Sticker DNA computer model ——PartⅡ: Application

Sticker model is one of the basic models in the DNA computer models. This model is coded with sin-gle-double stranded DNA molecules. It has the following advantages that the operations require no strands extension and use no enzymes; What抯 more, the materials are reusable. Therefore, it arouses attention and interest of scientists in many fields. In this paper, we extend and improve the sticker model, which will be definitely beneficial to the construction of DNA computer. This paper is the second part of our series paper, which mainly focuses on the application of sticker model. It mainly consists of the following three sections: the matrix representation of sticker model is first presented; then a brief review of the past research on graph and com-binatorial optimization, such as the minimal set covering problem, the vertex covering problem, Hamiltonian path or cycle problem, the maximal clique problem, the maximal independent problem and the Steiner spanning tree problem, is described; Finally a DNA algorithm for the graph iso-morphic problem based on the sticker model is given.     

Coordination chemistry mimics of nuclease-activity in the hydrolytic cleavage of phosphodiester bond

In vivo, there occurs the synthesis and degradation of the nucleic acids, involving the formation and cleavage of phosphodiester bond. The cleavage modes of phosphodiester bond can be divided into two types, oxidative and hydrolytic, only the hydrolytic products are sticky and connectable, allowing to be religated by ligases. In recent years, great progresses have been made in chemical mimics in the hydrolytic cleavage of phosphodiester bond. Among the found metal complexes with the activity of nucleic acid cleavage, there are mononuclear and dinuclear metal complexes, the adopted metal ions including transitional and lanthanide metal ions. However, the reaction rates are still several orders less than those of the natural enzymes. It should be a prosperous and expedient direction to mimic the hydrolytic cleavage of phosphodiester bond by taking the advantages of dinuclear metal complexes.     

Cloning and analysis of the antagonistic related genes of <Emphasis Type="Italic">Enterobacter cloacae</Emphasis> B8

To understand the antagonistic mechanism of the broad spectrum antagonistic Enterobacter cloacae B8,Tn5 transposon-mediated mutagenesis is performed using suicide plasmid pZJ25. Two mutant strains that lost antagonistic character are isolated. Tagging with kanr gene on Tn5,an antagonistic related DNA fragment, the F fragment, right of the Tn5 insertion site is cloned in a plasmid named pTLF,from one of the mutant strains B8F. The 733 bp F fragment is then sequenced after subcloning. Genomic DNA of the original B8 strain is isolated, digested with Pst I and ligated to Pst I cassette. DNA fragments left and right of the F fragment are amplified from the Pst I cassette library using cassette primer and specific primers designed according to known sequence. 1106 bp sequence left of the F fragment and 664bp sequence right of the F fragment are finally obtained. Bioinformatics analysis shows that the contig assembled from the sequences of the cloned antagonistic related DNA fragments of B8 encodes three ORFs and is homogeneous to admM,admN and admO genes of Pantoea agglomerans andrimid biosynthetic gene cluster (AY192157). The ORF, named anrF gene which encodes a polyketide synthase, knocked out by Tn5 insertion, is a homology of admM and the insertion site of Tn5 is at 214 bp upstream of the stop codon. It is concluded that the anrF gene is a gene related to the antagonistic activity of E. cloacae B8, and speculated that the antagonistic substance produced by B8 is an andrimid.     

The character of <Emphasis Type="Italic">EBNA1</Emphasis> gene variation in Cantonese and its association with nasopharyngeal carcinoma

Epstein-Barr virus (EBV) is closely associated with nasopharyngeal carcinoma (NPC), which occurs with highest incidence in Guangdong. However, EBV is ubiquitous and remains a life-long asymptomatic infection in the peripheral B lymphocytes of healthy carriers; thus it is supposed that there is a substrain of EBV with carcinogenesis potential in NPC high incidence area.     

