5′-Cyclic Phosphate Derivative1     

Seiichi Uesugi  Toshinori Kaneyasu  Jitsuhiro Matsugi  Morio Ikehara 《Nucleosides, nucleotides & nucleic acids》2013,32(4):373-385

Abstract

Some improvements were made on synthetic method for 2′-fluoro-2′-deoxyadenosine (11). Thus 11 was obtained in an overall yield of 9.3% starting from adenosine. 2′-Fluoro-2′-deoxyadenosine 3′,5′-cyclic phosphate (13), an analogue of cAMP, was synthesized from 11. The carbon-13 NMR spectrum was measured. The sugar carbon signals can be unambiguously assigned since the C1′ C2′ and C3′ have different ¹³C-¹⁹F coupling constants. Comparison of the data with those of other 3′,5′-cyclic phosphate derivatives confirms the assignments of C3′ and C4′ signals previously proposed by us.     

19.

Non-mycorrhizal uptake of amino acids by roots of the alpine sedge Kobresia myosuroides: implications for the alpine nitrogen cycle   总被引：5，自引：0，他引：5  

Theodore K. Raab  David A. Lipson  Russell K. Monson 《Oecologia》1996,108(3):488-494

Non-mycorrhizal plants of the alpine sedge, Kobresia myosuroides, take up the amino acid glycine from nutrient solutions at greater rates than NO _inf3 ^sup- or NH _inf4 ^sup+ . The amino acids glutamate and proline were also taken up at high rates. Total plant biomass was twice as high after 4 months of growth on glycine, compared to NH₄NO₃, with significant increases in both root and leaf biomass. By taking advantage of differences in the ¹³C signature of air in the growth chamber and the glycine used for growth, a two-member mixing model was used to estimate that a significant amount of the glycine was taken up as intact molecules, enough to contribute 16% of the total carbon assimilation over a 4-month growing period. Glycine uptake was inhibited when roots were exposed to N₂ in place of air, and when the protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP) was added to the root solution. From these results it is concluded that glycine uptake occurs through active transport. Glycine uptake exhibited a Q₁₀ of 2.0 over the temperature range 5–15° C, with relatively high rates maintained at the lowest temperature measured (5° C). Roots of Kobreasia were not capable of taking up NH _inf4 ^sup+ at measureable rates. To our knowledge, this is the first report of a plant whose non-mycorrhizal roots cannot take up NH _inf4 ^sup+ . Measurements of three N fractions (NO _inf3 ^sup- , NH _inf4 ^sup+ , and total amino acids) in the soil pore water were made over two growing seasons in two Kobresia dry meadows using microlysimeters. At the West Knoll site, which is characterized by soils with average amounts of organic matter, the dominant forms of N in the soil pore water were NO _inf3 ^sup- and NH _inf4 ^sup+ (0–450 mol L^-1). Amino acid concentrations were generally less than 20 mol L^-1 at this site. At the East Knoll site, which is characterized by soils with higher than average amounts of organic matter, amino acids were generally present at higher concentrations (17–100 mol L^-1), compared to NO _inf3 ^sup- and NH _inf4 ^sup+ . The most abundant amino acids were glycine (10–100 mol L^-1), glutamate (5–70 mol L^-1), and late in the season cystein (5–15 mol L^-1). The results demonstrate that this sedge, which dominates dry meadow communities in many alpine ecosystems, is capable of taking up intact amino acids as a principal N source, and has access to high amino acid concentrations in certain alpine soils. Such uptake of organic N may accommodate plant N demands in the face of slow alpine N mineralization rates due to cold soil temperatures.     

20.

Conformational Properties of Nucleotide-Based Template-Competitive HIV-1 Reverse Transcriptase Inhibitors: Analysis of Enzyme Binding Modes     

《Nucleosides, nucleotides & nucleic acids》2013,32(3):283-297

     

Partial purification and biochemical characterization of alkaline 5'-phosphodiesterase from barley malt sprouts

An alkaline 5-phosphodiesterase (5-PDE) from barley (Hordeum distichum) malt sprouts was partially purified by thermal treatment and acetone precipitation to diminish phosphomonoesterase (PME) activity. 5-PDE was purified 40-fold to a specific activity of 30 U mg^–1 protein with a final yield of about 32%. With synthetic substrate, the enzyme had an optimum pH of 8.9, maximum activity at 70 °C over 10 min, and a Km of 0.26 mM. The partially purified enzyme was activated by 10 mM Mg²⁺ up to 168% of the original activity, while Zn²⁺, Mn²⁺ and Cu²⁺ ions, chelating agent (EDTA) and NaN₃ (1–10 mM), and 5-ribonucleotides (1–5 mM) were inhibitory. Final enzyme preparation was stable over 8 d at 4 °C), at 70 °C for up to 120 min and without loss of activity over 90 d at –18 °C.     

