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Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set

Summary: Finding MFE Structures Formed by Nucleic
Acid Strands in a Combinatorial Set
Mirela Andronescu and Anne Condon
The Department of Computer Science, U. British Columbia
1 Introduction
When designing sets of DNA strands for biomolecular computations, it is
often desirable to have a "structure free" combinatorial set of strands, that
is, a set of long strands which do not form any secondary structure, obtained
by concatenating short strands in the designed set.
The ability to computationally predict the combination in a combinatorial
set of strands with lowest minumum free energy (MFE) secondary structure
is also useful in design of strands for directed mutagenesis and SELEX ex-
periments [3] biochemical analyses of a library of nucleic acid sequences, to
determine whether simple mutations of the sequences have desired properties.
The input sequence sets can be represented as strings of characters (DNA
or RNA nucleotides) and "wild cards", which can code for several different
characters using IUPAC (International Union of Pure and Applied Chemistry)
format or other format. In the case of SELEX, it is useful to be able to predict
not only the combination whose minimum energy structure has lowest energy,


Source: Andronescu, Mirela - Department of Genome Sciences, University of Washington at Seattle
Condon, Anne - Department of Computer Science, University of British Columbia


Collections: Biotechnology; Computer Technologies and Information Sciences