Synthesis of Peptide Nucleic Acid Monomers

Abstract

The chemical synthesis of peptide nucleic acid (PNA) monomers is described using Fmoc (backbone), anisoyl (cytosine, adenine), 4-tert-butylbenzoyl (cytosine) and isobutyryl/diphenylcarbamoyl (guanine) protecting group combinations. For the guanine monomer the alkylation was realized both in a Mitsunobu [DIAD, triphenylphosphine or (4-dimethylaminophenyl)diphenylphosphine, tert-butyl glycolate] and in a low-temperature, sodium-hydride mediated alkylation (tert-butyl bromoacetate) to give the N⁹ -substituted derivative.     

Design and Synthesis of Heterocyclic Conjugated Peptides as Novel Antimicrobial Agents

Antimicrobial peptides have been recognized as a novel class of antibiotics and several candidates are currently in clinical trials. In the present study, new antimicrobial compounds were synthesized by coupling quinazolinone moiety with the fragments of elastin sequences VP, GVP, VGVP and GVGVP. They were evaluated for their antibacterial activity against both gram positive and gram negative bacterial strains. We are here reporting that heterocyclic conjugated tetra peptide and penta peptide showed enhanced antibacterial activity compare to the conventional antimicrobial drugs.     

Liquid Phase Synthesis of Peptide Nucleic Acid (or Polyamide Nucleic Acid) Dimers

Abstract

The liquid phase synthesis of “polyamide nucleic acid” (PNA) dimers containing the purine nucleic acid bases adenine and guanine has been achieved in good yields. This strategy was elaborated in order to circumvent difficult direct coupling of protected PNA monomers. This method can be applied to the liquid phase synthesis of short protected polyPNAs fragments, which can then selectively be deprotected.     

Specific Features of Nucleic Acid Synthesis in Isolated Mitochondria of Elymus sibiricus from Different Natural Populations

Conditions and kinetic characteristics of nucleic acid synthesis were studied in the isolated mitochondria of Elymus sibiricus from different natural populations. The results showed the reciprocal dependence of RNA and DNA synthesis rates in the mitochondrial genetic system of E. sibiricus seedlings of different genotypes.     

Localization of Nucleic Acid Synthesis in Root Meristems

Adenine-8-C1¹⁴ was supplied to roots of Vicia faba and Alliumascalonicum and its incorporation into DNA was studied fromautoradiographs of hydrolysed sections. These roots have a quiescentcentre to the meristem where the cells do not synthesize DNAand probably, therefore, play no part in the construction ofthe root. The boundary between the quiescent centre and thecentral cap initials is clearly denned and this suggests thatthere is as little cell interchange between the histogens asthere is in roots with visibly discrete histogens.     

Solution Influence on Biomolecular Equilibria: Nucleic Acid Base Associations

Abstract

This paper consists of two parts. In the first part, the general problem of biomolecular equilibria in solution is considered, stressing that molecular interactions ultimately determine the answer to this problem. It is discussed how computer simulation techniques can reliably treat the problem and several pitfalls of computer simulation to be avoided are pointed out. Other approaches based on modeling and conceptual simplifications such as perturbative methods, long-range interaction approximations, surface thermodynamic approaches, and hydration shell models are discussed. In the second part, the results of Monte Carlo calculations on the associations of nucleic acid bases in water and carbon tetrachloride are presented. Stacked self-associations are found to be preferred in water and hydrogen-bonded complexes are favored in nonpolar solutions, in agreement with experimentell data. The influence of the solvent on base associations is explained in terms of solute-solvent and solvent-solvent contributions to the total energy. No enthalpic stabilization of the complexes by the solvent was found. The results are used to examine the validity of various approximations discussed in the first part of the paper.     

Mitotic Inhibition and Nucleic Acid Synthesis in Amoeba Nuclei

SEVERAL strains of large mononucleate amoebae contain specific proteins which inhibit mitosis and eventually kill amoebae of strains other than their own^1,2. We now describe experiments to show that this lethal antimitotic factor (AF) inhibits RNA synthesis when injected into susceptible cells.     