Stereochemistry of binding of thiophosphate analogs of ATP and ADP to carbamate kinase, glutamine synthetase, and carbamoyl-phosphate synthetase

Thiophosphate analogs of adenine nucleotides were used to establish the absolute stereochemistry of nucleotide substrates in the reactions of carbamate kinase (Streptococcus faecalis), unadenylylated glutamine synthetase (Escherichia coli), and carbamoyl-phosphate synthetase (E. coli). ³¹P NMR was used to determine that carbamate kinase uses the B isomer of Ado-5′-(2-thioPPP) in the presence of Mg²⁺. The stereospecificity of the reaction with carbamate kinase was not reversed by Cd²⁺ suggesting that the metal ion does not bind to the β-phosphoryl group or that both Mg²⁺ and Cd²⁺ bind to the sulfur atom. Carbamate kinase uses both A and B isomers of Ado-5′-(1-thioPP) with Mg²⁺ and Cd²⁺. We have previously reported that carbamoyl-phosphate synthetase uses the A isomer of Ado-5′-(2-thioPPP) at both ATP sites with Mg²⁺ (Raushel et al., 1978J. Biol. Chem.253, 6627). Current experiments show that the stereospecificity is reversed by Cd^2? and that both A and B isomers are used when Zn²⁺ is present. With Ado-5′-(1-thioPPP), the B isomer is used with Mg²⁺, the A isomer with Cd²⁺, and both isomers with Zn²⁺. Neither carbamate kinase nor carbamoyl-phosphate synthetase utilized Co(III)(NH₃)₄ATP as a substrate and thus we can only speculate that the Δ chelate ring configuration is the chelate structure utilized by carbamoyl-phosphate synthetase (based on the analogy between thiophosphate-ATP analogs and Co³⁺-ATP analogs utilized by hexokinase (E. K. Jaffe, and M. Cohn, 1978Biochemistry17, 652). If the sulfur of the β-phosphoryl of Ado-5′-(2-thioPPP) binds to the metal ion with carbamate kinase, then the Δ chelate ring is also used in this enzyme that catalyzes one of the steps in the overall reaction catalyzed by carbamoyl-phosphate synthetase. Glutamine synthetase reacts with the B isomer of both Ado-5′-(2-thioPPP) and Ado-5′-(1-thioPPP) in the presence of Mg²⁺. When Co²⁺ is used with this enzyme the A and B isomers of both thio-ATP compounds are substrates. Co(III)(NH₃)₄ATP is not a substrate for glutamine synthetase. Glutamine synthetase is therefore different from the two previously mentioned enzymes in that it used the opposite A ring configuration for the metal-ATP chelate.     

Oligomerization reactions of ribonucleotides: The reaction of the 5′-phosphorimidazolide of nucleosides on montmorillonite and other minerals

The reaction of ImpA in the presence of Na⁺-montmorillonite 22A or Na⁺-Volclay in aqueous, pH 8 solution gives a 50–60% yield of dimers and trimers (pA)₂ and (pA)₃. The ratio of 3,5-phosphodiester bond formation is twice as great as 2,5-bond formation. The reaction requires the presence of Mg²⁺ and is inhibited by 0.4 M imidazole. N-methylimidazole enhances the rate of the reaction but does not cause major changes in yield or product composition. Higher yields were obtained when Li⁺- or Ca²⁺-montmorillonites were used in place of Na⁺-montmorillonite. Little or no phosphodiester bond formation was observed with Mg²⁺- or Al³⁺-montmorillonite. Montmorillonites other than 22A and Volclay exhibited little or no catalysis. In addition, little or no catalysis was exhibited in ferrugenous smectite, nontronite, allophane, imogolite or sepiolite. Oligomers were also formed by the reaction of ImpG, 2-methylImpG, ImpC and ImpU in the presence of Na⁺-montmorillonite. The pyrimidine nucleotides gave significantly lower yields of oligomers.     

