Forschungszentrum Informationstechnik GmbH GMD

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  • Publication
    Optimization and design of oligonucleotide setup for strand displacement amplification
    ( 2005)
    Ehses, S.
    ;
    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
    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
    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.
  • Publication
    DNA library design for molecular computation
    ( 2003)
    Penchovsky, R.
    ;
    Ackermann, J.
    A novel approach to designing a DNA library for molecular computation is presented. The method is employed for encoding binary information in DNA molecules. It aims to achieve a practical discrimination between perfectly matched DNA oligomers and those with mismatches in a large pool of different molecules. The approach takes into account the ability of DNA strands to hybridize in complex structures like hairpins, internal loops, or bulge loops and computes the stability of the hybrids formed based on thermodynamic data. A dynamic programming algorithm is applied to calculate the partition function for the ensemble of structures, which play a role in the hybridization reaction. The applicability of the method is demonstrated by the design of a twelve-bit DNA library. The library is constructed and experimentally tested using molecular biology tools. The results show a high level of specific hybridization achieved for all library words under identical conditions. The method is also applicable for the design of primers for PCR, DNA sequences for isothermal amplification reactions, and capture probes in DNA-chip arrays. The library could be applied for integrated DNA computing of twelve-bit instances of NP-complete combinatorial problems by multi-step DNA selection in microflow reactors.
  • Publication
    Word Design for Biomolecular Information Processing
    ( 2003)
    Ackermann, J.
    ;
    Gast, F.-U.
    The design of DNA sequences plays a fundamental role for many biomolecular applications and is one of the most important theoretical tasks to fathom the potential of molecular information processing. Optimization strategies have been based on the model of stiff "digital" polymers by counting the number of base mismatches (Hamming distance and related distances). In this work we show the limitation of such a combinatorial approach because of the ability of DNA to build more complex structures. We develop a model platform to optimize word sets according to all possible secondary structures occurring for the relevant word-word interactions. The fidelity of the hybridization reactions can be improved significantly and as an example of a set of 24 words of 16-mers we show that the optimal set has unique physical properties, such as binding energy, melting temperature, and G+C content.
  • Publication
    Hybrid poly(dimethylsiloxane)-silicon microreactors used for molecular computing
    ( 2002)
    Noort, D. van
    ;
    Wagler, P.
    ;
    Mccaskill, J.S.
    The goal of this research is to improve the modular stability and programmability of DNA-based Computers and is a second step towards optical programmable DNA computing. The main focus here is on hydrodynamic stability. Clockable microreactors can be connected in various ways to solve combinatorial optimization problems, such as maximum clique or 3-SAT. This work demonstrates by construction how one microreactor design can be programmed to solve any instance of maximum clique up to its given maximum size (N). It reports on an implementation of the architecture proposed previously (McCaskill J S 2001 Biosystems 59 125-38). This contrasts with conventional DNA computing where the individual sequence of biochemical operations depends on the specific problem. In this pilot study we are tackling a graph for the maximum clique problem with N less than or equal to 12, with a special emphasis on N = 6. Furthermore, the design of the DNA solution space will be presented, which is symbolized by a set of bit-strings (words).
  • Publication
    Biochemical amplification waves in a one-dimensional microflow system
    ( 2002)
    Kirner, T.
    ;
    Steen, D.
    ;
    McCaskill, J.S.
    ;
    Ackermann, J.
    A cooperatively coupled, isothermal biochemical amplification system has been investigated under flow conditions in a microstructured reactor. The experimental setup provides for continuous amplification and on line detection of the reaction products in space and time. Spatially resolved fluorescence spectroscopy with an intercalating dye was used for detection of the double stranded DNA products. Biochemical amplification was observed under a wide range of flow rates. The total rate of amplification resulted from an interplay between the amplification of the biochemical system and a loss term produced by the flow. For flow rates above a critical value, the system was diluted out and the amplification reaction brought to a halt in the reactor. Homogeneous growth throughout the reactor was observed at intermediate flow rates. At low pump rates, additional biochemical amplification started at various locations. We interpret the spatially homogeneous Growth at low concentration and the local growth at high concentration to result from two different amplification phases because of noncooperative and cooperative amplification mechanisms, respectively. The consequences for long-term evolutionary experiments as well as for complex pattern formation are discussed.
  • Publication