Mutations stabilize small subunit ribosomal RNA in desiccation-tolerant cyanobacteria Nostoc

The ribosomal RNA molecule is an ideal model for evaluating the stability of a gene product under desiccation stress. We isolated 8 Nostoc strains that had the capacity to withstand desiccation in habitats and sequenced their 16S rRNA genes. The stabilities of 16S rRNAs secondary structures, indicated by free energy change of folding, were compared among Nostoc and other related species. The results suggested that 163 rRNA secondary structures of the desiccation-tolerant Nostoc strains were more stable than that of planktonic Nostocaceae species. The stabilizing mutations were divided into two categories: (1) those causing GC to replace other types of base pairs in stems and (2) those causing extension of stems. By mapping stabilizing mutations onto the Nostoc phylogenetic tree based on 16S rRNA gene, it was shown that most of stabilizing mutations had evolved during adaptive radiation among Nostoc spp. The evolution of 16S rRNA along the Nostoc lineage is suggested to be selectively advantageous under desiccation stress.

果树组织中总RNA提取的新方法

本研究设计了一种新的RNA提取方法 ,解决了RNA提取时容易被降解和污染这一关键问题。通过加入Rnase抑制剂 ,消除了同外源RNase对RNA的降解 ,结合DNA难呈低盐溶液(140mmol·L -1NaCl)的原理 ,去除了DNA对RNA提取液的污染 ;先后使用酚和氯仿 ,有效地去除了蛋白质和酚类物的污染 ,利用抗氧化剂PVP和巯基乙醇 ,消除了内源酚类物质氧化变色对病毒RNA逆转录的影响。采用上述方法可以在4～5h内得到纯度高、含量大、完整性好的果树总RNA ,并获得了逆转录活性较强的病毒RNA ,同时使提取RNA的成本降低。这些方法对苹果、葡萄、桃、樱桃等果树总RNA的提取均适用。

Self-assembly of single-stranded RNA on carbon nanotube: Polyadenylic acid to form a duplex structure

All messenger-RNA (mRNA) molecules in eukaryotic cells have a polyadenylic acid [poly (rA)] tail at the 3'-end and human poly (rA) polymerase (PAP) has been considered as a tumor-specific target. A ligand that is capable of recognizing and binding to the poly(M) tail of mRNA might interfere with the full processing of mRNA by PAP and can be a potential therapeutic agent. We report here for the first time that single-walled carbon nanotubes (SWNTs) can cause single-stranded poly (M) to self-structure and form a duplex structure, which is studied by UV melting, atomic force microscopy, circular dichroism spectroscopy, and NMR spectrometry.

Targeted RNA interference of cyclin A(2) mediated by functionalized single-walled carbon nanotubes induces proliferation arrest and apoptosis in chronic myelogenous leukemia K562 cells

Cyclin A(2) plays critical role in DNA replication, transcription, and cell cycle regulation. Its overexpression has been detected and related to many types of cancers including leukemia, suggesting that suppression of cyclin A(2) would be an attractive strategy to prevent tumor progression. Herein, we apply functionalized single wall carbon nanotubes (f-SWNTs) to carry small interfering RNA (siRNA) into K562 cells and determine whether inhibition of cyclin A(2) would be a potential therapeutic target for chronic myelogenous leukemia.

Atomic force microscopy and surface-enhanced Raman scattering detection of DNA based on DNA-nanoparticle complexes

We report a simple method for the label-free detection of double-stranded DNA using surface-enhanced Raman scattering (SERS). We prepared cetyltrimethylammonium bromide (CTAB)-capped silver nanoparticles and a DNA-nanoparticle complex by adding silver nanoparticles to lambda-DNA solutions. In the present study, the utilization of CTAB-capped silver nanoparticles facilitates the electrostatic interaction between DNA molecules and silver nanoparticles; at the same time, the introduction of DNA avoids adding aggregating agent for the formation of nanoparticle aggregates to obtain large enhancement of DNA, because the DNA acts as both the probe molecules and aggregating agent of Ag nanoparticles.