Conformation and Antiherpes Activity of 3′- and 5′-Azido and Amino Analogs of 5-Methoxymethyl-2′-Deoxyuridine

Abstract

The molecular conformations of 3′- and 5′-azido and amino derivatives of 5-methoxymethyl-2′-deoxyuridine, 1, were investigated by nmr. The glycosidic conformation of 5-methoxymethyl-5′-amino-2′,5′-dideoxy-uridine, 5 had a considerable population of the syn form. The 5′-derivatives show a preference for the S conformation of the furanose ring as in 1. In contrast, the 3′-derivatives show preference for the N conformation. For 5-methoxymethyl-3′-amino-2′,3′-dideoxyuridine, 3, the shift towards the N state is pH dependent. The preferred conformation for the exocyclic (C4′,C5′) side chain is g⁺ for all compounds except 5 which has a strong preference for the t rotamer (79%). Compounds 1, 3 and 5 inhibited growth of HSV-1 by 50% at 2, 18 and 70 μg/ml respectively, whereas 2 and 4 were not active up to 256 μg/ml (highest concentration tested). The compounds were not cytotoxic up to 3,000 μM.     

Synthesis and in vitro Biological Evaluation of Novel Thymidine Analogs Containing 1H-1,2,3-Triazolyl, 1H-Tetrazolyl,and 2H-Tetrazolyl Fragments

Abstract

3′-Azidothymidine (AZT) reacts with 1-propargyl-5-R-1H- and 2-propargyl-5-R-2H-tetrazoles (R?=?H, Me, CH₂COOEt, CH₂CON(CH₃)₂, Ph, 2-CH₃-C₆H₄, or 4-NO₂-C₆H₄) via the Cu(I)-catalyzed asymmetric [3?+?2] cycloaddition to give 3′-modified thymidine analogs incorporating 1H-1,2,3-triazolyl, 1H-, and 2H-tetrazolyl fragments in 41–76% yield. The structures of the obtained compounds have been elucidated by means of HRESI⁺-MS, ¹H and ¹³ Ostrovskii, V. A.; Popova, E. A.; Trifonov, R. E. Developments in Tetrazole Chemistry (2009–16). Advances in heterocyclic chemistry. 2017, 123, 2–62.[Web of Science ®] , [Google Scholar]C{¹H} NMR, and single crystal X-ray diffraction {for 3′-[4-(1H-5-N,N-dimethylaminocarbonylmethyltetrazol-1-yl)-1H-1,2,3-triazol-1-yl]thymidine 10d}. In vitro biological evaluation of the prepared compounds has been performed; they have exhibited low activity against phenotypic HIV-1_899A. Moderate anti-influenza activity against influenza virus A/Puerto Rico/8/34 (H1N1) strain has been observed in the cases of 3′-(4-(1H-tetrazol-1-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 10a (IC₅₀ 39.6?μg/mL), 3′-(4-(2H-5-ethoxycarbonyltetrazol-2-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 11c (IC₅₀ 31.6?μg/mL), and 3′-(4-(2H-5-(4-nitrophenyl)-tetrazol-2-ylmethyl)-1H-1,2,3-triazol-1-yl)thymidine 11g (IC₅₀ 46.4?μg/mL). The tested compounds possess very low cytotoxicity towards MDCK and MT4 cells as well as tumor human cervical carcinoma HeLa and promyelocytic leukemia HL-60 cells.     

Template-directed synthesis of oligoguanylates in the presence of metal ions

We have studied the condensation reaction of ImpG² on a poly(C) template, in the presence of various metal ions. With Mg²⁺ as co-catalyst we confirmed that Pb²⁺ and Zn²⁺ are effective catalysts. A catalytic effect was also observed for Bi³⁺, Sb³⁺ and Mn²⁺. Bi³⁺ and Sn²⁺, like Pb²⁺, favored the formation of 2′-5′ linkages. With Mn²⁺ a rather complex mixture of oligomers is formed, some of which contain pyrophosphate linkages. None of the metal ions investigated behaved like Zn²⁺ in favoring the formation of the naturally occurring 3′-5′ linkages.     

