Now showing 1 - 10 of 3752
  • Publication
    Optimization and design of oligonucleotide setup for strand displacement amplification
    ( 2005)
    Ehses, S.
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    Ackermann, J.
    ;
    McCaskill, J.S.
    Several advantages of strand displacement amplification (SDA) as an all-purpose DNA amplification reaction are due to it isothermal mechanism. The major problem of isothermal amplification mechanism is the accumulation of non-predictable byproduct especially for longer incubation time and low concentrations of initial template DNA. New theoretical strategies to tackle the difficulties regarding the specificity of the reaction are experimentally verified. Besides improving the reaction conditions, the stringency of primer hybridization can be distinctly improved by computer based sequence prediction algorithms based on the thermodynamic stability of DNA hybrid a described by the partition function of the hybridization reaction. An alternative SDA mechanism, with sequences developed by this means is also investigated.
  • Publication
    Folding stabilizes the evolution of catalysts
    ( 2004)
    Altmeyer, S.
    ;
    Füchslin, R.M.
    ;
    McCaskill, J.S.
    Sequence folding is known to determine the spatial structure and catalytic function of proteins and nucleic acids. We show here that folding also plays a key role in enhancing the evolutionary stability of the intermolecular recognition necessary for the prevalent mode of catalytic action in replication, namely, in trans, one molecule catalyzing the replication of another copy, rather than itself. This points to a novel aspect of why molecular life is structured as it is, in the context of life as it Could be: folding allows limited, structurally localized recognition to be strongly sensitive to global sequence changes, facilitating the evolution of cooperative interactions. RNA secondary structure folding, for example is shown to be able to stabilize the evolution of prolonged functional sequences, using only a part of this length extension for intermolecular recognition, beyond the limits of the (cooperative) error threshold. Such folding could facilitate the evolution of polymerases in spatially heterogeneous systems. This facilitation is, in fact, vital because physical limitations prevent complete sequence-dependent discrimination for any significant-size biopolymer substrate. The influence of partial sequence recognition between biopolymer catalysts and complex Substrates is investigated within a stochastic, spatially resolved evolutionary model of trans catalysis. We use an analytically tractable nonlinear master equation formulation called PRESS (McCaskill et at., Biol. Chem. 382: 1343-1363), which makes use of an extrapolation of the spatial dynamics clown from infinite dimensional space, and compare the results with Monte Carlo Simulations.
  • Publication
  • Publication
    Molecular systems-on-chip (MSoC) steps forward for programmable biosystems
    ( 2004)
    Wagler, P.F.
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    Tangen, U.
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    Maeke, T.
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    Chemnitz, S.
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    Juenger, M.
    ;
    McCaskill, J.S.
  • Publication
    Evolutionary stabilization of generous replicases by complex formation
    ( 2004)
    Füchslin, R.M.
    ;
    Altmeyer, S.
    ;
    McCaskill, J.S.
    The importance of spatial organization for the evolutionary stability of trans-acting replicase systems (T(X) under right arrow 2T), where T is a general member of a combinatorial family including the special catalyst X, is now well established, by analytical and Monte Carlo models [1,2]. Complex formation as an intermediate step in replication (X=Treversible arrowXT-->X+2T), besides refining the model, enhances co-localization of replicase X and templates T and is shown here to thereby contribute to the evolutionary stability of the catalyst. Applying the established individual molecule stochastic PRESS-framework [3], the performances of cooperative replication with and without intermediate complex formation are compared, and the beneficial effect of complex formation as enhancing stability is studied numerically under various conditions. The results obtained are of value for studies of prebiotic evolution, but also point towards a possible mechanism for stabilizing replication systems in adaptive molecular engineering.
  • Publication
    Construction of an integrated biomodule composed of microfluidics and digitally controlled microelectrodes for processing biomolecules
    ( 2003)
    Wagler, P.
    ;
    Tangen, U.
    ;
    Maeke, T.
    ;
    Mathis, H.P.
    ;
    McCaskill, J.S.
    This work focuses on the development of an online programmable microfluidic bioprocessing unit (BioModule) using digital logic microelectrodes for rapid pipelined selection and transfer of DNA molecules and other charged biopolymers. The design and construction technique for this hybrid programmable biopolymer processing device is presented along with the first proof of principle functionality. The electronically controlled collection, separation and channel transfer of the biomolecules is monitored by a sensitive fluorescence setup. This hybrid reconfigurable architecture couples electronic and biomolecular information processing via a single module combination of fluidics and electronics and opens new fields of applications not only in DNA computing and molecular diagnostics but also in applications of combinatorial chemistry and lab-on-a-chip biotechnology to the drug discovery process. Fundamentals of the design and silicon-PDMS-based construction of these electronic microfluidic devices and their functions are described as well as the experimental results.
  • Publication
    Molecular-systems-on-a-chip - steps forwards for programmable biosystems
    ( 2003)
    Wagler, P.F.
    ;
    Tangen, U.
    ;
    Maeke, T.
    ;
    Mathis, H.P.
    ;
    McCaskill, J.S.
  • Publication
    Microfabrication of a BioModule composed of microfluidics and digitally controlled microelectrodes for processing biomolecules
    ( 2003)
    Wagler, P.
    ;
    Tangen, U.
    ;
    Maeke, T.
    ;
    Mathis, H.P.
    ;
    McCaskill, J.S.
    This work focuses on the development of an online programmable microfluidic bioprocessing unit (BioModule) using digital logic microelectrodes for rapid pipelined selection and transfer of deoxyribonucleic acid (DNA) molecules and other charged biopolymers. The design and construction technique for this hybrid programmable biopolymer processing device is presented along with the first proof of principle functionality. The electronically controlled collection, separation and channel transfer of the biomolecules is monitored by a sensitive fluorescence set-up. This hybrid reconfigurable architecture couples electronic and biomolecular information processing via a single module combination of fluidics and electronics and opens new fields of applications not only in DNA computing and molecular diagnostics but also in applications of combinatorial chemistry and lab-on-a-chip biotechnology to the drug discovery process. Fundamentals of the design and silicon-polydimethylsiloxane (PDMS)-based construction of these electronic microfluidic devices and their functions are described as well as the experimental results.