A thermodynamic approach to designing structure-free combinatorial DNA word sets.
An algorithm is presented for the generation of sets of non-interacting DNA sequences, employing existing thermodynamic models for the prediction of duplex stabilities and secondary structures. A DNA 'word' structure is employed in which individual DNA 'words' of a given length (e.g. 12mer and 16mer) may be concatenated into longer sequences (e.g. four tandem words and six tandem words). This approach, where multiple word variants are used at each tandem word position, allows very large sets of non-interacting DNA strands to be assembled from combinations of the individual words. Word sets were generated and their figures of merit are compared to sets as described previously in the literature (e.g. 4, 8, 12, 15 and 16mer). The predicted hybridization behavior was experimentally verified on selected members of the sets using standard UV hyperchromism measurements of duplex melting temperatures (T(m)s). Additional experimental validation was obtained by using the sequences in formulating and solving a small example of a DNA computing problem.
Shortreed
Michael R
MR
Department of Chemistry, University of Wisconsin, Madison, WI 53706-1396, USA.
Chang
Seo Bong
SB
Hong
DongGee
D
Phillips
Maggie
M
Campion
Bridget
B
Tulpan
Dan C
DC
Andronescu
Mirela
M
Condon
Anne
A
Hoos
Holger H
HH
Smith
Lloyd M
LM
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods; D003596:Cytosine / Q000737:chemistry; D004247:DNA / Q000737:chemistry*; D006147:Guanine / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry; D009693:Nucleic Acid Hybridization; D017422:Sequence Analysis, DNA / Q000379:methods*; D013696:Temperature; D013816:Thermodynamics
D009692:Nucleic Acid Heteroduplexes; D006147:Guanine; D003596:Cytosine; D004247:DNA