重组包涵体蛋白质复性

基因工程技术的发展掀开了人类生命科学研究的崭新篇章，开辟了现代生物工业发展的新纪元。重组DNA技术为大规模生产目标蛋白质提供了可能，E．coli以其易于操作、遗传背景清楚、发酵成本低和蛋白表达水平高等优点，是生产重组蛋白的首选表达系统。但外源基因在E．coli中的高表达常常导致包涵体的形成，如何高效地复性包涵体蛋白是基因工程技术面临的一个难题。随着人类基因组计划的完成和蛋白组计划的实施，人们将会更多地面临这一问题的挑战。     

Algorithm of graph isomorphism with three dimensional DNA graph structures

An algorithm for solving the graph isomorphism problem with 3-D DNA structures is proposed in this paper. The karmed branched junction molecules are used to code k-degree vertices. Double stranded molecules are used to code edges. Then the molecules are mixed in a tube to be ligated. The result can be detected by gel electrophoresis. The time complexity of the algorithm is O(n2), where n is the number of vertices of the graph.     

电化学诱导铜（Ⅱ）-磺基水杨酸配合物对DNA的切割

研究了在铜(Ⅱ)-磺基水杨酸配合物存在情况下的电化学诱导DNA的切割．铜(Ⅱ)-磺基水杨酸配合物在控制的-0．4V电位下，Cu(ssal)2^2 作为媒介通过电化学反应产生活性氧自由基Q2^*,氧自由基可以切割DNA．被切割的DNA片断使用高效液相色谱可进行分离．实验结果表明，电化学诱导铜(Ⅱ)-磺基水杨酸配合物对DNA的切割方法简单，切割效果好．     

Cloning of a novel phosphateserine aminotransferase gene from a Triticum aestivum-Elytrigia elongatum alien substitution line with resistance to powdery mildew

Shannong 551, a T. aestivum-E, elongatum alien substitution line with resistance to powdery mildew, was inoculated with pathogenic spores of powdery mildew. The leaf samples were prepared 48 h after inoculation for scanning electron microscopy. The result showed that germination of spores and growth of young mycelia on leaves of Shannong 551 were suppressed at the early stage of infection. At the same time, RNAs were prepared from the leaves for the cloning of WRP1 and RPW2 by cDNA RDA and RACE technology. BLAST analysis of the sequences indicated that both WRP1 and RPW2 were novel genes. WRPI contains no complete ORE RPW2 contains the conserved structure domain of aminotransferase, and its DNA sequence shares high homology with genes of phosphateserine aminotransferase in many organisms. Therefore, it is speculated as a novel phosphateserine aminotransferase gene. The results of Northern blot suggested that expression of RPW2 occurred at the early stage of infection by powdery mildew. Southern blot using the probe of RPW2, in which there was strong hybridizing signals in both genome of Shannong 551 and E. elongatum, but not in those of Jinan 13 and Lumai No.5, indicated that RPW2 derived from the genome of E. elongatum.     

A family net of giant pandas in the Tangjiahe Natural Reserve： Assessment of current individual migration

In the present study, formalin-fixed feces, oligonucleotide fingerprinting and SRY-gene based sexing were used to construct a family net for giant pandas in the Tangjiahe Natural Reserve and to assess contemporary gene flow （migration） in this population. A total of 124 fecal samples were attributed to 37 individuals （22 females and 15 males） that were then analyzed for family relationships. Based on DNA fingerprints, the deduced family net revealed the following facts： （i） First-order relatives possessed similarities from 50% to 90%, and similarities between unrelated individuals or distant relatives were as high as 77%, indicating that the Tangjiahe pandas are characterized by high genetic similarity; （ii） 15 matings were identified and 5 ones occurred between close relatives, implying that there is potential for inbreeding to impact the pandas; （iii） four mating pairs and 5 offspring presented long distance migrations, demonstrating the intra-reserve habitat is continuous; （iv） four pairs of full sibs （also female-male dyads） dispersed short distance and all of them gave birth to highly inbred offspring, reflecting long distance migration is vital for inbreeding avoidance; （v） 17 adult individuals dispersed short or moderate distance and formed three clusters on the landscape, indicating that it is necessary to find out whether there is a negative factor impacting the pandas.