Abstract
DNA computing often requires oligonucleotides that do not produce erroneous cross-hybridizations. By using in vitro evolution, huge libraries of non-crosshybridizing oligonucleotides might be evolved in the test tube. As a first step, a fitness function that corresponds to non-crosshybridization has to be implemented in an experimental protocol. Therefore, a modified version of PCR that selects non-crosshybridizing oligonucleotides was designed and tested. Experiments confirmed that the PCR-based protocol did amplify maximally mismatched oligonucleotides selectively over those that were more closely matched. In addition, a reaction temperature window was identified in which discrimination between matched and mismatched might be obtained. These results are a first step toward practical manufacture of very large libraries of non-crosshybridizing oligonucleotides in the test tube.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Adleman, L.M.: Molecular computation of solutions to combinatorial problems. Science 266 (1994) 1021–1024
Lipton, R.J.: DNA solution of hard computational problems. Science 268 (1995) 542–545
Sakamoto, K., Gouzu, H., Komiya, K., Kiga, D., Yokoyama, S., Yokomori, T., Hagiya, M.: Molecular computation by DNA hairpin formation. Science 288 (2000) 1223–1226
Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two-dimensional DNA crystals. Nature 394 (1998) 539–544
Baum, E.B.: DNA sequences useful for computation. In Landweber, L.F., Baum, E.B., eds.: Proceedings of the Second Annual Meeting on DNA Based Computers. Volume 44., Providence, RI, DIMACS, American Mathematical Society (1998) 122–127 DIMACS Workshop, Princeton, NJ, June 10-12, 1996.
Marathe, A., Condon, A.E., Corn, R.M.: On combinatorial DNA word design. In Winfree, E., Gifford, D.K., eds.: DNA Based Computers V, Providence, RI, DIMACS, American Mathematical Society (1999) 75–90 DIMACS Workshop, Massachusetts Institute of Technology, Cambridge, MA, June 14-16, 1999.
Deaton, R., Murphy, R.C., Rose, J.A., Garzon, M., Franceschetti, D.R., Stevens Jr., S.E.: A DNA based implementation of an evolutionary searchfor good encodings for DNA computation. In: Proceedings of the 1997 IEEE International Conference on Evolutionary Computation, IEEE (1997) 267–272 Indianapolis, IN, April 13–16.
Osborne, S.E., Ellington, A.D.: Nucleic acid selection and the challenge of combinatorial chemistry. Chemical Review 97 (1997) 349–370
Deaton, R., Chen, J., Bi, H., Rose, J.: A software tool for generating noncrosshybridizing libraries of DNA oligonucleotides. In this volume (2002).
Santa Lucia, Jr., J.: A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. 95 (1998) 1460–1465
Smith, T.F., Waterman, M.S.: The identification of common molecular subsequences. J. Mol. Biol. 147 (1981) 195–197
Lipton, R.: DNA computing: does it compute? Plenary address at the Seventh International Meeting on DNA Based Computers (2001)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Deaton, R., Chen, J., Bi, H., Garzon, M., Rubin, H., Harlan Wood, D. (2003). A PCR-based Protocol for In Vitro Selection of Non-crosshybridizing Oligonucleotides. In: Hagiya, M., Ohuchi, A. (eds) DNA Computing. DNA 2002. Lecture Notes in Computer Science, vol 2568. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36440-4_17
Download citation
DOI: https://doi.org/10.1007/3-540-36440-4_17
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-00531-5
Online ISBN: 978-3-540-36440-5
eBook Packages: Springer Book Archive