Heteropolynucleotides as templates for non-enzymatic polymerizations

Summary We have studied a number of condensation reactions involving ImpU, ImpT, ImpC, ImpA, ImpG, ImpUpG and ImpCpA as activated nucleotide donors and a variety of homo- and hetero-polynucleotides as templates. We did not obtain any evidence of a template effect with ImpU and ImpT, but observed some condensation of ImpC with GpG on appropriate templates. ImpA and ImpG take part in a number of more or less efficient template-directed reactions, as do ImpUpG and ImpCpA.Our results suggest that, on the primitive Earth, pyrimidine nucleotides could most easily have been incorporated into polymers as constituents of short oligomers, which contained one or more purine nucleotide. The linkage of the product depends strongly on the nature of the substrates; the percentage of the natural 3-5-linkage was, in some cases, less than 10% and, in others, as high as 70%. Wobble-pairing was often very effective in promoting condensations, suggesting that transition mutations would have been very frequent in prebiotic polynucleotide replication.Abbreviations and Conventions U uridine - T thymidine - C cytidine - A adenosine - G guanosine - pN nucleoside-5-phosphate - Np a mixture of 2- and 3-phosphates of a nucleoside - pNp a mixture of the 2-5-diphosphate and 3-5-diphosphate of a nucleoside - N₁ ² pN₂ a 2-5-linked dinucleoside monophosphate - N₁ ³ pN₂ a 3-5-linked dinucleoside monophosphate - N⁵ ppN a pyrophosphate derived from a nucleoside-5-phosphate. ImpN and ImpN₁pN₂ are 5-phosphorimidazolides of nucleosides and 3-5-linked dinucleoside monophosphates, respectively - poly(N) a homopolynucleotide - poly (U₁ C₂ A₄ G₃) a random copolymer derived from a substrate mixture containing U, C, A, G in ratio 1:2:4:3 - ODU optical density units measured at 260 nm     

Oligonucleotide formation catalyzed by divalent metal ions. The uniqueness of the ribosyl system

Summary Polymerization of various nucleoside-5-phosphorimidazolides has been conducted in neutral aqueous solution using divalent metal ions as catalysts. Oligonucleotide formation took place from each of the ribonucleoside-5-phosphorimidazolides, ImpC, ImpU, ImpA, ImpG, and ImpI. The yields and distributions of the resulting oligonucleotides varied depending on the difference of the nucleic acid base and the metal ions used. The catalytic effect of divalent metal ions on the formation of oligocytidylates occurred in the following order: Pb²⁺>Zn²⁺>Co²⁺, Mn²⁺>Cd²⁺>Cu²⁺>Ni²⁺>Ca²⁺, Mg²⁺, none >Hg²⁺. The order changes slightly for other types of oligoribonucleotide formation. Oligoribonucleotides up to hexamers were obtained in 35–55% overall yield, when Pb²⁺ ion was used as a catalyst. Zn²⁺ ions yielded oligoribonucleotides up to tetramers in 10–20% overall yield. The resulting oligonucleotides contained mainly 2–5 internucleotide linkages.Little or no oligonucleotide was obtained from nucleoside-5-phosphorimidazolides modified in the sugars, Imp(3-dA), Imp(2-dA), Imp(Ara), Imp(Aris), and Imp(Nep). The results indicate that a ribosyl system is required for the metal ion-catalyzed synthesis of oligonucleotides. Abbreviations. EDTA, ethylenediaminetetraacetic acid; Versenol,N-hydroxyethylethylenediaminetriacetic acid; Tris, tris-(hydroxymethyl)aminomethane; pN (N is A, C, G, U, I, 3-dA, 2-dA, AraA, Aris, or Nep), nucleoside-5-phosphate; Np, nucleoside-2(3)-phosphate; I, inosine; 3-dA, 3-deoxyadenosine; 2-dA, 2-deoxyadenosine; AraA, arabinosyladenine; Aris, aristeromycin; Nep, neplanocin A; ImpN, nucleoside-5-phosphorimidazolide; NppN, P₁,P₂-dinucleoside-5,5-pyrophosphate; (pN)_n (n=2, 3, ...), oligomers of pN, numbers given between a nucleoside and a phosphate indicate the type of internucleotide linkage, e.g., pC₂ p₅C is 5-phosphorylcytidyl-(2–5)-cytidine; , cyclic dimers of pN; BAP, bacterial alkaline phosphatase; N.Pl, nuclease Pl; VPDase, venom phosphodiesterase; HPLC, high pressure liquid chromatography     

