Action Spectrum for Growth Delay Induced in Escherichia coli B/r by Far-Ultraviolet Radiation

An action spectrum for growth delay induced in Escherichia coli B/r by far-ultraviolet radiation (230 to 295 nm) was obtained. It resembles the action spectrum for killing obtained in the same experiments, indicating that the chromophore for growth delay is probably the same as the chromophore for killing. Another action spectrum for killing, obtained under conditions more suitable for chromophore identification, suggests that nucleic acid, either deoxyribonucleic acid or ribonucleic acid, is the chromophore for growth delay induced by far ultraviolet. Isoprenoid quinones, which seem to be important chromophores for growth delay induced by near-ultraviolet radiation (above 300 nm), appear to play a negligible role in growth delay induced by wavelengths below 300 nm.     

呼吸道病毒核酸快速检测方案的建立与应用

本研究旨在建立一套便携、准确、操作简便的呼吸道病毒核酸快速检测方案。通过实时荧光定量聚合酶链式反应(quantitative real-time polymerase chain reaction,qRT-PCR)验证免提取的呼吸道病毒处理试剂(extraction-free respiratory virus treatment reagent,RTU)对病毒核酸处理的效果以及超快速荧光定量PCR仪(FQ-8A)对核酸扩增的效果;将RTU和FQ-8A结合构建呼吸道病毒核酸快速检测方案,通过荧光定量PCR仪中Ct值判断阳性检出率,以验证该方案检测临床样本时的准确性。结果表明,RTU与全自动核酸提取仪在提取效果上灵敏度相当;RTU在提取不同病毒类型样本时,与其他3种提取方法效果相当,但RTU提取时间少于5 min;FQ-8A检测呼吸道合胞病毒(respiratory syncytial virus,RSV)及腺病毒(adenovirus,ADV)与对照仪器ABI-7500具有良好一致性,kappa系数分别为0.938(P<0.001)和0.887(P<0.001),但FQ-8A耗时更短,扩增时间仅在0.5 h左右;RTU和FQ-8A相结合的快检方案与常规检测方案具有高度一致的检出率,其灵敏度为91.70%,特异度为100%,kappa系数为0.944(P<0.001)。总之,通过RTU与FQ-8A的结合构建了一套可在35 min内完成全部流程的呼吸道病毒核酸快速检测方案。该方案准确性高、操作简便,可为呼吸道病毒快速诊断和治疗提供重要支持。     

Theoretical Modeling of DNA-Monocationic Lexitropsin Complexation: Influence of Ligand Binding on DNA Curvature

Abstract

A theoretical study is presented on the complexation to DNA of a monocationic lexitropsin. Energetics and the structures of the complexes formed are analyzed for three base pair sequences of a nucleic acid octamer. The influence of the ligand binding on the nucleic acid conformation is analysed in detail. It is found that whereas the uncomplexed nucleic acid segments have very irregular structures with an overall curvature varying between 15° and 20°, the DNA structure becomes more regular and the curvature is strongly reduced upon the binding of a monocationic lexitropsin.     

用于核酸递送的GSH响应型纳米粒构建

摘要 目的：核酸治疗近年来越来越受到关注,但是核酸药物易被快速清除、易被核酸酶降解、非特异性生物分布、以及不易被细胞摄取的缺点使其在体内难以发挥效果。本文提供了一种具有谷胱甘肽（GSH）响应性释放的纳米粒,能够进行有效核酸药物递送。方法：使用十六烷基三甲基氯化铵（CTAC）制备介孔硅纳米粒,在介孔硅纳米粒表面进行巯基修饰并活化,使其与巯基修饰的聚丙烯亚胺和聚乙二醇反应,形成具有GSH响应的介孔硅纳米粒,通过静电吸附进行核酸荷载。马尔文粒度仪测量表面电位、粒径,透射电镜观察纳米粒形态。核酸电泳检测其核酸负载效率,通过体外检测GSH响应释放聚乙烯亚胺（PEI）情况,共聚焦显微镜观察细胞摄取以及溶酶体逃逸情况。结果：成功构建了具有GSH响应的纳米粒,粒径为76.44±1.68 nm,表面电位为33.93±0.59 mV;通过透射电镜观察到纳米粒呈圆形带孔颗粒状;琼脂糖核酸负载试验观察到当氮磷比大于20时,能够有效进行核酸负载。共聚焦显微镜显示该纳米粒能够成功被MDA-MB-231乳腺癌细胞摄取。在溶酶体逃逸试验中观察到纳米粒进入细胞后3 h,Cy5-siRNA与溶酶体的荧光分离,证明构建的纳米粒成功从溶酶体逃脱。结论：成功构建了具有GSH响应的介孔硅纳米粒,能够有效用于核酸递送。     

