Synthesis of Polyaminooligonucleotides and Their Combinatorial Libraries

Abstract

A synthesis of phosphoramidites of 2′-deoxyadenosine and 2′-deoxyguanosine carrying a protected spermine moiety at N-6 and N-2 positions respectively is described. An approach to analyse properties of polyaminooligonucleotides using their synthetic combinatorial libraries is described and discussed. A synthesis of a polyaminooligonucleotide combinatorial library was carried out and the analysis of the library clearly showed that the presence of spermine moieties in oligodeoxyribonucleotides increases stability of their complexes.     

The Chemistry of C-Branched Spermine Tethered Oligo-DNAs and Their Properties in Forming Duplexes and Triplexes

Abstract

The first synthesis of 2′-, 5′- and centrally tethered C-branched spermine oligo-DNAs directly on the solid-support as well as their ability to stabilise DNA duplexes and triplexes are reported.     

Influence of Spermine on DNA Conformation in a Molecular Dynamics Trajectory of d(CGCGAATTCGCG)2: Major Groove Binding by One Spermine Molecule Delays the A→B Transition

Abstract

The effect of spermine on the A-DNA to B-DNA transition in d(CGCGAATTCGCG)₂ has been investigated by five A-start molecular dynamics simulations, using the Cornell et al. potential. In the absence of spermine an A→B transition is initiated immediately and the DNA becomes equidistant from the A- and B-forms at 200ps. In three DNA-spermine simulations, when a spermine is located across the major groove of A-DNA in one of three different initial locations, the time taken to reach equidistance from the A- and B-forms is delayed until 800, 950 or 1000ps. In each case the A-form appears to be temporarily stabilized by spermine's electrostatic interactions with phosphates on both sides of the major groove. The onset of the A→B transition can be correlated with the spermine losing contact with phosphates on one side of the groove and with A-like → B-like sugar pucker transitions in the vicinity of the spermine bridge. However in the fifth trajectory, in which the spermine initially threads from the major groove via the backbone into the minor groove, the B→A transition occurs rapidly once again and the DNA is equidistant between the A- and B-forms within 300ps. This indicates that the mere presence of spermine is insufficient to delay the transition and that major groove binding stabilizes A-DNA.     

Synthesis and Content of Polyamines in Bloodstream Trypanosoma brucei*

SYNOPSIS. The sensitive dansyl procedure was used to detect putrescine and spermidine, but not spermine and cadaverine, in pleomorphic Trypanosoma brucei. The polyamines were synthesized in vitro from [³H]ornithine, [¹⁴C]arginine and [¹⁴C]methionine. Proline, agmatine, and citrulline, but not glutamine, glutamic or pyroglutamic acids, stimulated spermidine formation from [¹⁴C]methionine. Putrescine and spermidine synthesis occurred rapidly from ornithine: putrescine synthesis peaked in 0.5 h, spermidine in 1 h. Trypanosoma brucei assimilated exogenous ¹⁴C-labeled putrescine, spermidine, and spermine; spermidine and spermine were taken up 5 times as rapidly as putrescine. Polyamine syntheses may therefore be a practical target for novel trypanocies.     

藤黄生孢链霉菌NRRL 2401遗传操作系统和基因文库的构建北大核心CSCD

【目的】建立藤黄生孢链霉菌NRRL 2401的遗传操作系统和基因文库,以便筛选次级代谢产物生物合成基因。【方法】利用大肠杆菌和链霉菌的属间接合转移的方法,以整合型载体pPM927、pSET152和复制型载体pJTU1278构建链霉菌遗传操作系统。以pCClFOS^(TM)载体,大肠杆菌EP1300^(TM)-T1~R为宿主菌构建Fosmid文库。随后,设计引物,利用"板池-行池-单克隆"的三级PCR方法对文库进行快速筛选。【结果】pPM927、pSET152和pJTU1278均成功转入藤黄生孢链霉菌NRRL 2401,其中pSET152载体的转化效率最高。构建了稳定高效的藤黄生孢链霉菌NRRL 2401的基因文库,含2880个克隆,平均插入片段大小约为35 kb,空载率小于1%,文库覆盖率为99.99%,覆盖基因组16.5倍。同时,初步筛选出可能含有吲哚霉素生物合成基因簇的9个阳性克隆。【结论】成功构建了稳定高效的藤黄生孢链霉菌NRRL 2401遗传操作系统和高质量的基因文库,为克隆该菌中次级代谢产物生物合成基因簇以及进一步遗传改造奠定了基础。     

