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Steady flow micro-reactor module for pipelined dna computations 1

6th international Workshop on dna-Based Computers, dna 2000

作者： McCaskill, John S. Penchovsky, Robert Gohlke, Marlies Ackermann, Jörg Rücker, thomas GMD-National Research Center for Information Technology Schloß Birlinghoven St Augustin53754 Germany

ISBN: (数字)9783540449928

ISBN: (纸本)3540420762

Microflow reactors provide a means of implementing dna computing as a whole, not just individual steps. Contrary to surface based dna Chips[1], microflow reactors with active components in closed flow systems can be used to integrate complete dna computations[2]. Microreactors allow complicated flow topologies to be realized which can implement a dataflowlike architecture for the processing of dna. A technologically feasible scalable approach with many reaction chambers however requires constant hydrodynamic flows. In this work, the experimental construction of a basic constant flow module for dna processing in such a context is addressed. Limited diffusional exchange in parallel flows is used to establish spatio-temporal segregation of reaction conditions which can be crossed by magnetic beads without barriers. As previously outlined[2], linked up with an optical programming technology, this will enable dna selection to be programmed and complex population selection to be performed. the basic first experimental step in the realization of this program is described here: the establishment of a stable hydrodynamic flow pattern which is scalable to many reactors in parallel and the demonstration of a scalable and synchronous clocking of magnetic beadbased processing. First results with fluorescently-labeled dna transfer will also be presented at the conference. the way in which this module may be integrated to solve the maximal clique problem has been proposed elsewhere[2]. © Springer-Verlag Berlin Heidelberg 2001.

关键词： dna

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three dimensional molecular modeling studies in AIDS research using high performance computing facilities: a ternary complex of HIV-1 RT

Three dimensional molecular modeling studies in AIDS researc...

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Proceedings of the 1996 18th Annual international conference of the IEEE Engineering in Medicine and Biology Society. Part 4 (of 5)

作者： Yadav, Prem N.S. Laxminarayan, Swamy Yadav, Janardan S. Pandey, Virendra N. Singh, Sunita Modak, Mukund J. UMDNJ Piscataway United States

We present here a complete three-dimensional molecular model structure of the ternary complex (Enzyme-dna-dNTP) of human immunodeficiency virus-type 1 reverse transcriptase (HIV-1 RT) using high performance computer simulation and molecular modeling techniques. the Ca coordinates of the crystal structure of HIV-1 RT-dna binary complex as well as biochemical properties of a number of mutant enzymes were used as the basis to model build a prepolymerase ternary complex in which Mg2 + ions are also accommodated. the side chains of amino acid residues interacting with the template and primer strands and those stabilizing the dNTP and Mg2+ ions in the active site pocket are clearly elucidated in the model. the structural information provided by this model should be useful in understanding the polymerase reaction mechanisms and should permit structure based drug design against HIV-1 RT.

关键词： Diseases

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three dimensional molecular modeling studies in AIDS research using high performance computing facilities: a ternary complex of HV-1 RT

Three dimensional molecular modeling studies in AIDS researc...

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Annual international conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

作者： N.S. Yadav S. Laxminarayan J.S. Yadav V.N. Pandey S. Singh M.J. Modak Dept. of Biochem. Acad. Comput. Center Piscataway NJ USA Biomedical Engineering Program New Jersey Institute of Technology and John von Neuman Computer Network Princeton USA Department of Biochemistry and Molecular Biology and Academic Computing Center University of Medicine and Dentistry of New Jersey Piscataway NJ USA

the authors present here a complete three-dimensional molecular model structure of the ternary complex (Enzyme-dna-dNTP) of human immunodeficiency virus-type 1 reverse transcriptase (HIV-1 RT) using high performance computer simulation and molecular modeling techniques. the Ca coordinates of the crystal structure of HIV-1 RT-dna binary complex as well as biochemical properties of a number of mutant enzymes were used as the basis to model build a prepolymerase ternary complex in which Mg/sup 2+/ ions are also accommodated. the side chains of amino acid residues interacting with the template and primer strands and those stabilizing the dNTP and Mg/sup 2+/ ions in the active site pocket are clearly elucidated in the model. the structural information provided by this model should be useful in understanding the polymerase reaction mechanisms and should permit structure based drug design against HIV-1 RT.

