DNA Extraction by XPCR

The extraction of DNA strands including a given sequence of bases is a crucial step in the Adleman-Lipton extract model of DNA computing. A special type of PCR is presented in this paper, with a related algorithm which performs a specified extraction from a given pool of DNA double stranded molecules. This kind of PCR, Cross Pairing PCR (or XPCR), was tested in several situations and used ina biotechnological procedure which implements the extraction algorithm

Efficient initial pool generation for weighted graph problems using parallel overlap assembly

Abstract. Most DNA computing algorithms for mathematical problems start with combinatorial generation of an initial pool. Several methods for initialpool generation have been proposed, including hybridization/ligation and mix/split methods. Here, we implement and compare parallel overlap assembly with the hybridization/ligation method. We applied these methods to the molecular algorithm to solve an instance of the graph problem with weighted edges. Our experimental results show that parallel overlap assembly is a better choice in terms of generation speed and material consumption than the hybridization/ligation method. Simulation of parallel overlap assembly was performed to investigate the potential and the limitation of the method.

Investigation of the reactions of bis stannyl furan 2(#ETA#) one

SIGLEAvailable from British Library Document Supply Centre- DSC:DXN060689 / BLDSC - British Library Document Supply CentreGBUnited Kingdo

Characterization of Non-crosshybridizing DNA Oligonucleotides Manufactured In Vitro

Libraries of DNA oligonucleotides manufactured by an In Vitro selection protocol were characterized for their non-crosshybridizing properties. Cloning and sequencing after several iterations of the protocol showed that the sequences, in general, became more non-crosshybridizing. Gel electrophoresis of protocol product, also, indicated non-crosshybridization, and showed evolution in the population of molecules under the non-crosshybridization selection pressure. Melting curves of protocol product also indicated non-crosshybridization when compared to control samples. Thus, it appears that the protocol does select populations of non-crosshybridizing sequences. © Springer-Verlag Berlin Heidelberg 2005

Writing information into DNA

Abstract. The time is approaching when information can be written into DNA. This tutorial work surveys the methods for designing code words using DNA, and proposes a simple code that avoids unwanted hybridization in the presence of shift and concatenation of DNA words and their complements.

Deterministic Polynomial-Time Algorithms for Designing Short DNA Words

LNCS v. 6108 is Proceedings of the 7th Annual Conference, TAMC 2010Designing short DNA words is a problem of constructing n DNA strings (words) with the minimum length such that the Hamming distance between each pair is at least k and the words satisfy a set of extra constraints. This problem has applications in DNA computing, DNA self-assembly, and DNA arrays. Previous works include those that extended results from coding theory to obtain bounds on code size for biologically motivated constraints and those that applied heuristic local searches, genetic algorithms, and randomized algorithms. In particular, Kao, Sanghi and Schweller developed polynomial-time randomized algorithms to construct n DNA words of length 9· max {logn,k} satisfying a sets of constraints with high probability. In this paper, we give deterministic polynomial-time algorithms to construct DNA words based on expander codes, Ramanujan graphs, and derandomization techniques. Our algorithms can construct n DNA words of length max {3logn, 4k} or 2.1 logn + 6.28 k satisfying the same sets of constraints as the words constructed by the algorithms of Kao et al. We have also extended these algorithms to construct words that satisfy a larger set of constraints for which the algorithms of Kao et al. do not work. © 2010 Springer-Verlag.link_to_subscribed_fulltextThe 7th Annual Conference on Theory and Applications of Models of Computation (TAMC 2010), Prague, Czech Republic, 7-11 June 2010. In Lecture Notes in Computer Science, 2010, v. 6108, p. 308-31