Abstract
We have developed a method for designing rapidly-hybridizing orthonormal DNA sequences. Two conditions were used in the prediction method. One condition concerned the stability of the self-folded secondary structures of forward and reverse strands. The other condition concerned the nucleation capability of complementary strands at the tails of their self-folded secondary structures. These conditions were derived from the complementary strands’ experimentally-determined hybridization rates’ dependence on their stability and nucleation capability. These dependences were examined for 37 orthonormal DNA sequences randomly selected from our set of 300 orthonormal DNA sequences. By applying this new method to the set of 300 orthonormal DNA sequences, more than 100 rapidly-hybridizing sequences were obtained.
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Kitajima, T., Takinoue, M., Shohda, Ki., Suyama, A. (2008). Design of Code Words for DNA Computers and Nanostructures with Consideration of Hybridization Kinetics . In: Garzon, M.H., Yan, H. (eds) DNA Computing. DNA 2007. Lecture Notes in Computer Science, vol 4848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77962-9_12
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DOI: https://doi.org/10.1007/978-3-540-77962-9_12
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-77961-2
Online ISBN: 978-3-540-77962-9
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