A novel invariant and sequence comparison for DNA

We consider numerical characterization of DNA primary sequence based on the positions of bases (a, t, c, g) and the pairs of bases X, Y in DNA (X, Y=a, t, c, g). This leads to a representation of DNA by a numerical sequence. Then, we extract a novel invariant (molecular connectivity index) from the derived numerical sequences. The suitable invariant can offer a characterization of DNA primary sequence. Finally, we provide an illustration of its utility by making a comparison between ten DNA sequences belonging to beta-globin gene in different species. The evolutionary relationships of ten species we have revealed in this contribution accord with phylogenetic tree properly.

DNA与生物碱类化合物非共价作用的负离子电喷雾质谱研究(Ⅰ)

目前 ,临床上使用的许多抗病毒药物均是通过与 DNA,RNA发生相互作用破坏其结构 ,进而影响基因调控与表达的功能 ,表现出抗病毒活性 [1,2 ] .因此 ,核酸与药物分子相互作用的研究对阐述抗病毒药物的作用机理 ,以及对药物的体外筛选都具有重要的意义 .电喷雾电离质谱作为一种软电离手段 ,可将溶液中生物分子与药物分子的非共价复合物转为气相进行分析 ,再现其生理状态 ,使其成为分子水平上进行药物筛选的最佳方法 [3～ 6 ] 和在分子水平上筛选中药抗病毒活性成分的理想工具 .本文选择合成了与 SARS病毒相关的 DNA片段作为抗病毒药物筛选的靶分子 ,用电喷雾质谱技术 ,通过对靶分子与 5种生物碱的非共价复合作用 ,探讨了生物质谱方法用于药物筛选的可行性 .1　实验部分1 .1　材料及样品制备　 DNA分子系人工合成 ,由 1 5个碱基组成 ,分子量为 470 4 ,结构为 GGTAA-GATGGAGAGC( 1 5 - mer) ;腺苷 ( Adenosine,Mw=2 67)、鸟苷 ( Guanosine,Mw=2 83)和胞苷 ( Cyti-dine,Mw=2 4 3)购自 Sigma公司 ;小檗碱、...

Structural features of the L-argininamide-binding DNA aptamer studied with ESI-FTMS

The 24-mer DNA aptamer of Harada and Frankel ( Harada, K.; Frankel, A. D. EMBO J. 1995, 14, 5798-5811) that binds L-argininamide (L-Arm) was studied by electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). This DNA folds into a stem and loop such that the loop is able to engulf L-Arm. As controls, two derivatives of the same base composition, one with the same stem but a scrambled loop and the other with no ability to form a secondary structure, were studied. The two DNAs that could fold into stem-loop structures showed a more negatively charged distribution of ions than the linear control. This tendency was preserved in the presence of ligand; complexes expected to have more secondary structure had ions with more negative charges. Distinct species corresponding to no, one, and two bound L-Arm molecules were observed for each DNA. The fractional peak intensities were fit to a straightforward binding model and binding constants were obtained. Thus, ESI-FTMS can provide both qualitative and quantitative data regarding the structure of DNA and its interactions with noncovalent ligands.

Reversible B/Z-DNA transition under the low salt condition and non-B-form polydApolydT selectivity by a cubane-like europium-L-aspartic acid complex

We report here that a cubane-like europium-L-aspartic acid complex at physiological pH can discriminate between DNA structures as judged by the comparison of thermal denaturation, binding stoichiometry, temperature-dependent fluorescence enhancement, and circular dichroism and gel electrophoresis studies. This complex can selectively stabilize non-B-form DNA polydApolydT but destabilize polydGdCpolydGdC and polydAdTpolydAdT. Further studies show that this complex can convert B-form polydGdCpolydGdC to Z-form under the low salt condition at physiological temperature 37 degrees C, and the transition is reversible, similar to RNA polymerase, which turns unwound DNA into Z-DNA and converts it back to B-DNA after transcription. The potential uses of a left-handed helix-selective probe in biology are obvious. Z-DNA is a transient structure and does not exist as a stable feature of the double helix. Therefore, probing this transient structure with a metal-amino acid complex under the low salt condition at physiological temperature would provide insights into their transitions in vivo and are of great interest.

