title: Calculating sequence-dependent melting stability of duplex DNA oligomers and multiplex sequence analysis by graphs.
abstract: The analytical methods for characterizing DNA sequence-dependent thermodynamic stability have been reviewed. A set of n-n sequence stability parameters is presented. Examples in which these values are used to calculate the thermodynamic stability of short duplex DNA oligomers are presented. The problem of determining sets of isothermal sequences is addressed by representing DNA sequences as graphs. Representing DNA sequences by a graph descriptor with special mathematical properties minimizes the computational difficulty of determining the number of DNA sequences with identical predicted thermodynamic stability. This is achieved by replacement of a whole set of sequences by a single representative. Applications of this concept were demonstrated for sequences assembled from individual bases and sequences assembled from oligomeric blocks.
authors.affiliation: Department of Chemistry, University of Illinois, Chicago, Illinois 60607, USA.
authors.forename: A S
authors.initials: AS
authors.lastname: Benight
authors.forename: P
authors.initials: P
authors.lastname: Pancoska
authors.forename: R
authors.initials: R
authors.lastname: Owczarzy
authors.forename: P M
authors.initials: PM
authors.lastname: Vallone
authors.forename: J
authors.initials: J
authors.lastname: Nesetril
authors.forename: P V
authors.initials: PV
authors.lastname: Riccelli
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D004247:DNA / Q000737:chemistry*; D066298:In Vitro Techniques; D008956:Models, Chemical; D009691:Nucleic Acid Denaturation; D013816:Thermodynamics
chemical_list: D004247:DNA