Udo Feldkamp - Academia.edu (original) (raw)

Papers by Udo Feldkamp

Die Erfindung betrifft Verfahren zur Herstellung informationstragender Polymere, nach diesen Verf... more Die Erfindung betrifft Verfahren zur Herstellung informationstragender Polymere, nach diesen Verfahren erhaltliche informationstragende Polymere; Verfahren zur Isolierung, zur Vervielfaltigung und zum Auslesen solcher informationstragender Polymere; polymere Datenspeicher und DNA-Computer, die informationstragende Polymere umfassen sowie die Verwendung informationstragender Polymere zur Herstellung von Molekulargewichtsstandards, als Marker oder Signaturen, zur Verschlusselung von Information, als molekulare Kleber oder zur Herstellung oder Bearbeitung kleinster molekularer Strukturen.

L'invention concerne un procede de production de polymeres permettant de supporter des inform... more L'invention concerne un procede de production de polymeres permettant de supporter des informations ; les polymeres porteurs d'informations ainsi obtenus; des procedes d'isolement, de multiplication et de lecture de tels polymperes supportant des informations; des memoires de donnees et des bioordinateurs polymeriques qui contiennent des polymeres supportant des informations ainsi que l'utilisation de polymeres supportant des informations comme marqueurs ou signatures pour la production de poids moleculaires standards, comme adhesifs moleculaires pour le codage d'informations, ou pour la production ou le traitement de structures moleculaires plus petites.

An approach based on programmable self-assembly of DNA oligonucleotides was used to create digita... more An approach based on programmable self-assembly of DNA oligonucleotides was used to create digital DNA molecules representing binary datastructures which are equivalent to those used in computers. Utilizing plasmids as a kind of computer memory, the digital molecules could be isolated, amplified and read out using common genetic techniques. Programmability allowed several applications to be realized in vitro such as a fast physical random number generator and digital DNA-“barcodes”. * Dept. of Computer Science, LS11, University of Dortmund, Joseph-von-Fraunhofer Str. 20, D-44227 Dortmund,

Designing oligonucleotide sequences that are suitable for applications in nanobiotechnology or DN... more Designing oligonucleotide sequences that are suitable for applications in nanobiotechnology or DNA Computing is not feasable without the help of computers. Such molecules have to hybridize specifically and with high and homogeneous efficiency to their respective complement. A computer program called dsc (DNA Sequence Compiler) translates specifications of physical, chemical and logical properties of DNA molecules into base sequences meeting these specifications. It maps the search for DNA sequences to the search for paths through a graph of base tuples with a fixed length. Two extensions of the underlying algorithm are described here, grouping sequences for a parallel path search and tolerating violations against the sequence dissimilarity rule that enforces hybridization specificity. The effects of these extensions on success probabilities and sequence quality is examined, and some strategic hints on how to use dsc are given.

AIP Conference Proceedings, 2008

ABSTRACT We here report on the developments of semisynthetic DNA‐protein conjugates and their ass... more ABSTRACT We here report on the developments of semisynthetic DNA‐protein conjugates and their assembly into multi‐component nanostructures. We describe the improvement of the DNA sequences embedded in such nanostructures by computational and analytical methods. Moreover, we report on the exploration of novel DNA conjugates of streptavidin or redox proteins with improved properties for the assembly of nucleic acid based nanostructures.

Lecture Notes in Computer Science, 2002

In DNA Computing and DNA nanotechnology the design of proper DNA sequences turned out to be an el... more In DNA Computing and DNA nanotechnology the design of proper DNA sequences turned out to be an elementary problem [1−9]. We here present a software program for the construction of sets ("pools") of DNA sequences. The program can create DNA sequences to meet logical and physical parameters such as uniqueness, melting temperature and GC ratio as required by the user. It can create sequences de novo, complete sequences with gaps and allows import and recycling of sequences that are still in use. The program always creates sequences that are − in terms of uniqueness, GC ratio and melting temperature − "compatible" to those already in the pool, no matter whether those were added manually or created or completed by the program itself. The software comes with a GUI and a Sequence Wizard. In vitro tests of the program's output were done by generating a set of oligomers designed for self−assembly. The software is available for download under http://LS11−www.cs.uni−dortmund.de/molcomp/Downloads/downloads.html.

The design of DNA sequences is a key problem for implementing molecular self-assembly with nuclei... more The design of DNA sequences is a key problem for implementing molecular self-assembly with nucleic acid molecules. These molecules must meet several physical, chemical and logical requirements, mainly to avoid mishybridization. Since manual selection of proper sequences is too time-consuming for more than a handful of molecules, the aid of computer programs is advisable. In this paper two software tools for designing DNA sequences are presented, the DNASequenceGenerator and the DNASequence-Compiler. Both employ an approach of sequence dissimilarity based on the uniqueness of overlapping subsequences and a graph based algorithm for sequence generation. Other sequence properties like melting temperature or forbidden subsequences are also regarded, but not secondary structure errors or equilibrium chemistry. Fields of application are DNA computing and DNA-based nanotechnology. In the second part of this paper, sequences generated with the DNASequenceGenerator are compared to those from several publications of other groups, an example application for the DNASequenceCompiler is presented, and the advantages and disadvantages of the presented approach are discussed.