In Vitro Membrane Penetration of Modified Peptide Nucleic Acid (PNA)

Abstract

Efficient cellular uptake is crucial for the success of any drug directed towards targets inside cells. Peptide nucleic acid (PNA), a DNA analog with a promising potential as a gene-directed drug, has been shown to display slow membrane penetration in cell cultures. We here used liposomes as an in vitro model of cell membranes to investigate the effect on penetration of a PNA molecule colvalently modified with a lipophilic group, an adamantyl moiety. The adamantyl attachment was found to increase the membrane-penetration rate of PNA three-fold, as compared to corresponding unmodified PNA. From the penetration behaviour of a number of small and large molecules we could conclude that passive diffusion is the mechanism for liposome-membrane passage. Flow linear dichroism (LD) of the modified PNA in presence of rod-shaped micelles, together with octanol-water distribution experiments, showed that the adamantyl-modified PNA is amphiphilic; the driving force behind the observed increased membrane-penetration rate appears to be an accumulation of the PNA in the lipid double layer.     

The Role of Structural Water in the Formation of Nucleotide Mispairs

Abstract

The results of NMR investigation of the double-helical nucleic acid fragments containing A · C, C · U, m⁶G · U and m⁶G · G mispairs can be explained on the assumption that the bases in such pairs being in usual tautomeric forms are linked via water bridges. A computer analysis of intermolecular interactions in the systems containing two bases and one or two water molecules shows that these pairs correspond to the energy minima. The formation of pairs with water bridges can be considered an intermediate step in mutagenesis caused by some spontaneous errors arising during nucleic acid biosynthesis as well in mutagenesis induced by alkylating agents.     

Structure-based model for light-harvesting properties of nucleic acid nanostructures

Programmed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary chromophore molecules with light-harvesting properties. Like in natural systems, the local and global spatial organization of these synthetic scaffolded chromophore systems plays a crucial role in their emergent excitonic and optical properties. Previously, we introduced a computational model to predict the large-scale 3D solution structure and flexibility of nucleic acid nanostructures programmed using the principle of scaffolded DNA origami. Here, we use Förster resonance energy transfer theory to simulate the temporal dynamics of dye excitation and energy transfer accounting both for overall DNA nanostructure architecture as well as atomic-level DNA and dye chemical structure and composition. Results are used to calculate emergent optical properties including effective absorption cross-section, absorption and emission spectra and total power transferred to a biomimetic reaction center in an existing seven-helix double stranded DNA-based antenna. This structure-based computational framework enables the efficient in silico evaluation of nucleic acid nanostructures for diverse light-harvesting and photonic applications.     

Synthesis of Nucleotide Lipophilic Prodrugs Containing Two Inhibitors Targeted Against Different Phases of the HIV Replication Cycle

Abstract

We describe the preparation of nucleoside acyl 5′-di or 5′-triphosphates, containing a nucleoside analog moiety and 13-oxa-myristic acid as lipophilic chain. At physiological pH these products liberated exclusively the corresponding nucleotides.     

Structure-Function Relationship of Three Triple-Helical Nucleic Acids

Abstract

The nucleic acid triplexes poly d(T)·poly d(A)·poly d(T), poly (U)·poly (A)·poly (U), and poly (I)·poly (A)·poly (I) display a sort of continuity between each other. However, their morphologies present their own individuality which, considering those of their parent duplexes, are quite unexpected. This comparison helps to understand triplex structure-function relationship. While helical parameters are functions of the sugar pucker, low values of WC and Hoogsteen base-pair propellers is commonplace for triplexes and the Hoogsteen base-pair geometry monitors the effects of the interstrand phosphates charge-charge repulsion.