THE NMR CONFORMATION STUDY OF THE COMPLEXES OF DEOXYCYTIDINE KINASE (dCK) AND 2′-DEOXYCYTIDINE/2′-DEOXYADENOSINE

The structures of the bound ¹³C/²H double-labelled 2′(R/S), 5′(R/S)-²H₂-1′,2′,3′,4′,5′-¹³C₅-2′-deoxyadenosine and the corresponding 2′-deoxycytidine moieties in the complexes with human deoxycytidine kinase (dCK) have been characterized for the first time by the solution NMR spectroscopy, using Transferred Dipole-Dipole Cross-correlated Relaxation and Transferred nOe experiments. It has been shown that the ligand adopts a South-type sugar conformation when bound to dCK.     

DNA binding,photocleavage, antimicrobial and cytotoxic properties of Ru(II) polypyridyl complexes containing BOPIP ligand, (BOPIP = {2-(4-(benzyloxy) phenyl)-1H-imidazo [4,5-f] [1,2]phenanthroline})

A novel ligand BOPIP (BOPIP?=?{2-(4-(benzyloxy)phenyl)-1H-imidazo[4,5-f][1,10]phenanthroline}) and its mononuclear Ru(II) polypyridyl complexes [Ru(phen)₂ BOPIP]²⁺(1) (phen?=?1,10-Phenanthrolene), [Ru(bpy)₂ BOPIP]²⁺(2) (bpy?=?2,2′ bipyridyl), [Ru(dmb)₂ BOPIP]²⁺(3) (dmb?=?4, 4′ -dimethyl 2, 2′ -bipyridine), [Ru(Hdpa)₂ BOPIP]²⁺(4) (Hdpa?=?2,2′dipyridylamine) have been synthesized successfully and characterized by elemental analysis, UV-vis, IR, ¹H, ¹³ Gill, M. R.; Garcia-Lara, J.; Foster, S. J.; Smythe, C.; Battaglia, G.; Thomas, J. A. A Ruthenium(II) polypyridyl Complex for Direct Imaging of DNA Structure in Living Cells. Nat. Chem. 2009, 1, 662–667.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]C-NMR, and ESI-MS Spectroscopy. The interaction of these complexes with CT-DNA was studied using absorption, emission techniques, viscosity measurements and molecular docking studies. The docking study also supports the binding ability of complexes obtained through the absorption and emission techniques. These studies reveal that the Four Ru(II) polypyridyl complexes bind to DNA predominantly by intercalation. The Antimicrobial activity and cytotoxicity of these complexes are also reported.     

Association of polymorphic markers of chemokine genes,their receptors,and <Emphasis Type="Italic">CD14</Emphasis> gene with coronary atherosclerosis

Atherosclerosis represents an inflammatory response to the disturbance of the endothelial layer in the arterial bloodstream. In the present study, an analysis of associations of polymorphic markers for the genes controlling synthesis of proteins involved in atherosclerosis pathogenesis in coronary atherosclerosis (CA) patients (217 subjects) and in a control group (250 subjects) was conducted. The following genes were examined: rs991804 (CCL2 gene), rs1126579 (CXCR2 gene), rs4074 (CXCL1 gene), rs4073 (CXCL8 gene), rs333 (CCR5 gene), rs2471859 (CXCR4 gene), rs1801157 (CXCL12 gene), and rs2569190 (CD14 gene). Using the Monte Carlo and Markov chain (APSampler) method, allele/genotype combinations associated with both low and high CA risk were revealed. The most important findings included the following: CXCR4*T/T + CCL2*C + CCR5*I/I (P_perm = 1 × 10^–6, OR = 0.44, 95% CI 0.3–0.63), CXCR2*C + CD14*C + CXCL12*G + CCL2*C + CCR5*D (P_perm = 4 × 10^–6, OR = 5.78, 95% CI 2.34–14.28), CD14*C + CCL2*C/C + CCR5*D (P_perm = 6.3 × 10^–6, OR = 5.81, 95% CI 2.17–15.56), CXCL8*A + CXCR2*C + CD14*T + CXCR4*C (P_perm = 0.01, OR = 3.21, 95% CI 1.63–6.31).     