Significance of Size and Nucleic Acid Content Heterogeneity as Measured by Flow Cytometry in Natural Planktonic Bacteria

Total bacterial abundances estimated with different epifluorescence microscopy methods (4′,6-diamidino-2-phenylindole [DAPI], SYBR Green, and Live/Dead) and with flow cytometry (Syto13) showed good correspondence throughout two microcosm experiments with coastal Mediterranean water. In the Syto13-stained samples we could differentiate bacteria with apparent high DNA (HDNA) content and bacteria with apparent low DNA (LDNA) content. HDNA bacteria, “live” bacteria (determined as such with the Molecular Probes Live/Dead BacLight bacterial viability kit), and nucleoid-containing bacteria (NuCC) comprised similar fractions of the total bacterial community. Similarly, LDNA bacteria and “dead” bacteria (determined with the kit) comprised a similar fraction of the total bacterial community in one of the experiments. The rates of change of each type of bacteria during the microcosm experiments were also positively correlated between methods. In various experiments where predator pressure on bacteria had been reduced, we detected growth of the HDNA bacteria without concomitant growth of the LDNA bacteria, such that the percentage contribution of HDNA bacteria to total bacterial numbers (%HDNA) increased. This indicates that the HDNA bacteria are the dynamic members of the bacterial assemblage. Given how quickly and easily the numbers of HDNA and LDNA bacteria can be obtained, and given the similarity to the numbers of “live” cells and NuCC, the %HDNA is suggested as a reference value for the percentage of actively growing bacteria in marine planktonic environments.     

Design,Synthesis, and Antifungal Activities of Novel Carboxamides Derivatives Bearing a Chalcone Scaffold as Potential SDHIs

In search for SDHIs fungicides, twenty-five novel carboxamides containing a chalcone scaffold were designed, synthesized, and evaluated for antifungal activities against five pathogenic fungi. The results showed that compound 5 k exhibited outstanding antifungal activity against R. solani with an EC₅₀ value of 0.20 μg/mL, which was much better than that of commercial SDHIs Boscalid (EC₅₀=0.74 μg/mL). Moreover, compound 5 k also displayed promising antifungal activities against S. sclerotiorum, B. cinerea, and A. alternate (IC₅₀=2.53–4.06 μg/mL), indicating that 5 k had broad-spectrum antifungal activity. Additionally, in vivo antifungal activities results showed that 5 k could significantly inhibit the growth of R. solani in rice leaves with good protective efficacy (57.78 %) and curative efficacy (58.45 %) at 100 μg/mL, both of which were much better than those of Boscalid, indicating a promising application prospect. Moreover, SEM analysis showed that compound 5 k could remarkably disrupt the typical structure and morphology of R. solani hyphae. Further SDH enzyme inhibition assay and molecular docking study revealed that lead compound 5 k had a similar mechanism of action as commercial SDHI Boscalid. These results indicated that compound 5 k showed potential as a SDHIs fungicide and deserved further investigation.     

Progress Towards a Submonomer Synthesis of Peptide Nucleic Acid

Abstract

We report recent developments in the optimization of a submonomer synthesis of peptide nucleic acid based on the Fukuyama-Mitsunobu reaction. The key steps in the submonomer synthesis are the installation of an appropriately protected 2-aminoethyl group on the α-nitrogen of an amino acid and its subsequent acylation with a protected nucleobase derivative. The aggressive alkylation conditions require a scheme of maximal protection for the nucleobases and that is proposed herein for the pyrimidines.     

Nucleic Acid Synthesis in the Chloroplasts of Acetabularia mediterranea

Radioautographic and radiochemical techniques were used to establish the presence of replicating DNA in the chloroplasts of Acetabularia mediterranea. These techniques also demonstrated that these chloroplasts synthesize RNA. It was found that label from thymine was also incorporated into DNA and RNA in these chloroplasts.