Induction of the pho regulon and polyphosphate synthesis against spermine stress in Pseudomonas aeruginosa

Growth of Pseudomonas aeruginosa on spermine requires a functional γ‐glutamylpolyamine synthetase PauA2. Not only subjected to growth inhibition by spermine, the pauA2 mutant became more sensitive to β‐lactam antibiotics in human serum. To explore PauA2 as a potential target of drug development, suppressors of the pauA2 mutant, which alleviated toxicity, were isolated from selection plates containing spermine. These suppressors share common phenotypic changes including delayed growth rate, retarded swarming motility, and pyocyanin overproduction. Genome resequencing of a representative suppressor revealed a unique C₅₉₉T mutation at the phoU gene that results in Ser₂₀₀Leu substitution and a constitutive expression of the Pho regulon. Identical phenotypes were also observed in a ΔpauA2ΔphoU double knockout mutant and complemented by the wild‐type phoU gene. Accumulation of polyphosphate granules and spermine resistance in the suppressor were reversed concomitantly when expressing exopolyphosphatase PPX from a recombinant plasmid, or by the introduction of deletion alleles in pstS pstC for phosphate uptake, phoB for Pho regulation, and ppk for polyphosphate synthesis. In conclusion, this study identifies polyphosphate accumulation due to an activated Pho regulon and phosphate uptake by the phoU mutation as a potential protection mechanism against spermine toxicity.     

Conformationally Restrained Chiral PNA Conjugates: Synthesis and DNA Complementation Studies

Abstract

In recent times, PNA (I), a structural mimic of DNA in which the sugar-phosphate backbone is replaced by N-(2-aminoethyl)glycine (aeg) linkage has emerged as a potential antisense therapeutic agent.¹ A major limitation of PNAs from an application perspective is their poor solubility in aqueous medium and being achiral, they bind to cDNA in both parallel (N-PNA/5′-DNA) and antiparallel (N-PNA/3′-DNA) modes. In this connection, we have designed spermine conjugated and conformationally constrained PNA analogues to generate the 4-aminoprolyl backbone (II).² These were synthesised and evaluated for their DNA binding abilities by using UV and CD spectroscopic studies. It is seen that incorporation of one 4-aminoprolyl unit at the N-terminus of a PNA chain not only enhances the inherent binding of PNA to DNA, but also imparts significant bias in parallel and antiparallel binding with cDNA. Conjugation of spermine at C-terminus enhanced the PNA solubility.     

小鼠衰老对不同组织中亚精胺的影响

目的:本研究以模式小鼠C57BL为对象,研究小鼠在衰老过程中不同组织器官内源性亚精胺含量的变化。方法:利用高效液相色谱检测小鼠心脏和肝脏组织中亚精胺含量,进一步应用qRT-PCR以及Western blot检测在衰老过程中,不同组织器官中亚精胺生物合成途径的关键基因表达变化,利用亚精胺处理细胞检测DNA损伤应答能力。结果:随着衰老的发生心脏(199.09±17.12)和肝脏组织(168.92±5.12)中亚精胺含量显著降低,分别为78.01±13.52、62.05±6.73,差异有统计学意义(P0.05);不同组织器官中亚精胺生物合成途径的关键基因Odc、Srm、Amd1的表达随衰老的发生明显下调,并且伴随着DNA损伤应答障碍;利用亚精胺处理细胞,能够增强细胞对DNA损伤的应答反应。结论:衰老的小鼠中内源性亚精胺含量降低,并且其合成途径的关键基因转录水平降低,导致细胞对DNA损伤应答能力减弱,从而加速机体衰老进程。     

Polyamines and ethylene in relation to adventitious root formation in Prunus avium shoot cultures