Temperature-dependent modification of divalent cation flux in the rat parotid gland basolateral membrane

Divalent cation (Mn²⁺, Ca²⁺) entry into rat parotid acinar cells is stimulated by the release of Ca²⁺ from the internal agonist-sensitive Ca²⁺ pool via a mechanism which is not yet defined. This study examines the effect of temperature on Mn²⁺ influx into internal Ca²⁺ pool-depleted acini (depl-acini, as a result of carbachol stimulation of acini in a Ca²⁺-free medium for 10 min) and passive ⁴⁵Ca²⁺ influx in basolateral membrane vesicles (BLMV). Mn²⁺ entry into deplacini was decreased when the incubation temperature was lowered from 37 to 4°C. At 4°C, Mn²⁺ entry appeared to be inactivated since it was not increased by raising extracellular [Mn²⁺] from 50 m up to 1 mm. The Arrhenius plot of depletion-activated Mn²⁺ entry between 37 and 8°C was nonlinear, with a change in the slope at about 21°C. The activation energy (Ea) increased from 10 kcal/mol (Q₁₀=1.7) at 21–37°C to 25 kcal/mol (Q₁₀=3.0) at 21-8°C. Under the same conditions, Mn²⁺ entry into basal (unstimulated) cells and ionomycin (5 m) permeabilized depl-acini exhibit a linear decrease, with E _a of 7.8 kcal/mol (Q₁₀=1.5) and 6.2 kcal/mol (Q₁₀ < 1.5), respectively. These data suggest that depletion-activated Mn²⁺ entry into parotid acini is regulated by a mechanism which is strongly temperature dependent and distinct from Mn²⁺ entry into unstimulated acini.As in intact acini, Ca²⁺ influx into BLMV was decreased (by 40%) when the temperature of the reaction medium was lowered from 37 to 4°C. Kinetic analysis of the initial rates of Ca²⁺ influx in BLMV at 37°C demonstrated the presence of two Ca²⁺ influx components: a saturable component, with K _Ca =279 ± 43 m, V_max = 3.38 ± 0.4 nmol Ca²⁺/mg protein/min, and an apparently unsaturable component. At 4°C, there was no significant change in the affinity of the saturable component, but V_max decreased by 61% to 1.3 ± 0.4 nmol Ca²⁺/mg protein/min. There was no detectable change in the unsaturable component. When BLMV were treated with DCCD (5 mm) or trypsin (1100, enzyme to membrane) for 30 min at 37°C there was a 40% decrease in Ca²⁺ influx. When BLMV were treated with DCCD or trypsin at 4°C and subsequently assayed for Ca²⁺ uptake at 37°C there was no significant loss of Ca²⁺ influx. These data suggest that the temperature sensitive high affinity Ca²⁺ flux component in BLMV is mediated by a protein which undergoes a modification at low temperatures, resulting in decreased Ca²⁺ transport.We thank Dr. Bruce Baum, Dr. Yukiharu Hiramatsu, Dr. Ofer Eidelman, and our other colleagues for their support during this work.     

Limiting concentrations of activated mononucleotides necessary for poly(C)-directed elongation of oligoguanylates

Summary Selected imidazolide-activated nucleotides have been subjected to hydrolysis under conditions similar to those that favor their template-directed oligomerization. Rate constants of hydrolysis of the P–N bond in guanosine 5-monophosphate 2-methylimidazolide (2-MeImpG) and in guanosine 5-monophosphate imidazolide (ImpG), k_h, have been determined in the presence/absence of magnesium ion as a function of temperature and polycytidylate [poly(C)] concentration. Using the rate constant of hydrolysis of 2-MeImpG and the rate constant of elongation, i.e., the reaction of an oligoguanylate with 2-MeImpG in the presence of poly(C) acting as template, the limiting concentration of 2-MeImpG necessary for oligonucleotide elongation to compete with hydrolysis can be calculated. The limiting concentration is defined as the initial concentration of monomer that results in its equal consumption by hydrolysis and by elongation. These limiting concentrations of 2-MeImpG are found to be 1.7 mM at 37°C and 0.36 mM at 1°C. Boundary conditions in the form of limiting concentration of activated nucleotide may be used to evaluate a prebiotic model for chemical synthesis of biopolymers. For instance, the limiting concentration of monomer can be used as a basis of comparison among catalytic, but nonenzymatic, RNA-type systems.We also determined the rate constant of dimerization of 2-MeImpG, k₂=0.45±0.06 M^–1 h^–1 in the absence of poly(C), and 0.45±0.06k₂0.97±0.13 M^–1 h^–1 in its presence at 37°C and pH 7.95. This dimerization, as well as the trimerization of 2-MeImpG, which represent the first steps in the oligomerization reaction, are markedly slower than the elongation of longer oligoguanylates, (pG) _n n>6. This means that in the presence of low concentrations of 2-MeImpG (1.7 mM) the system directs the elongation of longer oligomers more efficiently than the formation of short oligomers such as dimers and trimers. These results will be discussed as a possible example of chemical selection in template-directed reactions of nucleotides.     

