Optimization and design of oligonucleotide setup for strand displacement amplification B Sylvia Ehses a, * , Jo ¨ rg Ackermann b , John S. McCaskill c a Biomolecular Optical Systems (BioMOS), Fraunhofer-Gesellschaft, Schloss Birlinghoven, D-53754 Sankt Augustin, Germany b Plasma Analytics Systems, Technologiepark 1, 15236 Frankfurt/O., Germany c Biomolecular Information Processing (BioMIP), Ruhr-Universita ¨t Bochum, c/o Schloss Birlinghoven, D-53754 Sankt Augustin, Germany Received 10 March 2005; received in revised form 14 April 2005; accepted 17 April 2005 Abstract 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. D 2005 Elsevier B.V. All rights reserved. Keywords: Strand displacement amplification; Folding; Partition function; Hybridization 0165-022X/$ - see front matter D 2005 Elsevier B.V. All rights reserved. doi:10.1016/j.jbbm.2005.04.005 B This work was performed at Biomolecular Information Processing, BioMIP, Fraunhofer Gesellschaft, Schloss Birlinghoven, D-53754 Sankt Augustin, Germany. * Corresponding author. E-mail address: sylvia.ehses@biomos.fraunhofer.de (S. Ehses). J. Biochem. Biophys. Methods 63 (2005) 170 – 186 www.elsevier.com/locate/jbbm