Synopsis

The nucleic acid triplexes poly d(T)·poly d(A)·poly d(T), poly(U)·poly(A)·poly(U), and poly (I)·poly (A)·poly (I) present distinct morphologies. Considering those of their parent duplexes, they are also quite unexpected.     

Design of unsymmetrical azo initiators to increase radical generation efficiency in low-density lipoproteins

Lipid peroxidation studies often employ the use of azo initiators to produce a slow, steady source of free radicals, but the lack of initiators capable of efficiently generating radicals in lipid regions has created persistent problems in these investigations. For example, experiments with symmetrical lipophilic or symmetical hydrophilic azo initiators increasingly suggest that their initiation mechanisms in low-density lipoproteins (LDL) rely upon the presence of α-tocopherol to mediate peroxidation. We report here the synthesis and study of the new unsymmetrical azo compounds SA-1, SA-2, C-16, C-12, and C-8 that decompose over a range of convenient temperatures and improve radical generation efficiency and access to lipid compartments. The half-life for decomposition (τ_1/2) of the unsymmetrical initiators at 37°C in methanol covered a range of 121 hours for SA-1, 77 hours for SA-2, and ～ 25 hours for the series C-16, C-12, and C-8. Agarose gel electrophoresis of LDL incubated with these unsymmetrical initiators supports the conclusion that the initiators associate with lipoprotein without disrupting integrity of the particle. The unsymmetical initiator C-8 when compared to symmetical hydrophilic initiator C-0 is capable of providing increased peroxidation of LDL, as monitored by formation of cholesteryl linoleate oxidation products and consumption of α-tocopherol. Efficiency of radical generation in lipophilic and hydrophilic compartments was found to be represented with the use of the radical scavenger combination α-tocopherol and uric acid, but not with the use of N,N′-Diphenyl-p-phenylenediamine (DPPD) and uric acid. These unsymmetrical initiators, when compared to the widely used symmetrical azo initiators, provide an advantage of free radical production, lipophilic access, and constant radical generation in the investigation of lipid peroxidation in low-density lipoproteins.     

Molecular Dynamics in Protein—Single Stranded DNA Complexes. Two Distinct Nucleoside Mobilities in Poly(deoxythymidylic acid)—poly-L-lysine Complexes

Abstract

Stoichiometric amounts of poly-L-lysine were added to site-specifically spin labeled single stranded nucleic acids and the resulting complexes analyzed by electron spin resonance spectroscopy (ESR). The nucleic acids were spin labeled to different extents and with labels of varying tether length. The ESR data are used to determine nucleoside dynamics and some structural features in these complexes. It is concluded that two distinct base mobilities exist in the complexes; one set is characterized by a mean correlation time τR = 2 ns, and the other one by a τR ≤ 50 ns. A model is proposed which suggests that a poly-L-lys single stranded nucleic acid complex consists of low mobility segments flanked by more mobile bases. An interesting feature of the proposed model is its applicability to explain ESR data of single strand binding protein-spin labeled nucleic acid complexes, which can also be interpreted in terms of two distinct nucleoside mobility states. It is hypothesized that this phenomenon could be of biological significance for the release of protein ligands from a protein-nucleic acid complex.     

(S)-1-(Pent-4′-enoyl)-4-(hydroxymethyl)-azetidin-2-one derivatives as inhibitors of human fatty acid amide hydrolase (hFAAH): synthesis,biological evaluation and molecular modelling

Abstract

A series of lipophilic ester derivatives (2a–g) of (S)-1-(pent-4′-enoyl)-4-(hydroxymethyl)-azetidin-2-one has been synthesised in three steps from (S)-4-(benzyloxycarbonyl)-azetidin-2-one and evaluated as novel, reversible, β-lactamic inhibitors of endocannabinoid-degrading enzymes (human fatty acid amide hydrolase (hFAAH) and monoacylglycerol lipase (hMAGL)). The compounds showed IC₅₀ values in the micromolar range and selectivity for hFAAH versus hMAGL. The unexpected 1000-fold decrease in activity of 2a comparatively to the known regioisomeric structure 1a (i.e. lipophilic chains placed on N₁ and C₃ positions of the β-lactam core) could be explained on the basis of docking studies into a revisited model of hFAAH active site, considering one or two water molecules in interaction with the catalytic triad.     