Improved Synthesis of 2′-Fluoro-2′-Deoxyadenosine and Synthesis and Carbon-13 NMR Spectrum of Its 3′,5′-Cyclic Phosphate Derivative1

Abstract

Some improvements were made on synthetic method for 2′-fluoro-2′-deoxyadenosine (11). Thus 11 was obtained in an overall yield of 9.3% starting from adenosine. 2′-Fluoro-2′-deoxyadenosine 3′,5′-cyclic phosphate (13), an analogue of cAMP, was synthesized from 11. The carbon-13 NMR spectrum was measured. The sugar carbon signals can be unambiguously assigned since the C1′ C2′ and C3′ have different ¹³C-¹⁹F coupling constants. Comparison of the data with those of other 3′,5′-cyclic phosphate derivatives confirms the assignments of C3′ and C4′ signals previously proposed by us.     

Non-mycorrhizal uptake of amino acids by roots of the alpine sedge Kobresia myosuroides: implications for the alpine nitrogen cycle

Non-mycorrhizal plants of the alpine sedge, Kobresia myosuroides, take up the amino acid glycine from nutrient solutions at greater rates than NO _inf3 ^sup- or NH _inf4 ^sup+ . The amino acids glutamate and proline were also taken up at high rates. Total plant biomass was twice as high after 4 months of growth on glycine, compared to NH₄NO₃, with significant increases in both root and leaf biomass. By taking advantage of differences in the ¹³C signature of air in the growth chamber and the glycine used for growth, a two-member mixing model was used to estimate that a significant amount of the glycine was taken up as intact molecules, enough to contribute 16% of the total carbon assimilation over a 4-month growing period. Glycine uptake was inhibited when roots were exposed to N₂ in place of air, and when the protonophore carbonyl cyanide m-chlorophenylhydrazone (CCCP) was added to the root solution. From these results it is concluded that glycine uptake occurs through active transport. Glycine uptake exhibited a Q₁₀ of 2.0 over the temperature range 5–15° C, with relatively high rates maintained at the lowest temperature measured (5° C). Roots of Kobreasia were not capable of taking up NH _inf4 ^sup+ at measureable rates. To our knowledge, this is the first report of a plant whose non-mycorrhizal roots cannot take up NH _inf4 ^sup+ . Measurements of three N fractions (NO _inf3 ^sup- , NH _inf4 ^sup+ , and total amino acids) in the soil pore water were made over two growing seasons in two Kobresia dry meadows using microlysimeters. At the West Knoll site, which is characterized by soils with average amounts of organic matter, the dominant forms of N in the soil pore water were NO _inf3 ^sup- and NH _inf4 ^sup+ (0–450 mol L^-1). Amino acid concentrations were generally less than 20 mol L^-1 at this site. At the East Knoll site, which is characterized by soils with higher than average amounts of organic matter, amino acids were generally present at higher concentrations (17–100 mol L^-1), compared to NO _inf3 ^sup- and NH _inf4 ^sup+ . The most abundant amino acids were glycine (10–100 mol L^-1), glutamate (5–70 mol L^-1), and late in the season cystein (5–15 mol L^-1). The results demonstrate that this sedge, which dominates dry meadow communities in many alpine ecosystems, is capable of taking up intact amino acids as a principal N source, and has access to high amino acid concentrations in certain alpine soils. Such uptake of organic N may accommodate plant N demands in the face of slow alpine N mineralization rates due to cold soil temperatures.