With the establishment of protein and nucleic acid synthesis in Acetabularia chloroplasts, it is clear that these chloroplasts carry out those metabolic processes which are most characteristic of autonomous cells.

     

末端脱氧核苷酸转移酶在生物传感及核酸合成领域的应用*

末端脱氧核苷酸转移酶(terminal deoxynucleotidyl transferase, TdT)是聚合酶X家族中的一员,与典型的DNA聚合酶不同,TdT以恒温的无模板依赖的方式催化脱氧核糖核苷三磷酸(dNTP)聚合到寡核苷酸的3'羟基端来合成DNA。并且TdT对底物的耐受性高具有聚合修饰型dNTP的能力,如荧光修饰的dNTP、生物素修饰的dNTP,甚至人工碱基均可作为其良好底物。TdT的这些生化特性使其被广泛的应用在生物传感和核酸合成领域中,促进了许多基于核酸的工具和方法的发展,并为酶促从头合成DNA技术的发展奠定基础。介绍了TdT的性质,重点总结了它在其介导的生物检测技术、核酸的修饰技术以及酶促合成DNA技术三个方面的核心作用、目前面临的挑战以及未来研究的方向,以期促进TdT在生物传感器和核酸合成中的进一步应用。     

The Synthesis of Branched Oligonucleotides as Signal Amplification Multimers for Use in Nucleic Acid Assays

Abstract

Branched oligonucleotides have been synthesized using phosphoramidite derivatives with two protected hydroxyl functions. These molecules are employed for a label amplification strategy used in DNA probe diagnostics.     

An Improved Screening Method for Inhibitors of Nucleic Acid Synthesis

A screening method for the antibiotics capable of inhibiting synthesis of nucleic acid in bacterial cells or mammalian tumor cells was investigated. The DNA and RNA syntheses in Bacillus subtilis 168 thymine^?, indole^? were studied by the assay of incorporations of ³H-thymine and ¹⁴C-uracil into the cells, respectively. With known antibiotics against nucleic acid synthesis, the adequacy of the method was examined, and the result proved that this method is more sensitive and specific than the conventional assay methods.

It was found as a new fact that cellocidin is a potent and specific inhibitor to the thymine incorporation into DNA.

By an almost similar procedure, an inhibitory effect of several antibiotics on the incorporations of ³H-thymidine and ¹⁴C-uridme into Ehrlich ascites carcinoma cells was also studied.     

Nucleic Acid and Histone Synthesis by Ethanol-Treated Cleavage-Arrested Sea Urchin Embryos

Abstract. It has been found that fertilized sea urchin eggs prevented from normal cleavage by solutions of isosmotic ethanol in sea water are able to complete some cellular and molecular aspects of the normal developmental program that are observed in control cultures. In both treated and control cultures, the type of RNA transcribed changes at 24 h (early gastrula) in favor of higher molecular weight rRNA. Ultrastructural studies reveal the presence of nucleoli in ethanol-treated as well as control embryos. The type of H1 histone synthesized also shifts at 24 h in favor of a higher molecular weight H1 in both ethanol-treated and control embryos. Replication of DNA proceeds at a slower rate in ethanol-treated embryos than in controls, resulting in DNA/embryo values in ethanol which are 20–30% of control values after 24 h. The results relate to the problem of differentiation without cleavage, and the role of normal partitioning, cell-cell interaction, and DNA synthesis in triggering the sequence of events in the developmental program.     

Synthesis of Protein and Nucleic Acid by Disrupted Spheroplasts of Pseudomonas schuylkilliensis