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.     

A New Model for the Comparison of the Efficiency and Selectivity of Photoreactive Groups Towards the Nucleic Acid and Protein Functional Groups

Abstract

A new model for the comparison of the efficiency and selectivity of photoreactive groups towards the nucleic acid and protein functional groups is described. It was shown that reagents carrying p-azidoaniline residue are the most efficient and selective for the modiication of the side radicals of amino acids.     

Anticandidal properties of N-acylpeptides containing an inhibitor of glucosamine-6-phosphate synthase

A series of N-acyl peptides 1–9, containing an inhibitor of glucosamine-6-phosphate synthase have been synthesised and tested against Candida strains. N-Acylated peptides inhibit glucosamine-6-phosphate synthase in cell free extracts from Candida albicans. Antifungal activities of the tested compounds correlated with their lipophilic properties. Peptides acylated with decanoic acid were found to be the most potent in the series. N-decanoylpeptides also showed activity against Candida albicans Gu5 resistant mutant with Cdr1 and Cdr2 drug extrusion proteins that causes MDR by an active efflux mechanism.     

Phosphono Peptide Nucleic Acids with a Constrained Hydroxyproline-Based Backbone

Abstract

DNA mimics representing negatively charged analogues of peptide nucleic acids (PNAs), particularly hetero-oligomers constructed from alternating phosphono-PNA residues (pPNA) and monomers on the base of trans-4-hydroxy-L-proline (HypNA) as well as mimics composed of phosphono-HypNA monomers (pHypNA) were tested in a set of in vitro and in vivo assays, and they demonstrated a high potential for the use in nucleic acid based diagnostic, isolation of nucleic acids and antisense experiments.     

Interaction of Nucleic Acids with Lipid Membranes

Abstract

The thermodynamics of nucleic acids which were enclosed in reverse-phase evaporation vesicles was studied by thermal denaturation with optical recording. The denaturation curves were recorded with a dual wavelength spectrophotometer. The sum of the hypochromicity of the nucleic acid and of the change in turbidity of the vesicles was measured at 260 nm and was corrected for the change in turbidity at 320 nm. Cloned fragments of double-stranded DNA containing 180 base pairs and poly A:poly U were enclosed in REV with a yield up to every vesicle containing five nucleic acid molecules. Vesicles were prepared from egg- lecithin, and the surface charge of the vesicles was varied by addition of stearic acid, phosphatidyl-glycerol and phosphatidyl-serine. The helix-coil transition of the nucleic acid enclosed in the vesicle could be resolved from that of the free nucleic acid. Due to the enclosure into the egg-lecithin REV the transition is stabilized from 70.5° to 74°C, the transition is broadened from 0.7°C to 2.7°C. Varying the phosphatidyl-serine-lecithin-ratio from 0–100%, an optimum in the yield of enclosure at 20% was obtained, a further broadening of the transition to 5.5°C and a decrease of the stabilization down to a small destabilization at 100% phosphatidyl serine was observed. Qualitatively, similar effects were observed with poly A:poly U. Variation of the ionic strength led to the conclusion that the replacement of the counterions of the phosphate backbone by the surface charge of the membrane, as well as a direct contact between the nucleic acid and the membrane have to be assumed. At present, the biological relevance of the results may be more in the drastic decrease in cooperativity than in the slight modulation of the stability. From nearly 180 base pairs opening up cooperatively in free nucleic acid this number is lowered to less than 50, a size in the range of promotor regions.     

From Pro-nucleotides to Pro-oligonucleotides

Abstract

Consequences of masking the phosphate functions of nucleic acid derivatives by enzyme labile bioreversible protecting groups are discussed.     

Conformationally Restricted Chiral Peptide Nucleic Acids Derived from Azetidines

Abstract

The initial experiments towards the chemical synthesis of conformationally rigid peptide nucleic acid analogues with azetidine moieties have been described.