关键词： Acquired immune deficiency syndrome High performance computing Biochemistry Spine Biological system modeling Biology computing dna Computer networks Amino acids Polymers

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molecular DAMAGE-INDUCED DIRECTLY AND INDIRECTLY BY IONIZING-RADIATION IN dna

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 459-465页

作者： ZAIDER, M BARDASH, M FUNG, A COLUMBIA UNIV DEPT RADIAT ONCOLNEW YORKNY 10032

We describe the interaction of radiation with a double-stranded dna molecule and with the structural water surrounding it. the results, which include a detailed picture of dna molecular alterations, as well as their yield and spatial disposition, were obtained with the aid of Monte Carlo codes that simulate, event-by-event and simultaneously, direct and indirect effects. these calculations make use of explicit quantum-mechanical descriptions of the electronic structure of condensed water and of a homopolynucleotide chain. From these we obtain, via the dielectric response function of the two systems, epsilon (q, omega), the interaction probabilities necessary in the transport codes.

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METAL-ION ASSISTED, RADIATION-INDUCED CONVERSION OF B-dna TO Z-dna IN POLY (DGDC) AND 2 NATURAL dnaS

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 479-483页

作者： TRUMBORE, CN MYERS, YN HYDE, CK HUDSON, RD RHODES, CN MASSELINK, JK Department of Chemistry and Biochemistry University of Delaware Newark 19716.

Metal-ion assisted, gamma-radiation-induced B-Z conformation changes have been observed with UV and circular dichroism spectroscopy for poly (dGdC), calf thymus and herring testis dna. these conformational changes are similar to those induced by increasing multivalent metal ion concentrations in dna containing alternating purine and pyrimidine base sequences. In both the metal-ion-induced and the metal-ion-assisted, radiation-induced conformation changes, the conversions were from the right-handed B-dna to the left-handed Z-dna conformation. It is proposed that radiation-induced dna strand breaks markedly reduce the high activation energy barrier in the metal ion-driven B-Z conformation conversion and allow much smaller metal ion concentrations to induce this conversion than in the absence of strand breaks. the biological importance of such radiation-induced conformational changes is discussed in terms of the potential significance of the Z-dna conformation in the control of the dna transcription process.

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P53 STATUS, dna DOUBLE-STRAND BREAK REPAIR PROFICIENCY, AND RADIATION RESPONSE OF MOUSE LYMPHOID AND MYELOID CELL-LINES

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 557-560页

作者： RADFORD, IR Research Division Peter MacCallum Cancer Institute East Melbourne Victoria Australia.

the p53 status of a panel of 10 mouse lymphoid or myeloid cell lines was determined by immunoprecipitation with mutant- and wild-type-specific antibodies and was compared with the radiation response of the lines. the more rapidly dying cell lines all contained p53 displaying the wild-type epitope. By contrast, four of six more slowly dying cell lines contained either no or mutant p53 protein. It was of interest that radiation-induced apoptosis occurred, albeit at a considerable time after irradiation, in cells ostensibly lacking p53 protein. dna double-strand break (dsb) repair was examined in both a rapidly and more slowly dying cell line. the rapidly dying cell line was capable of dna dsb rejoining, however this repair was interrupted by postirradiation dna degradation.

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COMBINATION IS thE DOMINANT FREE-RADICAL PROCESS INITIATED IN dna BY IONIZING-RADIATION - AN OVERVIEW BASED ON SOLID-STATE EPR STUDIES

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 491-497页

作者： BERNHARD, WA MROCZKA, N BARNES, J Department of Biophysics University of Rochester NY 14642.

An overview of the early processes initiated in dna by ionizing radiation is given from the perspective of studies done by solid-state EPR with the focus on radical combination. Comparisons with free radical formation and trapping in crystalline pyrimidines (1-methylcytosine, thymine, 1-methylthymine, 1-methyluracil, and cytosine monohydrate) provide insight into the processes occurring in dna. Between 25 and 50% of low LET ionizations in fully hydrated dna at 4K lead to trapped free radicals, the remaining unobserved radicals are assumed to have combined. the majority of the radicals trapped in dna at 4K (G similar to 0.3 mu mol/J) are believed to be in clusters. Based on the value of G, it is argued that the range of holes and bound electrons in dna at 4K are, in the main, limited to within the cluster diameter, similar to 4 nm. Proton transfer across hydrogen bonds promotes radical trapping and inhibits combination but is thermally reversible. Warming to room temperature mobilizes the reversibly trapped radicals and gives additional combination (50-80% of those trapped at 4K). the yield of free radicals, after anneal, is sufficient to account for the yield of single-strand breaks produced by direct effects.