Direct electrochemistry and surface plasmon resonance characterization of alternate layer-by-layer self-assembled DNA-myoglobin thin films on chemically modified gold surfaces

Alternate layer-by-layer (L-by-L) polyion adsorption onto gold electrodes coated with chemisorbed cysteamine gave stable, electroactive multilayer films containing calf thymus double stranded DNA (CT ds-DNA) and myoglobin (Mb). Direct, quasi-reversible electron exchange between gold electrodes and proteins involved the Mb heme Fe2+/Fe3+ redox couple. The formation of L-by-L (DNA/Mb), films was characterized by both in situ surface plasmon resonance (SPR) monitoring and cyclic voltammetry (CV). The effective thickness of DNA and Mb monolayers in the (DNA/Mb)l bilayer were 1.0 +/- 0.1 and 2.5 +/- 0.1 mn, corresponding to the surface coverage of similar to65% and similar to89% of its full packed monolayer, respectively. A linear increase of film thickness with increasing number of layers was confirmed by SPR characterizations. At pH 5.5, the electroactive Mb in films are those closest to the electrode surface; additional protein layers did not communicate with the electrode. CV studies showed that electrical communication might occur through hopping conduction via the electrode/base pair/Mb channel, thanks to the DNA-Mb interaction. After the uptake of Zn2+, a special electrochemical behavior, where MbFe(2+) acts as a DNA-binding reduction catalyst in the Zn2+-DNA/Mb assembly, takes place.

Liposome-mediated conformation transition of DNA detected by molecular probe: methyl green

Recent studies have focused on the structural features of DNA-lipid assemblies. In this paper, we take methyl green (MG) as a probe molecule to detect the conformational change of DNA molecule induced by dimethyldioctadecylammonium bromide (DDAB) liposomes before the condensation process of DNA begins. DDAB-induced DNA topology changes were investigated by cyclic voltammetry (CV), circular dichroism (CD) and UV-VIS spectrometry. We find that upon binding to DNA, positively charged liposomes induce a conformational transition of DNA molecules from the native B-form to the C motif. Conformational transition in DNA results in the binding modes of MG to DNA, changing and being isolated from DNA to the solution. More stable complexes are formed between DNA and DDAB. That is also proved by the melting study of DNA.

DNA分子与生物碱类化合物的非共价复合作用的电喷雾质谱研究

临床上使用的很多抗病毒药物都是以DNA或RNA为作用的主要靶点,通过与DNA、RNA发生相互作用破坏其结构,进而影响基因调控与表达的功能,表现出抗病毒活性.因此,核酸与其靶向药物分子相互作用的研究不论对阐述抗病毒药物的作用机理,还是对药物的体外筛选都具有非常重要的意义.

Binuclear lanthanide complexes as catalysts for the hydrolysis of double-stranded DNA

The efficient cleavage of plasmid DNA ( pCAT) by binuclear lanthanide complexes was investigated. At 37 degrees C and neutral pH, both Ho23+L and Er23+L promoted 100% conversion of supercoiled plasmid to the nicked circular form and linear form in 1 h. The corresponding saturation kinetics curve of cleavage of pCAT plasmid by binuclear lanthanide complexes showed the expected increase with catalyst concentration. (C) 1999 Elsevier Science S.A. All rights reserved.

Lanthanide binuclear macrocyclic complexes as synthetic enzymes for the cleavage of DNA

Lanthanide binuclear complexes can accelerate the cleavage of pUC19 plasmid DNA, yielding predominantly linear form. The saturation kinetics of the cleavage of pUC19 was studied. The observed rates with lanthanide binuclear complexes showed the expected increase with the catalyst concentration. The rate of cleavage is greater than that of lanthanide ions alone. (C) 1998 Elsevier Science B.V. All rights reserved.