Nucleic Acids Research, Vol 25, Issue 23 4748-4757, Copyright © 1997 by Oxford University Press
AG Frutos, Q Liu, AJ Thiel, AM Sanner, AE Condon, LM Smith and RM Corn
A strategy for DNA computing on surfaces using linked sets of 'DNA words'
that are short oligonucleotides (16mers) is proposed. The 16mer words have
the format 5'-FFFFvvvvvvvvFFFF-3' in which 4-8 bits of data are stored in 8
variable ('v') base locations, and the remaining fixed ('F') base locations
are used as a word label. Using a template and map strategy, a set of 108
8mers each of which possesses at least a 4 base mismatch with the
complements to all the other members of the set (4bm complements) are
identified for use as a variable base sequence set. In addition, sets of 4
and 12 word labels of the form ABCD....DCBA that are respectively 8bm and
6bm complements with each other are identified. The 16mers are chosen to
have a G/C content of 50% in order to make the thermodynamic stability of
the perfectly matched hybridized DNA duplexes similar; a simple pairwise
additive method is used to estimate the perfect match and mismatch
hybridization thermodynamics. A series of preliminary experiments are
presented that use small arrays of 16mers attached to chemically modified
gold surfaces and fluorescently labeled complements to study the
hybridization adsorption and enzymatic manipulation of the
oligonucleotides.
ARTICLES
Demonstration of a word design strategy for DNA computing on surfaces
Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA. corn@chem.wosc.edu
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