An attempt was made to identify some of the hormonal factors that control adventitious root formation in our Prunus avium micropropagation system in order to improve rooting in difficult-to-root genotypes. Changes in endogenous contents of free polyamines were determined at intervals during auxin-induced rooting of shoot cultures. Accumulation of putrescine and spermidine peaked between days 9 and 11. Spermine was only present in traces, Exogenously supplied putrescine or spermine (50-500 μM), in the presence of optimal or suboptimal levels of indolebutyric acid (IBA), had no effect on rooting percentage or root density, except for spermine at 500 μM. At this external concentration spermine caused a substantial accumulation in both free spermine and putrescine. The use of several inhibitors of polyamine biosynthesis, namely α-difluoromethylornithine (DFMO), α-difluoromethylarginine (DFMA), dicyclohexylammonium sulphate (DCHA) and methylglyoxal-bis-guanyl-hydrazone (MGBG) alone or in combination in the 0.1 to 5 μM range, resulted in an inhibition of rooting that was partially reversed by the addition of the corresponding polyamine. Cellular polyamine levels were significantly reduced by DFMO and DFMA but not by DCHA and MGBG, Labeled putrescine incorporation into spermidine increased somewhat in the presence of the ethylene synthesis inhibitor aminoethoxyvinylglycine (AVG). A system based on [3,4-¹⁴C]methionine incorporation was used to measure ethylene synthesis by the in vitro cultured shoots. Label incorporation was drastically reduced by 10 μM AVG and increased 3.5-fold in the presence of 50 μM IBA with respect to controls (no IBA). Labeled methionine incorporation into spermidine increased to some extent when ethylene synthesis was inhibited by AVG. Adding the ethylene precursor 1-aminocyclopropane-l-carboxylic acid (ACC) to the rooting medium significantly inhibited rooting percentage; AVG caused the formation of a greater number of roots per shoot but delayed their growth. Supplying the shoots with both compounds resulted in an intermediate rooting response, in which both rooting percentage and root density were affected. These results indicate that polyamines may play a significant role at least in some stages of root formation. The polyamine and ethylene biosynthetic pathways seem to be competitive but under our conditions, the enhancement of one pathway when the other was inhibited, was not dramatic. Although IBA promoted ethylene synthesis, AVG, which drastically reduced it, also promoted root formation. Thus, the auxin effect on root induction cannot be directly related to its ability to enhance ethylene synthesis.     

Inhibition of the polyadenylation reaction in vitro by polyamines

The effect of polyamines on the polyadenylation reaction in vitro was investigated. Varying concentrations of spermine were added to the reaction catalyzed by purified poly(A) polymerase using rat liver nuclear RNA, poly(A), Escherichia coli tRNA or (Ap)₃A as exogenous primers. The enzyme activity decreased progressively with increasing concentrations of polyamines; complete inhibition was obtained at 0.4 and 1.2 mm spermine for the nuclear RNA- and poly(A)-primed reactions, respectively. No inhibition was observed for the (Ap)₃A-primed reaction. Spermidine and putrescine also inhibited polyadenylation but to a lesser extent than spermine. The degree of inhibition by spermine was related to the polynucleotide primer concentrations. Spermine prevented polyadenylation by binding to the primer but not to the poly(A) polymerase molecule as shown by the migration of [¹⁴C]spermine through glycerol gradients after preincubation with enzyme or tRNA. At concentrations inhibitory to polyadenylation in vitro, spermine could stimulate the DNA-dependent RNA synthesis catalyzed by RNA polymerase II. The present study suggests that low levels of polyamines could be used as specific inhibitors of the poly(A) synthesis in vitro.     

转录组分析罗伯茨绿僵菌精胺合成酶MrSPS介导真菌血腔定殖功能

【背景】精胺在植物应对逆境胁迫、动物抵抗疲劳和衰老、真菌生长代谢等过程中发挥重要作用,但目前在昆虫病原真菌中的研究未见报道。【目的】在分子水平上探究罗伯茨绿僵菌精胺合成关键酶——精胺合成酶在昆虫血腔定殖中的作用机制。【方法】显微注射法测定Mrsps敲除株ΔMrsps的致病力变化,并观察血腔中ΔMrsps生长状态;收集ΔMrsps和野生型WT注射侵染30 h后的大蜡螟血淋巴进行转录组测序,分别与罗伯茨绿僵菌和大蜡螟参考基因组进行比对分析,并结合定量PCR进行验证。【结果】与WT和回补株ΔMrsps-cp相比较,ΔMrsps致病力显著下降,而且随着注射浓度的降低,ΔMrsps致病力下降越显著。侵染36 h后WT和ΔMrsps孢子都能正常萌发且开始以类酵母状态生长,60 h后,相较于WT,ΔMrsps的生长繁殖数量较少。转录组共检测到3 202个罗伯茨绿僵菌基因,其中1 769个基因在ΔMrsps中表达上调,922个基因表达下调;差异表达基因涉及碳水化合物代谢、运输、分解代谢、翻译和氨基酸代谢等多条途径;筛选出28个血腔致病相关基因全部在ΔMrsps中表达下调;定量PCR检测发现在整个血腔定殖阶段免疫逃避蛋白Mcl1基因和血腔定殖Colonization of hemocoel 1基因在WT和ΔMrsps-cp中的表达量高于ΔMrsps。共检测到13 249个大蜡螟基因,其中4 026个差异表达基因;KEGG注释分析显示大量差异表达基因富集到内分泌系统和免疫系统等途径;深入分析发现22个差异表达基因归属于Toll和Imd信号通路,其中18个基因在ΔMrsps侵染的大蜡螟中表达上调,表明ΔMrsps侵染大蜡螟过程中更易引起免疫系统的激活。【结论】揭示了Mrsps在罗伯茨绿僵菌血腔定殖阶段作用的分子机制,为进一步揭示精胺在真菌中的作用机理提供了理论基础。     