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ON thE LINEARITY OF thE DOSE-EFFECT RELATIONSHIP OF dna DOUBLE-STRAND BREAKS

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 549-552页

作者： CHADWICK, KH LEENHOUTS, HP RIVM LSO3720 BA BILTHOVENNETHERLANDS

Most radiation biologists believe that dna double-strand breaks are induced linearly with radiation dose for all. types of radiation. Since 1985, with the advent of elution and gel electrophoresis techniques which permit the measurement of dna double-strand breaks induced in mammalian cells at doses having radiobiological relevance, the true nature of the dose-effect relationship has been brought into some doubt. Many investigators measured curvilinear dose-effect relationships and a few found good correlations between the induction of the dna double-strand breaks and cell survival. We approach the problem pragmatically by assuming that the induction of dna double-strand breaks by I-125 Auger electron emitters incorporated into the dna of the cells is a linear function of the number of I-125 decays, and by comparing the dose-effect relationship for sparsely ionizing radiation against this standard. the conclusion drawn in that the curvilinear dose-effect relationships and the correlations with survival are real. the problem of why the dose-effect relationship is curvilinear when microdosimetric considerations predict that even for sparsely ionizing radiation energy deposition in and close to the Watson-Crick double helix should give a linear dose-effect relationship remains.

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CLONING HUMAN dna-REPAIR GENES

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 573-577页

作者： JEGGO, PA CARR, AM LEHMANN, AR UNIV SUSSEX MRCCELL MUTAT UNITBRIGHTON BN1 9RRE SUSSEXENGLAND

Many human genes involved in the repair of UV damage have been cloned using different procedures and they have been of great value in assisting the understanding of the mechanism of nucleotide excision-repair. Genes involved in repair of ionizing- radiation damage have proved more difficult to isolate. Positional cloning has localized the XRCC5 gene to a small region of chromosome 2q33-35, and a series of yeast artificial chromosomes covering this region have been isolated. Very recent work has shown that the XRCC5 gene encodes the 80 kDa subunit of the Ku dna-binding protein. the Ku80 gene also maps to this region. Studies with fission yeast have shown that radiation sensitivity can result not only from defective dna repair but also from abnormal cell cycle control following dna damage. Several genes involved in this 'checkpoint' control in fission yeast have been isolated and characterized in detail. It is likely that a similar checkpoint control mechanism exists in human cells.

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dna IN GLASSES AT 77 K - HIGH-ENERGY IONIZING-RADIATION VERSUS UV ELECTRON EJECTION

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international JOURNAL OF RADIATION BIOLOGY 1994年第5期66卷 511-515页

作者： MALONE, ME SYMONS, MCR PARKER, AW UNIV ESSEX DEPT CHEM & BIOL CHEMCOLCHESTER CO4 3SQESSEXENGLAND UNIV LEICESTER DEPT CHEMLEICESTER LE1 7RHLEICSENGLAND RUTHERFORD APPLETON LAB CENT LASER SUPPORT FACILDIDCOT OX11 0QXOXONENGLAND

Most in the field of ionizing radiation damage to dna in frozen aqueous solutions agree that two major types of radical ions are formed, i.e.(.)G(+)/(.)A(+) and T-.(-)/C-.(-). the main evidence stems from EPR and strand break studies. Fluid solutions exposed to laser light are known to give G(.+) and e(solv)(-) with low yields of single strand breaks. We have explored this contrast by photoionizing dna solutions at 77 K, in the expectation that this would prevent the formation of e(solv)(-) and hence that the results might be similar to those for high energy radiation. they are not: the results show only the formation of G(.)+ (or) A(.+)). the fate of the ejected electrons is unclear except for sodium perchlorate glasses when they react to give O-.-.

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