Schneider/De novo Molecular Design, 2013

ABSTRACT

Journal of Computational Chemistry, 2009

The design of nucleic acid sequences for a highly specific and efficient hybridization is a cruci... more The design of nucleic acid sequences for a highly specific and efficient hybridization is a crucial step in DNA computing and DNA-based nanotechnology applications. The CANADA package contains software tools for designing DNA sequences that meet these and other requirements, as well as for analyzing and handling sequences. CANADA is freely available, including a detailed manual and example input files, at http://ls11-www.cs.unidortmund.de/molcomp/downloads.

Journal of Biomolecular Structure and Dynamics, 2006

Due to the exceptional molecular recognition properties of nucleic acids, the computational desig... more Due to the exceptional molecular recognition properties of nucleic acids, the computational design of DNA sequence motifs is of paramount interest for a wide variety of applications, ranging from DNA-based nanotechnology and DNA computing to the broad field of DNA microarray technologies. These applications rely on the specificity of Watson-Crick base-pairing, and thus, are highly sensitive to non-specific interactions and the formation of any undesired secondary structures, which contradict an efficient intermolecular hybridization. Here we report on the in silico design and in vitro evaluation of single-stranded DNA (ssDNA) carrier strands for the directional DNA-based positioning of streptavidin (STV) conjugates covalently tagged with short ssDNA oligonucleotides. Each such carrier strand consists of four hybridization sites complementary to the conjugate DNA strands. The high and homogeneous hybridization efficiency measured in vitro by microarray hybridization assays confirms the quality of our in silico sequence design method. Hybridization efficiency of DNA-STV-conjugates depends on the position of the hybridization site in the carrier sequence, where the positions nearest to and farthest from the microarray surface proved to be most favorable.

ChemPhysChem, 2004

We report on the microarray-based in vitro evaluation of two libraries of DNA oligonucleotide seq... more We report on the microarray-based in vitro evaluation of two libraries of DNA oligonucleotide sequences, designed in silico for applications in supramolecular self-assembly, such as DNA computing and DNA-based nanosciences. In this first study which is devoted to the comparison of sequence motif properties theoretically predicted with their performance in real-life, the DNAdirected immobilization (DDI) of proteins was used as an example of DNA-based self-assembly. Since DDI technologies, DNA computing, and DNA nanoconstruction essentially depend on similar prerequisites, in particular, large and uniform hybridization efficiencies combined with low nonspecific cross-reactivity between individual sequences, we anticipate that the microarray approach demonstrated here will enable rapid evaluation of other DNA sequence libraries.

In this study the advantages of statistical gene selection are combined with the power of Genetic... more In this study the advantages of statistical gene selection are combined with the power of Genetic Programming (GP) to build classifiers for assigning gene expression microarray data samples to categories characteristic of certain cell states. To that end we implemented different statistical measures in a program called GE- NEACTIVATOR and tested their applicability to gene selection. Subsequently we used the general purpose GP-system DISCIPULUS to train classifiers. We applied our approach to four different human cancer gene expression datasets publicly avail- able, including multi-class sets. The results indicate that using gene selection and GP as implemented in DISCIPULUS is an appropriate method for gene expression data analysis.

Various approaches to the self-assembly of molecules have been introduced already 1), 2), 3), 4),... more Various approaches to the self-assembly of molecules have been introduced already 1), 2), 3), 4), 5), 6), 7). A step further toward flexible design and construction of precisely defined molecules are approaches to programmable self-assembly 5), 10). In order to allow arbitrary programming, a sufficient solution of the negative design problem 8), 5), 9) is needed. We present a computer program which translates formal grammars directly into DNA molecules. It allows the construction of DNA molecules with defined logical structure and physical properties. Applications of the compiler are DNA-computing algorithms, nano-frameworks and the construction of biochips.

Angewandte Chemie, 2006

DNA hat viele physikalische und chemische Eigenschaften, die sie zu einem leistungsfahigen Materi... more DNA hat viele physikalische und chemische Eigenschaften, die sie zu einem leistungsfahigen Material fur molekulare Konstruktionen im Nanometer-Masstab machen. Insbesondere ihre Fahigkeit, Duplexe und andere Sekundarstrukturen durch vorhersagbare, Nucleotidsequenz-gesteuerte Hybridisierung zu bilden, ermoglicht den Entwurf programmierbarer Strukturmotive, die wiederum zu grosen supramolekularen Anordnungen, Gerusten und sogar zu mechanischen und logischen Funktionseinheiten zusammengefugt werden konnen. Trotz der breiten Vielfalt solcher Strukturmotive, die als Bausteine beim programmierten Zusammenbau von supramolekularen DNA-Nanoarchitekturen verwendet werden, sind den unterschiedlichen Modulen einige grundlegende Prinzipien des Entwurfs ihrer hierarchischen Konfiguration und der eingesetzten Nucleotidsequenzen gemein. Dieser Aufsatz gibt einen Uberblick uber dieses faszinierende und schnell wachsende Forschungsgebiet unter besonderer Berucksichtigung strukturchemischer Aspekte.