Osmotically shocked spheroplasts obtained from Pseudomonas schuylkilliensis strain P contained about 54, 32, 28, and 82% of the total cellular protein, ribonucleic acid (RNA), deoxyribonucleic acid (DNA), and phospholipid, respectively. This preparation was capable of incorporating (32)P-orthophosphate into RNA and DNA, (3)H-adenosine or (3)H-uridine into RNA, and (3)H-leucine or (14)C-phenylalanine into protein. These activities were not found in the cytoplasmic fraction which contained most of the glucose-6-phosphate dehydrogenase activity. The synthesis of RNA by intact and disrupted spheroplast preparations was sensitive to actinomycin D, chromomycin A(3), streptovaricin, rifampin, Lubrol W, Triton X-100, and sodium deoxycholate, whereas RNA synthesis by intact cells was insensitive to these agents. Ethylenediaminetetraacetic acid, porcine pancreatic lipase, the protoplast-bursting factor, high concentrations of salts, and washing the preparation inhibited the synthesis of RNA by disrupted spheroplasts but had little or no effect on intact spheroplasts. Most of the newly synthesized RNA made by disrupted spheroplasts had the characteristics of messenger RNA. The DNA present in this preparation functioned as a template for RNA synthesis; continued protein synthesis was dependent on concomitant RNA synthesis. An unusual feature of the preparation was the finding that the synthesis of macromolecules was completely dependent on oxidative phosphorylation.     

Macromolecular Design,Nucleic Acid Junctions,and Crystal Formation

Abstract

The simplest form of macromolecular design involves the ligation of nucleic acids. Recent results on the concatenation of nucleic acid junctions show that these molecules can act as fairly rigid macromolecular valence clusters on the nanometer scale. These clusters can be joined to form closed stick figures in which each edge is double helical DNA or RNA and each vertex is a nucleic acid junction. The geometrical criteria for forming discrete-closed and periodic structures from these components are established. The helicity of each edge limits the possible structures that can be formed.

The formation of a periodic array from nucleic acid junction building blocks is compared with the crystallization of molecular systems. This comparison leads to a new interpretation of the nature of order in the solid state for molecular crystals. The suggestion is made that the structure of a solid molecular system described by the fewest unique orthogonal (Fourier) components is the one which will be entropically favored, since it contains the least information. This is the crystalline state, with a small number of molecules per asymmetric unit. The free energy from the proposed entropie driving force responsible for this behavior is available, in principle, to correct small deviations from ideality in forming covalent crystals from nucleic acid junction components, as well as in non-bonded molecular systems. Nucleic acid junction periodic arrays provide an appropriate vehicle with which to test this interpretation.     

蛋白核酸合成抑制剂和蛋白磷酸化对基因表达的调节

环己酰亚胺和放线菌素D明显降低小麦幼苗中BADH基因的表达,表明BADH基因表达在转录和转译水平上受到调控。氯霉素则有增加表达的效应。线粒体可能形成阻遏蛋白参与调节。H7和甘露糖降低BADH基因表达,相应地冈田酸(Okadaic acid)明显增加表达,说明蛋白磷酸化积极参与小麦幼苗中BADH基因表达的调节。     

Stimulatory Effects of Some Nucleic Acid Base Analogues on the Growth of Anabaena doliolum

8-azaguanine, 5-aminouracil, and 2, 6-diaminopurine, like thenatural base, adenine, apparently increase the growth rate ofAnabaena doliolum and transiently inhibit heterocyst production.Possible reasons for these effects are discussed in the lightof reports of similar effects of other combined nitrogen sourceson Anabaena doliolum.     

Nucleic Acid Synthesis in Cytoplasm of Yaba Monkey Tumor Virus-Infected Cells

Yaba tumor virus progeny appeared in cynomolgus monkey kidney cells at 24 h postinfection and reached a plateau at 72 h in the first cycle of replication. Viral DNA synthesis was first detected at about 3 h and reached a peak in 18 h. Maximum coating of viral DNA in infected cells occurred at 4 days postinfection. Rapidly labeled RNA was synthesized in the cytoplasm of virus-infected cells. At 6 h postinfection 7 to 10S RNA was present; this species was present in greater amount at 12 h; at 24 h a truncated peak indicated the presence of 14 to 15S as well as 7 to 10S RNA. Hybridization data indicated that the largest peak of messenger RNA synthesis occurred at 11 to 13 h postinfection and a second, slightly smaller, peak occurred at 21 to 23 h.