Spermine as a possible endogenous allosteric activator of carboxypeptidase A: multispectroscopic and molecular simulation studies

Abstract

Carboxypeptidase A (EC.3.4.17.1) is a zinc-containing proteolytic enzyme that removes the C-terminal amino acid from a peptide chain with the free carboxylate-terminal. In this study, the effect of spermine interaction on the structure and thermal stability of Carboxypeptidase A was investigated by ultraviolet???visible spectroscopy, fluorescence spectroscopy, circular dichroism, Kinetic measurement, molecular docking and simulation studies have also been followed at the pH of 7.5. The transition temperature of Carboxypeptidase A, as a criterion of protein thermal stability, in the presence of spermine was enhanced by increasing the concentration of spermine. The results of fluorescence intensity changes, at two temperatures of 308 and 318?K, also suggested that spermine had a great ability to quench the fluorescence of Carboxypeptidase A through the static quenching procedure. The thermodynamic parameters changes, including standard Gibbs free-energy, entropy and enthalpy, showed that the binding of spermine to Carboxypeptidase A was spontaneous and the hydrogen bonding and van der Waals interactions played a major role in stabilizing the Carboxypeptidase A–spermine complex. The changes in the content of the α-helix and the β-sheet of the Carboxypeptidase A with binding to spermine were shown by the CD spectra method. Further, kinetic studies revealed that by increasing concentration of spermine, the activity of Carboxypeptidase A was enhanced. Also, the docking study revealed that the hydrogen bonding and van der Waals interactions played a major role in stabilizing the Carboxypeptidase A–spermine complex. As a result, spermine could be considered as an activator and a stabilizer for Carboxypeptidase A.

Communicated by Ramaswamy H. Sarma     

The synthesis and turnover of spermidine and spermine in mouse brain

Following the administration to mice of radiolabeled putrescine by intraventricular injection, changes in the specific radioactivity of putrescine, spermidine, and spermine have been measured. Putrescine decline was biphasic, being more rapid over the first 12 hr(t _1/2=5 hr) than over the remainder of the 48-hr period (t _1/2=11 hr) that significant labeling was detected. Spermidine was rapidly labeled during the decline in putrescine radioactivity and maximum incòrporation of label occurred at 18 hr. Subsequently, spermidine specific activity declined with a half-life of 22 days. Spermine synthesis was slower, with maximum labeling occurring after 4 days. Spermine turnover, measured at a time when spermidine radioactivity had substantially declined, was extremely slow (t _1/2=92 days). The data supports the view that putrescine is a precursor of spermidine which in turn is required for spermine synthesis.     

Synthesis of Oligodeoxynucleotides Containing 2-Substituted Guanine Derivatives Using 2-Fluoro-2′-Deoxyinosine as Common Nucleoside Precursor

Abstract

Oligonucleotides containing 2-substituted guanine derivatives with double-helix stabilizing molecules such as spermine, spermidine and propylimidazole have been prepared using protected 2-fluoro-2′-deoxyinosine phosphoramidite and two different protective strategies: the p-nitrophenylethyl (NPE) and the t-butylphenoxyacetyl groups. Melting studies show a large increase on the melting temperatures of duplexes containing these 2-substituted guanine derivatives.     

Effect of polyamines on prostaglandin synthesis in various cell-free systems

Synthesis of PGF_2α by bovine uterus and guinea pig lung microsomes and that of TXB₂ by human platelet and rat spleen microsomes were stimulated by spermine. PGE₂ synthesis by bovine seminal vesicle and porcine lung microsomes, and 6-keto-PGF_1α synthesis by bovine seminal vesicle and uterus microsomes were inhibited by spermine. When phospholipid-free prostaglandin synthetase from bovine seminal vesicle was used instead of microsomes, the inhibition of PGE₂ synthesis by spermine disappeared. The inhibition of PGE₂ synthesis by spermine gradually appeared with an increase of phospholipid added. Among phospholipids tested, phosphatidylcholine was the most effective for the inhibition of PGE₂ synthesis by spermine.     

A New Synthesis of α-Methylspermidine

A five-step synthesis of -methylspermidine (1,8-diamino-5-azanonane), the first polyamine analogue preventing pathological consequences of spermidine depletion in transgenic rats overproducing spermine/spermidine N ¹-acetyltransferase, from ethyl 3-aminobutyrate was achieved in a high overall yield.     

Enzymatic Synthesis of a Branched Trisaccharide, 2,4-di-α-Glucosyl-glucose

New procedures for determining putrescine, spermidine and spermine were first established here by the end point assay method using polyamine oxidase from Penicillium chrysogenum or Aspergillus terreus and putrescine oxidase from Micrococcus rubens. Method 1: Spermidine and spermine were first oxidized with polyamine oxidase (step A). To the reaction mixture, putrescine oxidase was added to oxidize putrescine (step B). Putrescine and spermidine in another reaction mixture were oxidized with putrescine oxidase (step C). Method 2 : Putrescine and spermidine were first oxidized with putrescine oxidase (step A). To the reaction mixture, polyamine oxidase was added to oxidize spermine (step B). Spermidine and spermine in another reaction mixture were oxidized with polyamine oxidase (step C). The amounts of putrescine, spermidine and spermine were determined from the absorbance values at each steps A, B and C.     

Spermine as a porcine pancreatic elastase activator: spectroscopic and molecular simulation studies

Abstract

The aim of this study was to investigate the spermine effect on the thermal denaturation, conformation and activity of elastase at three temperatures of 303, 313 and 323?K in the Tris buffer, at pH 8.5, using UV–vis spectrophotometry, spectrofluorometry and circular dichroism as well as molecular docking and molecular simulation. The increased absorption of elastase in the presence of spermine suggested a change in the environment of tryptophan. It was found that under the influence of spermine, the emission intensity of elastase extremely was reduced, and the use of the Stern-Volmer equation showed that some static quenching had occurred. The thermodynamic parameters values (enthalpy and entropy) and the molecular docking technique also revealed that van der Waals forces or hydrogen bonding interactions played an important role in the binding process. The spermine–elastase complex formation led to increasing the value of the catalytic constant (k_cat). So it could be considered as an activator. Slight changes were observed in the second structure of elastase (1.06% increase for the α-helix and 0.048% decrease the β-sheet) and the thermal stability effect. Molecular docking results also demonstrated that spermine could bind to porcine pancreatic elastase, and van der Waals forces or hydrogen bonding interactions played the major role in the binding process. Overall, our results showed that spermine could induce structural alterations in elastase, acting as a partial stabilizer and an activator for the enzyme.

Communicated by Ramaswamy H. Sarma     

A possible involvement of polyamines in the initiation of DNA synthesis by human WI-38 and mouse BALB/3T3 cells

Changing the medium, or adding fresh serum, induces a large proportion of the proliferatively quiescent cells in confluent monolayers of human WI-38 and mouse BALB/3T3 cells to initiate a growth-division cycle. Exposure at the time of the medium change or serum addition to MGBG (methyl glyoxal bis [guanylhydrazone]), an inhibitor of spermidine and spermine synthesis and function, reduces or stops the subsequent flow of cells into the DNA-synthetic phase, without grossly affecting RNA synthesis. Mediation of MGBG action by an actual or functional shortage of spermidine or spermine (but not putrescine), and consequently an involvement of these polyamines in DNA synthesis, is strongly suggested by the reduction of the inhibitor's effectiveness by a brief (1-hour), early prereplicative exposure of the treated cells to exogenous spermidine and spermine (but not putrescine).     

Ultrastructural changes in vitro of rat liver nucleoli in response to polyamines

Summary Structural alterations of the nucleoli of rat liver cells were noted when these nuclei were isolated with spermidine or spermine rather than magnesium. When 5–10 mM spermidine or spermine were used to isolate the nuclei, the nucleoli were a) larger, b) contained numerous and sometimes large lacunae, and c) were less aggregated and had prominent chromatin caps. These chromatin caps gave the nucleolus a ring-shaped appearance in the light microscope. These findings, coupled with physiological data that indicate that polyamines enhance nucleolar RNA polymerase activity (Russell et al., 1971), suggest that spermidine and spermine may be involved in the control of ribosomal RNA synthesis. To our knowledge, this is the first instance of the direct stimulation of ribosomal RNA synthesis during nuclear isolation.Supported by USPHS Grant NS-07934.